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Protein

Sex-determining transformer protein 1

Gene

tra-1

Organism
Caenorhabditis elegans
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Plays a major role in controlling sexual phenotype (PubMed:1339311). Terminal global regulator in a well-characterized cascade of sex-determining genes (PubMed:8367286). Promotes female development (PubMed:11124807). Interacts with tra-2 to promote spermatogenesis (PubMed:11250902). Promotes spermatogenesis through the Tip60 HAT complex and by regulating the expression of genes, such as fog-3, required for male development (By similarity). With trr-1, activates the fog-3 gene to determine sperm/oocyte cell fate (By similarity). In hermaphrodites, binds to an intronic regulatory site in the ceh-30 gene, preventing ceh-30 transcription and thereby preventing survival of the CEM (cephalic male) sensory neurons (PubMed:18056428).By similarity5 Publications

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri208 – 23326C2H2-type 1; low DNA-binding affinityPROSITE-ProRule annotationAdd
BLAST
Zinc fingeri244 – 27027C2H2-type 2; low DNA-binding affinityPROSITE-ProRule annotationAdd
BLAST
Zinc fingeri276 – 30025C2H2-type 3PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri306 – 33126C2H2-type 4PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri337 – 36226C2H2-type 5PROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

  • metal ion binding Source: UniProtKB-KW
  • protein C-terminus binding Source: UniProtKB
  • RNA polymerase II distal enhancer sequence-specific DNA binding Source: WormBase
  • RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding Source: WormBase
  • RNA polymerase II regulatory region sequence-specific DNA binding Source: WormBase
  • sequence-specific DNA binding Source: WormBase

GO - Biological processi

  • cell differentiation Source: UniProtKB-KW
  • female germ-line sex determination Source: UniProtKB
  • female somatic sex determination Source: UniProtKB
  • gonad development Source: UniProtKB
  • negative regulation of transcription from RNA polymerase II promoter Source: WormBase
  • positive regulation of neuron apoptotic process Source: WormBase
  • spermatogenesis Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Developmental protein

Keywords - Biological processi

Differentiation, Sexual differentiation, Spermatogenesis

Keywords - Ligandi

DNA-binding, Metal-binding, Zinc

Enzyme and pathway databases

ReactomeiR-CEL-5610787. Hedgehog 'off' state.
R-CEL-5632684. Hedgehog 'on' state.
SignaLinkiP34708.

Names & Taxonomyi

Protein namesi
Recommended name:
Sex-determining transformer protein 1Imported
Alternative name(s):
Hermaphrodization of XO animals protein 2Imported
Gene namesi
Name:tra-1Imported
Synonyms:her-2
ORF Names:Y47D3A.6Imported
OrganismiCaenorhabditis elegans
Taxonomic identifieri6239 [NCBI]
Taxonomic lineageiEukaryotaMetazoaEcdysozoaNematodaChromadoreaRhabditidaRhabditoideaRhabditidaePeloderinaeCaenorhabditis
Proteomesi
  • UP000001940 Componenti: Chromosome III

Organism-specific databases

WormBaseiY47D3A.6a; CE28129; WBGene00006604; tra-1.
Y47D3A.6b; CE28130; WBGene00006604; tra-1.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: UniProtKB
  • nucleus Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 11101110Sex-determining transformer protein 1PRO_0000046895Add
BLAST

Proteomic databases

EPDiP34708.
PaxDbiP34708.
PRIDEiP34708.

Expressioni

Tissue specificityi

Expressed in intestine and gonads (at protein level).1 Publication

Developmental stagei

Isoform b is expressed abundantly in second larval (L2) stage. Isoform a is more abundant in embryos.1 Publication

Interactioni

Subunit structurei

Interacts with the MX regulatory domain of tra-2.2 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
fem-1P172212EBI-367214,EBI-1998155
fem-2P495942EBI-367214,EBI-1998402
fem-3P346912EBI-367214,EBI-445465
tra-2P347095EBI-367204,EBI-367223

GO - Molecular functioni

  • protein C-terminus binding Source: UniProtKB

Protein-protein interaction databases

BioGridi41731. 5 interactions.
IntActiP34708. 37 interactions.
MINTiMINT-154380.
STRINGi6239.Y47D3A.6a.

