GENBANK FLATFILE GENERATOR

A new flatfile generator has been written to replace the old asn2ff code.
It is provided both as a stand-alone application, asn2gb, and as a pair of
C functions in the NCBI software toolkit. There are several command-line
arguments, with equivalent function parameters, that customize the behavior
of the new flatfile generator and optimize its performance.

NCBI maintains the GenBank nucleotide sequence database, and is part of the
International Nucleotide Sequence Database (INSD) collaboration. The list
of biological features and qualifiers approved by the collaborators for
official release and exchange of GenBank, EMBL, and DDBJ records can be
found at http://www.ncbi.nlm.nih.gov/projects/collab/FT/index.html

NCBI converts all direct sequence submissions, as well as records supplied
by our collaborators and other data sources, into a data model specified in
Abstract Syntax Notation 1 (ASN.1) format, regardless of the original form
of the data. From this common data representation we can generate GenBank
or FASTA files, populate BLAST sequence databases, or build indices for the
Entrez retrieval system.

Since the ASN.1 data is structured for ease of computation, asn2gb and the
underlying toolkit functions are able to provide useful derived information
at the request of the user. For example, the sequence of bases encoding an
mRNA feature can be presented in a /transcription qualifier. Because this
is not an INSD-approved qualifier, it will not be present in the official
flatfile release of a record. It can only be provided as an extension of
the collaboration-approved format, such as in "Sequin mode" below.


ASN2GB STANDALONE APPLICATION

An asn2gb executable is now available on all platforms, and is distributed
in the asn1-converters area of the NCBI public ftp site. The most commonly
used arguments are explained below. A more detailed discussion of various
parameter values is in the section on calling the SeqEntryToGnbk function
from within your own program code.

An input file and output file are required, but default to stdin and
stdout, respectively, if not specified in the command-line.

  -i  Input File Name
  -o  Output File Name

GenBank format produces the conventional GenBank flatfile on nucleotide
sequences. GenPept is the equivalent on protein sequences. INSDSet is a set
of one or more INSDSeq elements, which is an XML structured view of the
information in the flatfile. INSDSeq contains additional fields, derived
from the underlying data, provided as a convenience for computing on the
sequences and their feature annotations.

  -f  Format (b GenBank, e EMBL, p GenPept, t Feature Table, x INSDSet)

Sequin mode produces a relaxed flatfile that allows unapproved qualifiers
and database cross-references present in the record to be shown. It is
typically used while constructing a sequence record for submission. The
stricter modes are used for official GenBank releases and display of
flatfiles on the Entrez web site.

  -m  Mode (r Release, e Entrez, s Sequin, d Dump)

Normal style examines each record for "far" references (accessions not
packaged along with the sequence being formatted), and shows the CONTIG
block instead of separately fetching the underlying components. Master
style forces the components to be fetched and displays the actual sequence
letters.

  -s  Style (n Normal, s Segment, m Master, c Contig)

Bit flags and custom flags modify the appearance of the flatfile, such as
adding /transcription and /peptide extended qualifiers, eliminating the
need for writing programs to extract these subsequences. Locks are used to
preload "far" sequence components or lookup their accession numbers, and
can greatly speed up processing of records with far references. The values
are decimal numbers generated by combination of the appropriate binary
bits, which are described in the section on calling the SeqEntryToGnbk
function.

  -g  Bit Flags (1 HTML, 2 XML, 4 ContigFeats, 8 ContigSrcs, 16 FarTransl)
  -h  Lock/Lookup Flags (8 LockProd, 16 LookupComp, 64 LookupProd)
  -u Custom Flags (2 HideMostImpFeats, 4 HideSnpFeats)

Batch processing of Bioseq-set ASN.1 release files is also supported. The
gb*.aso.gz compressed binary files from the NCBI public ftp site can also
be uncompressed on-the-fly on UNIX platforms.

  -a  ASN.1 Type
      Single Record: a Any, e Seq-entry, b Bioseq, s Bioseq-set, m Seq-submit
      Release File: t Batch Bioseq-set, u Batch Seq-submit
  -b  Bioseq-set is Binary [T/F]
  -c  Bioseq-set is Compressed [T/F]
  -p  Propagate Top Descriptors [T/F]

  -l  Log file

(Release files package many independent Seq-entry objects in a Bioseq-set.
Using -a t causes asn2gb to read one component at a time, processing it and
freeing it from memory before reading the next one.  Otherwise it would try
to process the entire file at once, almost certainly running out of memory.)

Remote fetching allows accession lookups and fetching of far components
from the NCBI network server. An indicated accession can also be fetched
for formatting.

  -r  Remote Fetching [T/F]
  -A  Accession to Fetch

Remote features should be fetched by using a modified form of -A:

  -A "<accession>,0,-1"

The middle number is the desired set structure complexity, which normally
should be 0. If the last number is -1, it will fetch all external feature
annotations and package them with the returned sequence record.


