Swissprot sequence format

Description

The following is an example of Swissprot "flat" format, the only swissprot format flavor that BioPerl is capable of parsing as of version 1.5.1. The Bio::SeqIO system can parse these files with the Bio::SeqIO::swiss module.

Swissprot also releases an XML formatted database.

Example

ID   MA32_HUMAN     STANDARD;      PRT;   282 AA.
AC   Q07021;
DT   01-FEB-1995 (Rel. 31, Created)
DT   01-FEB-1995 (Rel. 31, Last sequence update)
DT   01-OCT-2000 (Rel. 40, Last annotation update)
DE   COMPLEMENT COMPONENT 1, Q SUBCOMPONENT BINDING PROTEIN, MITOCHONDRIAL
DE   PRECURSOR (GLYCOPROTEIN GC1QBP) (GC1Q-R PROTEIN) (HYALURONAN-BINDING
DE   PROTEIN 1) (PRE-MRNA SPLICING FACTOR SF2, P32 SUBUNIT) (P33).
GN   GC1QBP OR HABP1 OR SF2P32 OR C1QBP.
OS   Homo sapiens (Human).
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC   Mammalia; Eutheria; Primates; Catarrhini; Hominidae; Homo.
OX   NCBI_TaxID=9606;
RN   [1]
RP   SEQUENCE FROM N.A., AND SEQUENCE OF 74; 76-93 AND 208-216.
RC   TISSUE=FIBROBLAST;
RX   MEDLINE=94085792; PubMed=8262387;
RA   Honore B., Madsen P., Rasmussen H.H., Vandekerckhove J., Celis J.E.,
RA   Leffers H.;
RT   "Cloning and expression of a cDNA covering the complete coding region
RT   of the P32 subunit of human pre-mRNA splicing factor SF2.";
RL   Gene 134:283-287(1993).
RN   [2]
RP   SEQUENCE OF 5-282 FROM N.A., AND SEQUENCE OF 74-114.
RX   MEDLINE=91309150; PubMed=1830244;
RA   Krainer A.R., Mayeda A., Kozak D., Binns G.;
RT   "Functional expression of cloned human splicing factor SF2: homology
RT   to RNA-binding proteins, U1 70K, and Drosophila splicing regulators.";
RL   Cell 66:383-394(1991).
RN   [3]
RP   SEQUENCE FROM N.A., AND PARTIAL SEQUENCE.
RX   MEDLINE=94253723; PubMed=8195709;
RA   Ghebrehiwet B., Lim B.L., Peerschke E.I., Willis A.C., Reid K.B.;
RT   "Isolation, cDNA cloning, and overexpression of a 33-kD cell surface
RT   glycoprotein that binds to the globular 'heads' of C1q.";
RL   J. Exp. Med. 179:1809-1821(1994).
RN   [4]
RP   X-RAY CRYSTALLOGRAPHY (2.25 ANGSTROMS).
RX   MEDLINE=99199225; PubMed=10097078;
RA   Jiang J., Zhang Y., Krainer A.R., Xu R.-M.;
RT   "Crystal structure of human p32, a doughnut-shaped acidic
RT   mitochondrial matrix protein.";
RL   Proc. Natl. Acad. Sci. U.S.A. 96:3572-3577(1999).
CC   -!- FUNCTION: NOT KNOWN. BINDS TO THE GLOBULAR "HEADS" OF C1Q THUS
CC       INHIBITING C1 ACTIVATION.
CC   -!- SUBCELLULAR LOCATION: MITOCHONDRIAL MATRIX.
CC   -!- SIMILARITY: BELONGS TO THE MAM33 FAMILY.
CC   -!- CAUTION: WAS ORIGINALLY (REF.1 AND REF.2) THOUGHT TO BE A PRE-MRNA
CC       SPLICING FACTOR THAT PLAYS A ROLE IN PREVENTING EXON SKIPPING,
CC       ENSURING THE ACCURACY OF SPLICING AND REGULATING ALTERNATIVE
CC       SPLICING.
CC   --------------------------------------------------------------------------
CC   This SWISS-PROT entry is copyright. It is produced through a collaboration
CC   between  the Swiss Institute of Bioinformatics  and the  EMBL outstation -
CC   the European Bioinformatics Institute.  There are no  restrictions on  its
CC   use  by  non-profit  institutions as long  as its content  is  in  no  way
CC   modified and this statement is not removed.  Usage  by  and for commercial
CC   entities requires a license agreement (See http://www.isb-sib.ch/announce/
CC   or send an email to license@isb-sib.ch).
CC   --------------------------------------------------------------------------
DR   EMBL; L04636; AAA16315.1; -.
DR   EMBL; M69039; AAA73055.1; -.
DR   EMBL; X75913; CAA53512.1; -.
DR   PIR; JT0762; JT0762.
DR   PIR; S44104; S44104.
DR   PDB; 1P32; 06-APR-99.
DR   MIM; 601269; -.
KW   Mitochondrion; Transit peptide; 3D-structure.
FT   TRANSIT       1     73       MITOCHONDRION.
FT   CHAIN        74    282       COMPLEMENT COMPONENT 1, Q SUBCOMPONENT
FT                                BINDING PROTEIN.
SQ   SEQUENCE   282 AA;  31362 MW;  2F747FA73BB1314B CRC64;
     MLPLLRCVPR VLGSSVAGLR AAAPASPFRQ LLQPAPRLCT RPFGLLSVRA GSERRPGLLR
     PRGPCACGCG CGSLHTDGDK AFVDFLSDEI KEERKIQKHK TLPKMSGGWE LELNGTEAKL
     VRKVAGEKIT VTFNINNSIP PTFDGEEEPS QGQKVEEQEP ELTSTPNFVV EVIKNDDGKK
     ALVLDCHYPE DEVGQEDEAE SDIFSIREVS FQSTGESEWK DTNYTLNTDS LDWALYDHLM
     DFLADRGVDN TFADELVELS TALEHQEYIT FLEDLKSFVK SQ
//