Structurei

3D structure databases

ProteinModelPortaliP34708.
SMRiP34708. Positions 210-363.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi424 – 50582Ala-richPROSITE-ProRule annotationAdd
BLAST
Compositional biasi522 – 58362Pro-richPROSITE-ProRule annotationAdd
BLAST
Compositional biasi1069 – 108719Pro-richPROSITE-ProRule annotationAdd
BLAST

Domaini

Only isoform a (Tra-1L), is thought to bind DNA. Zinc fingers 3, 4 and 5 are the most important for DNA binding; removal of finger 5 almost abolishes DNA binding and prevents the selection of binding sites.1 Publication

Sequence similaritiesi

Contains 5 C2H2-type zinc fingers.PROSITE-ProRule annotation

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri208 – 23326C2H2-type 1; low DNA-binding affinityPROSITE-ProRule annotationAdd
BLAST
Zinc fingeri244 – 27027C2H2-type 2; low DNA-binding affinityPROSITE-ProRule annotationAdd
BLAST
Zinc fingeri276 – 30025C2H2-type 3PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri306 – 33126C2H2-type 4PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri337 – 36226C2H2-type 5PROSITE-ProRule annotationAdd
BLAST

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

eggNOGiKOG1721. Eukaryota.
COG5048. LUCA.
HOGENOMiHOG000154672.
InParanoidiP34708.
KOiK06230.
OrthoDBiEOG7X6KZ8.

Family and domain databases

Gene3Di3.30.160.60. 5 hits.
InterProiIPR007087. Znf_C2H2.
IPR015880. Znf_C2H2-like.
IPR013087. Znf_C2H2/integrase_DNA-bd.
[Graphical view]
SMARTiSM00355. ZnF_C2H2. 5 hits.
[Graphical view]
PROSITEiPS00028. ZINC_FINGER_C2H2_1. 4 hits.
PS50157. ZINC_FINGER_C2H2_2. 4 hits.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform a (identifier: P34708-1) [UniParc]FASTAAdd to basket