SEQENTRYTOGNBK FUNCTION

The NCBI software toolkit provides flatfile generation functions for
programmers to incorporate into their own computer applications.

SeqEntryToGnbk takes a SeqEntryPtr or SeqLocPtr and calls asn2gnbk_setup,
asn2gnbk_format, and asn2gnbk_cleanup, which are available from a private
header. It returns FALSE if there was a problem generating the flatfile.
BioseqToGnbk is simply a convenience function that takes a BioseqPtr, looks
up the parent SeqEntryPtr, and then calls SeqEntryToGnbk. To use these
functions, #include <asn2gnbk.h> in your program code.

NLM_EXTERN Boolean SeqEntryToGnbk (
  SeqEntryPtr sep,
  SeqLocPtr slp,
  FmtType format,
  ModType mode,
  StlType style,
  FlgType flags,
  LckType locks,
  CstType custom,
  XtraPtr extra,
  FILE *fp
);

NLM_EXTERN Boolean BioseqToGnbk (
  BioseqPtr bsp,
  SeqLocPtr slp,
  FmtType format,
  ModType mode,
  StlType style,
  FlgType flags,
  LckType locks,
  CstType custom,
  XtraPtr extra,
  FILE *fp
);

In the asn2gb application, format, mode, style, flags, locks, and custom
parameters are specified by the -f, -m, -s, -g, -h and -u arguments,
respectively.


FORMATS include GENBANK_FMT, EMBL_FMT, GENPEPT_FMT, and FTABLE_FMT
(Sequin's 5-column parsable feature table). If the SeqEntryPtr argument
passed to SeqEntryToGnbk points to a Bioseq-set, the function processes all
Bioseqs of the appropriate molecule type (nucleotide or protein) for the
specified format.


MODES are RELEASE_MODE, ENTREZ_MODE (release mode strictness except that it
allows local IDs and does not require a valid CDS /protein_id accession),
SEQUIN_MODE, and DUMP_MODE. RefSeq records can have certain qualifiers
(e.g., /transcript_id) and db_xrefs show up in release mode beyond those
approved by INSD agreement. Entrez mode is used for web display, and can
show new elements that haven't yet finished their 4-month quarantine period.


STYLES are NORMAL_STYLE, SEGMENT_STYLE, MASTER_STYLE, and CONTIG_STYLE.
Segment style is the traditional representation of segmented sequences,
while contig style displays a CONTIG line with a join of accessions instead
of a sequence. Normal style automatically chooses between segment and
contig style, depending upon the kind of data. (Near segmented records will
be done in segment style. Far segmented sequences or delta sequences with
no literals will be done as if you chose contig style.) Master style shows
features mapped to the segmented Bioseq's coordinates.


FLAGS are bit flags controlling appearance or behavior, and are ORed
together.

One 2-bit flag tells asn2gnbk to create HTML with web links, flatfile in
XML form, or flatfile in ASN.1 form. These settings are mutually exclusive.
The setup for creating HTML links is within SeqEntryToGnbk itself.

#define CREATE_HTML_FLATFILE       1
#define CREATE_XML_GBSEQ_FILE      2
#define CREATE_ASN_GBSEQ_FILE      3

Others control feature display behavior in contig style, whether it was
explicitly chosen or was called when a far segmented or far delta record
was processed in normal style.

#define SHOW_CONTIG_FEATURES       4
#define SHOW_CONTIG_SOURCES        8

A 2-bit flag set controls translation of CDS features with far products.

#define SHOW_FAR_TRANSLATION      16
#define TRANSLATE_IF_NO_PRODUCT   32
#define ALWAYS_TRANSLATE_CDS      48

The same set of flags also apply to transcription of mRNA features with far
products if the SHOW_TRANCRIPTION flag is also set.

#define SHOW_FAR_TRANSCRIPTION    16
#define TRANSCRIBE_IF_NO_PRODUCT  32
#define ALWAYS_TRANSCRIBE_MRNA    48

Any record can be shown with RefSeq policies for exception, source, and
other qualifiers, values, and db_xrefs that are not necessarily part of the
INSD agreement.

#define REFSEQ_CONVENTIONS        64

Another 2-bit flag controls where to get features when using far segmented
parts or far component delta Bioseqs.

#define ONLY_NEAR_FEATURES       128
#define FAR_FEATURES_SUPPRESS    256
#define NEAR_FEATURES_SUPPRESS   384

Other flags allow customization of reports from genomic product sets.

#define COPY_GPS_CDS_UP          512
#define COPY_GPS_GENE_DOWN      1024

The CONTIG block can be shown along with the sequence block in master or
segment style, when appropriate.

#define SHOW_CONTIG_AND_SEQ     2048

mRNAs and peptide features can show /transcription or /peptide sequence
qualifiers. This is most useful when generating INSDSeq XML so users do not
have to compute on the data themselves.

#define SHOW_TRANCRIPTION       4096
#define SHOW_PEPTIDE            8192

GBSeq XML has been replaced by INSDSeq XML.  The CREATE_XML_GBSEQ_FILE flag
will actually produce INSDSeq.  The original GBSeq can be generated during
the transition period by adding the following flag.

#define PRODUCE_OLD_GBSEQ      16384

Still others are expected to be rarely used, or are for testing new features.

#define DDBJ_VARIANT_FORMAT    32768
#define SPECIAL_GAP_DISPLAY    65536
#define FORCE_PRIMARY_BLOCK   131072
#define FORCE_ALLOW_FAR_FEATS 262144
#define RELAXED_MAPPING       524288


LOCKS are bits for controlling program performance, and are also ORed
together.

One flag set is for locking far segmented or delta components, far feature
location Bioseqs, or far feature product Bioseqs in advance. This prevents
the object manager from uncaching components at an inopportune time,
causing unnecessary thrashing. Far component Bioseqs are needed for
displaying the sequence.

#define LOCK_FAR_COMPONENTS        2
#define LOCK_FAR_LOCATIONS         4
#define LOCK_FAR_PRODUCTS          8

Another set attempts to do bulk accession to gi lookups in advance, which
is possible if PubSeqFetchEnable was called by the application. Remote
fetching in asn2gb uses this new access mechanism. Far component IDs are
needed for the CONTIG line, far location IDs for feature location joins,
and far product IDs for the /protein_id and /transcript_id accessions.

#define LOOKUP_FAR_COMPONENTS     16
#define LOOKUP_FAR_LOCATIONS      32
#define LOOKUP_FAR_PRODUCTS       64
#define LOOKUP_FAR_HISTORY       128
#define LOOKUP_FAR_INFERENCE     256
#define LOOKUP_FAR_OTHERS        512

To use PubSeqFetchEnable, the application should #include <pmfapi.h>.


CUSTOM are bit flags suppressing specific features, and are also ORed
together.

One set enables display of statistics for features and references.

#define SHOW_FEATURE_STATS         1
#define SHOW_REFERENCE_STATS       2

Another set suppresses common feature types or all features.

#define HIDE_FEATURES              4

#define HIDE_IMP_FEATS             8
#define HIDE_VARS_AND_REPT_REGNS  16
#define HIDE_SITES_BONDS_REGIONS  32
#define HIDE_CDD_FEATS            64
#define HIDE_CDS_PROD_FEATS      128

A 3-bit flag controls selective display of GeneRIF references or review
articles in RefSeq records.

#define HIDE_GENE_RIFS           256
#define ONLY_GENE_RIFS           512
#define ONLY_REVIEW_PUBS         768
#define NEWEST_PUBS             1024
#define OLDEST_PUBS             1280
#define HIDE_ALL_PUBS           1792

Protein feature tables and References in feature tables can also be shown.

#define SHOW_PROT_FTABLE        2048
#define SHOW_FTABLE_REFS        4096

Source features, instantiated Gap features, and the sequence itself can
also be suppressed.

#define HIDE_SOURCE_FEATS       8192
#define HIDE_GAP_FEATS         16384
#define HIDE_SEQUENCE          32768

Gaps in far delta sequences in Web Entrez are normally converted to a
shorthand notation. These can be forced to expand to runs of Ns.

#define EXPANDED_GAP_DISPLAY   65536

Gene Ontology terms can be suppressed if desired.

#define HIDE_GO_TERMS         131072

The CDS /translation can also be suppressed, even with near products.

#define HIDE_TRANSLATION      262144

Evidence qualifiers, including experiment and inference, can be suppressed.

#define HIDE_EVIDENCE_QUALS   524288

Other custom flags modify the output to support internal NCBI processing.

#define NEW_XML_POLICY       1048576
#define OLD_GBSEQ_XML        2097152
#define FORCE_SEQ_SPANS      4194304


EXTRA is an opaque pointer used for preparing internal NCBI indices.  Most
programs will pass NULL for this parameter.


SAMPLE GENBANK FLATFILE

A sample genomic sequence encoding a spliced mRNA is shown below in GenBank
format. The exon features in the original record have been removed from
this example.