Also known as: Tra-1L1 Publication

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MMAPSTEDPD TVVEAQRRGS FSKKKNANGW NKVELVDQCA KQMGSEDKQP
60 70 80 90 100
GGGDVKTEND PSKNGLGSAT SNFIQSSVPP SHQTLSNPLQ LSPPAEASVA
110 120 130 140 150
QQSGASQVFP TFQAALGASS DELLQPNATS SSTSSSASTS SIVPVVKFTN
160 170 180 190 200
QTAPNGSTVA TSVGQNVRLT INGKRVGRPP GTFKRPQNNA ANSSNSGNDS
210 220 230 240 250
DMMGDHDLTC RWKSCNSSFQ TLKALVDHVQ ESHVQSTEQE HHAWRCEWEG
260 270 280 290 300
CDRNETFKAL YMLIVHVRRH TGEKPNKCEY PGCGKEYSRL ENLKTHRRTH
310 320 330 340 350
TGEKPYKCEF ADCEKAFSNA SDRAKHQNRT HSNLKPYSCQ IPQCTKSYTD
360 370 380 390 400
PSSLRKHIKA VHGDDEYEKA KKSRPANYSN RRRPDHRLAP PTGAMSHPYL
410 420 430 440 450
ATPNSGASVV AHSSVHQQNF INMALAQHHH NAQRAQQLMA ATGNVMPMMD
460 470 480 490 500
PASAAAAAQA QAHHQAQAQM LQTHMMQQAQ IQAAAQMQAQ VQHQAAMQAH
510 520 530 540 550
AMQQAQMVLQ NNLLGAQSLL SPFSPLLPPS RAPNVMAMLQ TPPTPTSVAP
560 570 580 590 600
MFDIMTSRAP MAPVVSAPTA PAPLVPAPVP ASPVFDELRE QMREVEPLQQ
610 620 630 640 650
QQQQEPMDQD LQDIRVDGDS DDEDEEEPRT PSGALLLPRG GNNGDGGFGG
660 670 680 690 700
SGSSRASSGS GTMELSAAPI SQNGSRASGS GERGMRSFLI ADILQLAADF
710 720 730 740 750
QNERLLSDVL DLAIFDTRDV RSLHNIYQVY IRAHKAIPIT RRPLDWNETH
760 770 780 790 800
QLHNLYHDPR FNRAEHQDSP AIRDRDTRFW RTIAEANTMR QRQIEPVPLD
810 820 830 840 850
DDDEGYFDEM VHRVQNGRLN EQFMEGFESD DDDGFEDEDD VPGLGIAVYR
860 870 880 890 900
GRRRVRREAL KQANLDIQEA ETAGRNVGGF GDEEDRNNRG HDQDRSFLDH
910 920 930 940 950
YYPPMVVVVE TESPQIVRDQ EMMRQFEEAK KNVETDEIKK RAEAMQFGTS
960 970 980 990 1000
SSHHHTKTLL IQRALFDKTS SVRRSLLQFI TISVDQEELR QSCHATSAPQ
1010 1020 1030 1040 1050
GAHVVHNVVD EFDSIMRAQE DSNNRILLSL DIPAPSAVTG VSGSITHADN
1060 1070 1080 1090 1100
SALQLQQEQP TSSFSSWFPE DDPIYALPPP PPPPAPPRRR RSADNKDDSE
1110
NIPKKPRHQF
Length:1,110
Mass (Da):122,804
Last modified:February 1, 1994 - v1
Checksum:iEEE72C82841ECD7A
GO
Isoform b (identifier: P34708-2) [UniParc]FASTAAdd to basket

Also known as: Tra-1S1 Publication

The sequence of this isoform differs from the canonical sequence as follows:
     280-288: YPGCGKEYS → VGFGGDNEI
     289-1110: Missing.

Show »
Length:288
Mass (Da):30,905
Checksum:iE3790E446DCE0B42
GO

Sequence cautioni

The sequence CAB61040.2 differs from that shown. Reason: Erroneous initiation. Curated
The sequence CAC42377.1 differs from that shown. Reason: Erroneous initiation. Curated

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei280 – 2889YPGCGKEYS → VGFGGDNEI in isoform b. 1 PublicationVSP_006821
Alternative sequencei289 – 1110822Missing in isoform b. 1 PublicationVSP_006822Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M93256 mRNA. Translation: AAB59181.1.
M94130 mRNA. Translation: AAA91281.1.
AL117202 Genomic DNA. Translation: CAB61040.2. Different initiation.
AL117202 Genomic DNA. Translation: CAC42377.1. Different initiation.
PIRiA43253.
B43253.
RefSeqiNP_001022880.1. NM_001027709.1.
NP_001022881.1. NM_001027710.2.
UniGeneiCel.9756.

Genome annotation databases

GeneIDi176548.
KEGGicel:CELE_Y47D3A.6.
UCSCiY47D3A.6a. c. elegans. [P34708-1]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M93256 mRNA. Translation: AAB59181.1.
M94130 mRNA. Translation: AAA91281.1.
AL117202 Genomic DNA. Translation: CAB61040.2. Different initiation.
AL117202 Genomic DNA. Translation: CAC42377.1. Different initiation.
PIRiA43253.
B43253.
RefSeqiNP_001022880.1. NM_001027709.1.
NP_001022881.1. NM_001027710.2.
UniGeneiCel.9756.