LOCUS       AF012431                2141 bp    DNA     linear   ROD 07-FEB-2000
DEFINITION  Mus musculus D-dopachrome tautomerase (Ddt) gene, complete cds.
ACCESSION   AF012431
VERSION     AF012431.1  GI:2352907
KEYWORDS    .
SOURCE      Mus musculus (house mouse)
  ORGANISM  Mus musculus
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia;
            Sciurognathi; Muridae; Murinae; Mus.
REFERENCE   1  (bases 1 to 2141)
  AUTHORS   Esumi,N., Budarf,M., Ciccarelli,L., Sellinger,B., Kozak,C.A. and
            Wistow,G.
  TITLE     Conserved gene structure and genomic linkage for D-dopachrome
            tautomerase (DDT) and MIF
  JOURNAL   Mamm. Genome 9 (9), 753-757 (1998)
   PUBMED   9716662
REFERENCE   2  (bases 1 to 2141)
  AUTHORS   Esumi,N. and Wistow,G.
  TITLE     Direct Submission
  JOURNAL   Submitted (03-JUL-1997) Molecular Structure and Function, NEI,
            Building 6, Rm. 331, NIH, Bethesda, MD 20892, USA
FEATURES             Location/Qualifiers
     source          1..2141
                     /organism="Mus musculus"
                     /mol_type="genomic DNA"
                     /db_xref="taxon:10090"
                     /chromosome="10"
     gene            1..2141
                     /gene="Ddt"
     mRNA            join(1..159,462..637,1868..2141)
                     /gene="Ddt"
                     /product="D-dopachrome tautomerase"
     CDS             join(52..159,462..637,1868..1940)
                     /gene="Ddt"
                     /note="related to macrophage migration inhibitory factor
                     (MIF); in vitro activity on D-dopachrome"
                     /codon_start=1
                     /product="D-dopachrome tautomerase"
                     /protein_id="AAC77467.1"
                     /db_xref="GI:2352908"
                     /translation="MPFVELETNLPASRIPAGLENRLCAATATILDKPEDRVSVTIRP
                     GMTLLMNKSTEPCAHLLVSSIGVVGTAEQNRTHSASFFKFLTEELSLDQDRIVIRFFP
                     LEAWQIGKKGTVMTFL"
BASE COUNT      473 a    567 c    570 g    531 t
ORIGIN
        1 agctcacccg gtgcagttac cgtttggcga tcccactctt ctcccgctaa catgccattc
       61 gttgagttgg aaacaaactt gccggctagc cgcatacccg cggggctgga gaaccggctg
      121 tgtgcggcca cagccaccat cctggacaaa cccgaagacg tgagtgaggg tcggcgagaa
      181 cttgtgggct agggtcggac ctcccaatga cccgttccca tccccaggga ccccactccc
      241 ctggtaacct ctgaccttcc gtgtcctatc ctcccttcct agatcccttc ctggttgtct
      301 ttcccaggcg tgaccctgac gtgactgact cccaaggatc ctgggcagtg tcccagaccc
      361 ggagccctcg gacccccacg ttaagaattt ggcgcgcccc cttctgaaca ccagccatgc
      421 cctgcccaag cttcaggatt taacttttgt gttccttgca gcgcgtgagc gttacgatac
      481 gacctggcat gaccctgttg atgaacaaat ccacagagcc ttgtgctcac cttctggtct
      541 cttccatcgg ggttgtgggc accgcggagc agaaccgcac tcacagcgcc agcttcttca
      601 agttcctcac cgaggagctg tccctggacc aggaccggta tgcagggcca gtgagggaac
      661 gtatttgtgc gtctggagtc aggactcagt ctctctgtat gaggttgggg ggggggaggg
      721 gtcactattt gctggttcca gaaagcactc agtgtccttg tccacgaagg tggactcctc
      781 aggcactgga atggtgagtc tgtgatcaga atgatagcaa gatttcaatt ccttcgactc
      841 tctacagccc cgagaaagga tggtttggga agccccagtg ttgtcttgtg tgtactgaga
      901 atctacttag gcaccctctt aaccactgtg atagtggcct cctcaccgtc actgaaccag
      961 ggggtctggt tttttaaggg agaacttttc caggctggtc cgagggaatc tggttgtgtc
     1021 ctgaggcaga taacctttga actagataag gctccgggag agttgctgga tgataaaaag
     1081 acctccccca caaggtgacc ctaccctccc ccctccccat ccttacattc tgaggcagag
     1141 ttagagtctc atattcctga ggctggagcg ggcctgtgaa gaactacgga gataagtttg
     1201 aaagagcctt ccaaaatgga gtcctagtgg gctcaggaaa gttggtattg gctgcttttg
     1261 ttggatgctc aaatgctgtc ctttagttga ggggacaata cttcttaacg gtaatgctcg
     1321 tgcacacagc acagggcaga tttggtagct tcctgacata gataactgta ttgggccagt
     1381 tttacagatg gaaacctgag ggtgtcagcc ctgtgcacaa ccaccctggt gccagacgat
     1441 cgccagggac ttcctctgag tcctgtgatt gagcaattgc tgattcccac agatttgaat
     1501 cagatttgaa cctgcgcctc acttagagct gggctttggt tcaaaactaa gtgcctggta
     1561 ccctgggcac gcctttagga gcatgcagtt agttagaagc agggggactg tttgttagcc
     1621 cgtaagcagc ctaacatgct cacctgagca cagagcacag gtattgaagc cattgcgtta
     1681 agtctgcact gggaccggta tagccatcac ctttcttctg acttgtcttt ggtgcaagga
     1741 tcattagctg gggtgggcag attggcaaaa tatcctgcag gctgatatgg gctggcctgt
     1801 ctggcaggga ccttaacaaa tgaggggtgt atgcaggagt tgacatctct ccttcttcct
     1861 cctaaaggat cgttatccgc ttcttcccct tggaggcttg gcagatcgga aagaaaggaa
     1921 ctgtcatgac atttctgtga cggaaacaaa gaacccaggg tgtttgctcg aaccgggcca
     1981 gagcccttcc agagaggccc tcccggcaga atcgtggcct ggtagatagg atggtaaatc
     2041 cctcttttgc ctaaacgtct gcgacttcag tggtccattt ttctcttccc cagcctcgtg
     2101 aataattgaa agagagcaaa taaatgaaga gaatatcatt c
//


SAMPLE INSDSET XML

The same record is shown in INSDSet XML format. INSDSeq XML is a data
distribution format meant to be read by a computer, not a display format
intended for human reading, so sequence letters are single strings of
characters with no spaces or newlines. (The sequences and other long lines
are word-wrapped here only for printing.)

The INSDFeature_location is the string displayed exactly as it was in the
GenBank flatfile.

  join(1..159,462..637,1868..2141)

For the convenience of users who wish to compute on features without having
to parse these string, the individual feature intervals are also presented
individually.

        <INSDFeature_intervals>
          <INSDInterval>
            <INSDInterval_from>1</INSDInterval_from>
            <INSDInterval_to>159</INSDInterval_to>
            <INSDInterval_accession>AF012431.1</INSDInterval_accession>
          </INSDInterval>
          <INSDInterval>
            <INSDInterval_from>462</INSDInterval_from>
            <INSDInterval_to>637</INSDInterval_to>
            <INSDInterval_accession>AF012431.1</INSDInterval_accession>
          </INSDInterval>
          <INSDInterval>
          ...

The record here was generated with the SHOW_TRANCRIPTION flag set to
extract the bases under the mRNA feature interval and display them in a
transcription qualifier. This eliminates the need to process feature
intervals for the common task of obtaining the mRNA bases. SHOW_PEPTIDE
does the same for extracting peptide sequences from under sig_peptide or
mat_peptide features. The transcription and peptide qualifiers are
extensions of those approved by the INSD for official releases.