3D structure databases

ProteinModelPortaliP34708.
SMRiP34708. Positions 210-363.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi41731. 5 interactions.
IntActiP34708. 37 interactions.
MINTiMINT-154380.
STRINGi6239.Y47D3A.6a.

Proteomic databases

EPDiP34708.
PaxDbiP34708.
PRIDEiP34708.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi176548.
KEGGicel:CELE_Y47D3A.6.
UCSCiY47D3A.6a. c. elegans. [P34708-1]

Organism-specific databases

CTDi176548.
WormBaseiY47D3A.6a; CE28129; WBGene00006604; tra-1.
Y47D3A.6b; CE28130; WBGene00006604; tra-1.

Phylogenomic databases

eggNOGiKOG1721. Eukaryota.
COG5048. LUCA.
HOGENOMiHOG000154672.
InParanoidiP34708.
KOiK06230.
OrthoDBiEOG7X6KZ8.

Enzyme and pathway databases

ReactomeiR-CEL-5610787. Hedgehog 'off' state.
R-CEL-5632684. Hedgehog 'on' state.
SignaLinkiP34708.

Miscellaneous databases

NextBioi893034.
PROiP34708.

Family and domain databases

Gene3Di3.30.160.60. 5 hits.
InterProiIPR007087. Znf_C2H2.
IPR015880. Znf_C2H2-like.
IPR013087. Znf_C2H2/integrase_DNA-bd.
[Graphical view]
SMARTiSM00355. ZnF_C2H2. 5 hits.
[Graphical view]
PROSITEiPS00028. ZINC_FINGER_C2H2_1. 4 hits.
PS50157. ZINC_FINGER_C2H2_2. 4 hits.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Molecular analysis of the C. elegans sex-determining gene tra-1: a gene encoding two zinc finger proteins."
    Zarkower D., Hodgkin J.
    Cell 70:237-249(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS A AND B), FUNCTION, DEVELOPMENTAL STAGE.
    Strain: Bristol N2.
  2. "Genome sequence of the nematode C. elegans: a platform for investigating biology."
    The C. elegans sequencing consortium
    Science 282:2012-2018(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA], ALTERNATIVE SPLICING.
    Strain: Bristol N2.
  3. "Zinc fingers in sex determination: only one of the two C. elegans Tra-1 proteins binds DNA in vitro."
    Zarkower D., Hodgkin J.
    Nucleic Acids Res. 21:3691-3698(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  4. "Direct protein-protein interaction between the intracellular domain of TRA-2 and the transcription factor TRA-1A modulates feminizing activity in C. elegans."
    Lum D.H., Kuwabara P.E., Zarkower D., Spence A.M.
    Genes Dev. 14:3153-3165(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, INTERACTION WITH TRA-2.
  5. "RNA-Regulated TRA-1 nuclear export controls sexual fate."
    Segal S.P., Graves L.E., Verheyden J., Goodwin E.B.
    Dev. Cell 1:539-551(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBCELLULAR LOCATION, TISSUE SPECIFICITY.
  6. "The TRA-1 transcription factor binds TRA-2 to regulate sexual fates in Caenorhabditis elegans."
    Wang S., Kimble J.
    EMBO J. 20:1363-1372(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, INTERACTION WITH TRA-2.
  7. "The C. elegans protein CEH-30 protects male-specific neurons from apoptosis independently of the Bcl-2 homolog CED-9."
    Schwartz H.T., Horvitz H.R.
    Genes Dev. 21:3181-3194(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.

Entry informationi

Entry nameiTRA1_CAEEL
AccessioniPrimary (citable) accession number: P34708
Secondary accession number(s): Q95Q22, Q9U2C0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1994
Last sequence update: February 1, 1994
Last modified: May 11, 2016
This is version 139 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programCaenorhabditis annotation project

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Caenorhabditis elegans
    Caenorhabditis elegans: entries, gene names and cross-references to WormBase
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.