<?xml version="1.0"?>
<!DOCTYPE INSDSet PUBLIC "-//NCBI//INSD INSDSeq/EN"
"http://www.ncbi.nlm.nih.gov/INSD_INSDSeq.dtd">
<INSDSet>
  <INSDSeq>
    <INSDSeq_locus>AF012431</INSDSeq_locus>
    <INSDSeq_length>2141</INSDSeq_length>
    <INSDSeq_moltype>DNA</INSDSeq_moltype>
    <INSDSeq_topology>linear</INSDSeq_topology>
    <INSDSeq_division>ROD</INSDSeq_division>
    <INSDSeq_update-date>07-FEB-2000</INSDSeq_update-date>
    <INSDSeq_create-date>03-SEP-1997</INSDSeq_create-date>
    <INSDSeq_definition>Mus musculus D-dopachrome tautomerase (Ddt) gene,
complete cds</INSDSeq_definition>
    <INSDSeq_primary-accession>AF012431</INSDSeq_primary-accession>
    <INSDSeq_accession-version>AF012431.1</INSDSeq_accession-version>
    <INSDSeq_other-seqids>
      <INSDSeqid>gb|AF012431.1|AF012431</INSDSeqid>
      <INSDSeqid>gi|2352907</INSDSeqid>
    </INSDSeq_other-seqids>
    <INSDSeq_source>Mus musculus (house mouse)</INSDSeq_source>
    <INSDSeq_organism>Mus musculus</INSDSeq_organism>
    <INSDSeq_taxonomy>Eukaryota; Metazoa; Chordata; Craniata; Vertebrata;
Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia;
Sciurognathi; Muridae; Murinae; Mus</INSDSeq_taxonomy>
    <INSDSeq_references>
      <INSDReference>
        <INSDReference_reference>1 (bases 1 to 2141)</INSDReference_reference>
        <INSDReference_authors>
          <INSDAuthor>Esumi,N.</INSDAuthor>
          <INSDAuthor>Budarf,M.</INSDAuthor>
          <INSDAuthor>Ciccarelli,L.</INSDAuthor>
          <INSDAuthor>Sellinger,B.</INSDAuthor>
          <INSDAuthor>Kozak,C.A.</INSDAuthor>
          <INSDAuthor>Wistow,G.</INSDAuthor>
        </INSDReference_authors>
        <INSDReference_title>Conserved gene structure and genomic linkage for
D-dopachrome tautomerase (DDT) and MIF</INSDReference_title>
        <INSDReference_journal>Mamm. Genome 9 (9), 753-757 (1998)
</INSDReference_journal>
        <INSDReference_pubmed>9716662</INSDReference_pubmed>
      </INSDReference>
      <INSDReference>
        <INSDReference_reference>2 (bases 1 to 2141)</INSDReference_reference>
        <INSDReference_authors>
          <INSDAuthor>Esumi,N.</INSDAuthor>
          <INSDAuthor>Wistow,G.</INSDAuthor>
        </INSDReference_authors>
        <INSDReference_title>Direct Submission</INSDReference_title>
        <INSDReference_journal>Submitted (03-JUL-1997) Molecular Structure and
Function, NEI, Building 6, Rm. 331, NIH, Bethesda, MD 20892, USA
</INSDReference_journal>
      </INSDReference>
    </INSDSeq_references>
    <INSDSeq_feature-table>
      <INSDFeature>
        <INSDFeature_key>source</INSDFeature_key>
        <INSDFeature_location>1..2141</INSDFeature_location>
        <INSDFeature_quals>
          <INSDQualifier>
            <INSDQualifier_name>organism</INSDQualifier_name>
            <INSDQualifier_value>Mus musculus</INSDQualifier_value>
          </INSDQualifier>
          <INSDQualifier>
            <INSDQualifier_name>mol_type</INSDQualifier_name>
            <INSDQualifier_value>genomic DNA</INSDQualifier_value>
          </INSDQualifier>
          <INSDQualifier>
            <INSDQualifier_name>db_xref</INSDQualifier_name>
            <INSDQualifier_value>taxon:10090</INSDQualifier_value>
          </INSDQualifier>
          <INSDQualifier>
            <INSDQualifier_name>chromosome</INSDQualifier_name>
            <INSDQualifier_value>10</INSDQualifier_value>
          </INSDQualifier>
        </INSDFeature_quals>
      </INSDFeature>
      <INSDFeature>
        <INSDFeature_key>gene</INSDFeature_key>
        <INSDFeature_location>1..2141</INSDFeature_location>
        <INSDFeature_intervals>
          <INSDInterval>
            <INSDInterval_from>1</INSDInterval_from>
            <INSDInterval_to>2141</INSDInterval_to>
            <INSDInterval_accession>AF012431.1</INSDInterval_accession>
          </INSDInterval>
        </INSDFeature_intervals>
        <INSDFeature_quals>
          <INSDQualifier>
            <INSDQualifier_name>gene</INSDQualifier_name>
            <INSDQualifier_value>Ddt</INSDQualifier_value>
          </INSDQualifier>
        </INSDFeature_quals>
      </INSDFeature>
      <INSDFeature>
        <INSDFeature_key>mRNA</INSDFeature_key>
        <INSDFeature_location>join(1..159,462..637,1868..2141)
</INSDFeature_location>
        <INSDFeature_intervals>
          <INSDInterval>
            <INSDInterval_from>1</INSDInterval_from>
            <INSDInterval_to>159</INSDInterval_to>
            <INSDInterval_accession>AF012431.1</INSDInterval_accession>
          </INSDInterval>
          <INSDInterval>
            <INSDInterval_from>462</INSDInterval_from>
            <INSDInterval_to>637</INSDInterval_to>
            <INSDInterval_accession>AF012431.1</INSDInterval_accession>
          </INSDInterval>
          <INSDInterval>
            <INSDInterval_from>1868</INSDInterval_from>
            <INSDInterval_to>2141</INSDInterval_to>
            <INSDInterval_accession>AF012431.1</INSDInterval_accession>
          </INSDInterval>
        </INSDFeature_intervals>
        <INSDFeature_quals>
          <INSDQualifier>
            <INSDQualifier_name>gene</INSDQualifier_name>
            <INSDQualifier_value>Ddt</INSDQualifier_value>
          </INSDQualifier>
          <INSDQualifier>
            <INSDQualifier_name>product</INSDQualifier_name>
            <INSDQualifier_value>D-dopachrome tautomerase</INSDQualifier_value>
          </INSDQualifier>
          <INSDQualifier>
            <INSDQualifier_name>transcription</INSDQualifier_name>
            <INSDQualifier_value>AGCTCACCCGGTGCAGTTACCGTTTGGCGATCCCACTCTTCT
CCCGCTAACATGCCATTCGTTGAGTTGGAAACAAACTTGCCGGCTAGCCGCATACCCGCGGGGCTGGAGAACCGG
CTGTGTGCGGCCACAGCCACCATCCTGGACAAACCCGAAGACCGCGTGAGCGTTACGATACGACCTGGCATGACC
CTGTTGATGAACAAATCCACAGAGCCTTGTGCTCACCTTCTGGTCTCTTCCATCGGGGTTGTGGGCACCGCGGAG
CAGAACCGCACTCACAGCGCCAGCTTCTTCAAGTTCCTCACCGAGGAGCTGTCCCTGGACCAGGACCGGATCGTT
ATCCGCTTCTTCCCCTTGGAGGCTTGGCAGATCGGAAAGAAAGGAACTGTCATGACATTTCTGTGACGGAAACAA
AGAACCCAGGGTGTTTGCTCGAACCGGGCCAGAGCCCTTCCAGAGAGGCCCTCCCGGCAGAATCGTGGCCTGGTA
GATAGGATGGTAAATCCCTCTTTTGCCTAAACGTCTGCGACTTCAGTGGTCCATTTTTCTCTTCCCCAGCCTCGT
GAATAATTGAAAGAGAGCAAATAAATGAAGAGAATATCATTC</INSDQualifier_value>
          </INSDQualifier>
        </INSDFeature_quals>
      </INSDFeature>
      <INSDFeature>
        <INSDFeature_key>CDS</INSDFeature_key>
        <INSDFeature_location>join(52..159,462..637,1868..1940)
</INSDFeature_location>
        <INSDFeature_intervals>
          <INSDInterval>
            <INSDInterval_from>52</INSDInterval_from>
            <INSDInterval_to>159</INSDInterval_to>
            <INSDInterval_accession>AF012431.1</INSDInterval_accession>
          </INSDInterval>
          <INSDInterval>
            <INSDInterval_from>462</INSDInterval_from>
            <INSDInterval_to>637</INSDInterval_to>
            <INSDInterval_accession>AF012431.1</INSDInterval_accession>
          </INSDInterval>
          <INSDInterval>
            <INSDInterval_from>1868</INSDInterval_from>
            <INSDInterval_to>1940</INSDInterval_to>
            <INSDInterval_accession>AF012431.1</INSDInterval_accession>
          </INSDInterval>
        </INSDFeature_intervals>
        <INSDFeature_quals>
          <INSDQualifier>
            <INSDQualifier_name>gene</INSDQualifier_name>
            <INSDQualifier_value>Ddt</INSDQualifier_value>
          </INSDQualifier>
          <INSDQualifier>
            <INSDQualifier_name>note</INSDQualifier_name>
            <INSDQualifier_value>related to macrophage migration inhibitory
factor (MIF); in vitro activity on D-dopachrome</INSDQualifier_value>
          </INSDQualifier>
          <INSDQualifier>
            <INSDQualifier_name>codon_start</INSDQualifier_name>
            <INSDQualifier_value>1</INSDQualifier_value>
          </INSDQualifier>
          <INSDQualifier>
            <INSDQualifier_name>transl_table</INSDQualifier_name>
            <INSDQualifier_value>1</INSDQualifier_value>
          </INSDQualifier>
          <INSDQualifier>
            <INSDQualifier_name>product</INSDQualifier_name>
            <INSDQualifier_value>D-dopachrome tautomerase</INSDQualifier_value>
          </INSDQualifier>
          <INSDQualifier>
            <INSDQualifier_name>protein_id</INSDQualifier_name>
            <INSDQualifier_value>AAC77467.1</INSDQualifier_value>
          </INSDQualifier>
          <INSDQualifier>
            <INSDQualifier_name>db_xref</INSDQualifier_name>
            <INSDQualifier_value>GI:2352908</INSDQualifier_value>
          </INSDQualifier>
          <INSDQualifier>
            <INSDQualifier_name>translation</INSDQualifier_name>
            <INSDQualifier_value>MPFVELETNLPASRIPAGLENRLCAATATILDKPEDRVSVTI
RPGMTLLMNKSTEPCAHLLVSSIGVVGTAEQNRTHSASFFKFLTEELSLDQDRIVIRFFPLEAWQIGKKGTVMTF
L</INSDQualifier_value>
          </INSDQualifier>
        </INSDFeature_quals>
      </INSDFeature>
    </INSDSeq_feature-table>
    <INSDSeq_sequence>AGCTCACCCGGTGCAGTTACCGTTTGGCGATCCCACTCTTCTCCCGCTAACAT
GCCATTCGTTGAGTTGGAAACAAACTTGCCGGCTAGCCGCATACCCGCGGGGCTGGAGAACCGGCTGTGTGCGGC
CACAGCCACCATCCTGGACAAACCCGAAGACGTGAGTGAGGGTCGGCGAGAACTTGTGGGCTAGGGTCGGACCTC
CCAATGACCCGTTCCCATCCCCAGGGACCCCACTCCCCTGGTAACCTCTGACCTTCCGTGTCCTATCCTCCCTTC
CTAGATCCCTTCCTGGTTGTCTTTCCCAGGCGTGACCCTGACGTGACTGACTCCCAAGGATCCTGGGCAGTGTCC
CAGACCCGGAGCCCTCGGACCCCCACGTTAAGAATTTGGCGCGCCCCCTTCTGAACACCAGCCATGCCCTGCCCA
AGCTTCAGGATTTAACTTTTGTGTTCCTTGCAGCGCGTGAGCGTTACGATACGACCTGGCATGACCCTGTTGATG
AACAAATCCACAGAGCCTTGTGCTCACCTTCTGGTCTCTTCCATCGGGGTTGTGGGCACCGCGGAGCAGAACCGC
ACTCACAGCGCCAGCTTCTTCAAGTTCCTCACCGAGGAGCTGTCCCTGGACCAGGACCGGTATGCAGGGCCAGTG
AGGGAACGTATTTGTGCGTCTGGAGTCAGGACTCAGTCTCTCTGTATGAGGTTGGGGGGGGGGAGGGGTCACTAT
TTGCTGGTTCCAGAAAGCACTCAGTGTCCTTGTCCACGAAGGTGGACTCCTCAGGCACTGGAATGGTGAGTCTGT
GATCAGAATGATAGCAAGATTTCAATTCCTTCGACTCTCTACAGCCCCGAGAAAGGATGGTTTGGGAAGCCCCAG
TGTTGTCTTGTGTGTACTGAGAATCTACTTAGGCACCCTCTTAACCACTGTGATAGTGGCCTCCTCACCGTCACT
GAACCAGGGGGTCTGGTTTTTTAAGGGAGAACTTTTCCAGGCTGGTCCGAGGGAATCTGGTTGTGTCCTGAGGCA
GATAACCTTTGAACTAGATAAGGCTCCGGGAGAGTTGCTGGATGATAAAAAGACCTCCCCCACAAGGTGACCCTA
CCCTCCCCCCTCCCCATCCTTACATTCTGAGGCAGAGTTAGAGTCTCATATTCCTGAGGCTGGAGCGGGCCTGTG
AAGAACTACGGAGATAAGTTTGAAAGAGCCTTCCAAAATGGAGTCCTAGTGGGCTCAGGAAAGTTGGTATTGGCT
GCTTTTGTTGGATGCTCAAATGCTGTCCTTTAGTTGAGGGGACAATACTTCTTAACGGTAATGCTCGTGCACACA
GCACAGGGCAGATTTGGTAGCTTCCTGACATAGATAACTGTATTGGGCCAGTTTTACAGATGGAAACCTGAGGGT
GTCAGCCCTGTGCACAACCACCCTGGTGCCAGACGATCGCCAGGGACTTCCTCTGAGTCCTGTGATTGAGCAATT
GCTGATTCCCACAGATTTGAATCAGATTTGAACCTGCGCCTCACTTAGAGCTGGGCTTTGGTTCAAAACTAAGTG
CCTGGTACCCTGGGCACGCCTTTAGGAGCATGCAGTTAGTTAGAAGCAGGGGGACTGTTTGTTAGCCCGTAAGCA
GCCTAACATGCTCACCTGAGCACAGAGCACAGGTATTGAAGCCATTGCGTTAAGTCTGCACTGGGACCGGTATAG
CCATCACCTTTCTTCTGACTTGTCTTTGGTGCAAGGATCATTAGCTGGGGTGGGCAGATTGGCAAAATATCCTGC
AGGCTGATATGGGCTGGCCTGTCTGGCAGGGACCTTAACAAATGAGGGGTGTATGCAGGAGTTGACATCTCTCCT
TCTTCCTCCTAAAGGATCGTTATCCGCTTCTTCCCCTTGGAGGCTTGGCAGATCGGAAAGAAAGGAACTGTCATG
ACATTTCTGTGACGGAAACAAAGAACCCAGGGTGTTTGCTCGAACCGGGCCAGAGCCCTTCCAGAGAGGCCCTCC
CGGCAGAATCGTGGCCTGGTAGATAGGATGGTAAATCCCTCTTTTGCCTAAACGTCTGCGACTTCAGTGGTCCAT
TTTTCTCTTCCCCAGCCTCGTGAATAATTGAAAGAGAGCAAATAAATGAAGAGAATATCATTC
</INSDSeq_sequence>
  </INSDSeq>
</INSDSet>

