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Protein

Semaphorin-3F

Gene

SEMA3F

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at transcript leveli

Functioni

May play a role in cell motility and cell adhesion.

GO - Molecular functioni

  • chemorepellent activity Source: MGI
  • receptor activity Source: InterPro

GO - Biological processi

Complete GO annotation...

Names & Taxonomyi

Protein namesi
Recommended name:
Semaphorin-3F
Alternative name(s):
Sema III/F
Semaphorin IV
Short name:
Sema IV
Gene namesi
Name:SEMA3F
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640 Componenti: Chromosome 3

Organism-specific databases

HGNCiHGNC:10728. SEMA3F.

Subcellular locationi

GO - Cellular componenti

  • extracellular space Source: ProtInc
  • membrane Source: InterPro
Complete GO annotation...

Keywords - Cellular componenti

Secreted

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA35650.

Polymorphism and mutation databases

BioMutaiSEMA3F.
DMDMi8134696.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 1818Sequence AnalysisAdd
BLAST
Chaini19 – 785767Semaphorin-3FPRO_0000032320Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Glycosylationi53 – 531N-linked (GlcNAc...)Sequence Analysis
Disulfide bondi104 ↔ 115By similarity
Glycosylationi126 – 1261N-linked (GlcNAc...)Sequence Analysis
Disulfide bondi133 ↔ 142By similarity
Disulfide bondi300 ↔ 412By similarity
Disulfide bondi324 ↔ 372By similarity
Disulfide bondi548 ↔ 566By similarity
Disulfide bondi678 ↔ 746By similarity

Keywords - PTMi

Disulfide bond, Glycoprotein

Proteomic databases

MaxQBiQ13275.
PaxDbiQ13275.
PRIDEiQ13275.

PTM databases

PhosphoSiteiQ13275.

Expressioni

Tissue specificityi

Expressed abundantly but differentially in a variety of neural and nonneural tissues. There is high expression in mammary gland, kidney, fetal brain, and lung and lower expression in heart and liver.

Developmental stagei

Detected as early as embryonic day 10.

Gene expression databases

BgeeiQ13275.
CleanExiHS_SEMA3F.
ExpressionAtlasiQ13275. baseline and differential.
GenevestigatoriQ13275.

Organism-specific databases

HPAiHPA035008.

Interactioni

Protein-protein interaction databases

BioGridi112305. 5 interactions.
IntActiQ13275. 2 interactions.
MINTiMINT-1392156.
STRINGi9606.ENSP00000002829.

Structurei

3D structure databases

ProteinModelPortaliQ13275.
SMRiQ13275. Positions 30-697.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini31 – 545515SemaPROSITE-ProRule annotationAdd
BLAST
Domaini605 – 69086Ig-like C2-typeAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi758 – 77922Arg/Lys-rich (basic)Add
BLAST

Sequence similaritiesi

Belongs to the semaphorin family.Curated
Contains 1 Sema domain.PROSITE-ProRule annotation

Keywords - Domaini

Immunoglobulin domain, Signal

Phylogenomic databases

eggNOGiNOG320723.
GeneTreeiENSGT00760000118854.
HOGENOMiHOG000039964.
HOVERGENiHBG055071.
InParanoidiQ13275.
KOiK06840.
OMAiCAWDGQA.
PhylomeDBiQ13275.
TreeFamiTF352628.

Family and domain databases

Gene3Di2.130.10.10. 2 hits.
2.60.40.10. 1 hit.
InterProiIPR007110. Ig-like_dom.
IPR013783. Ig-like_fold.
IPR003599. Ig_sub.
IPR016201. Plexin-like_fold.
IPR001627. Semap_dom.
IPR027231. Semaphorin.
IPR015943. WD40/YVTN_repeat-like_dom.
[Graphical view]
PANTHERiPTHR11036. PTHR11036. 1 hit.
PfamiPF01403. Sema. 1 hit.
[Graphical view]
SMARTiSM00409. IG. 1 hit.
SM00423. PSI. 1 hit.
SM00630. Sema. 1 hit.
[Graphical view]
SUPFAMiSSF101912. SSF101912. 2 hits.
SSF103575. SSF103575. 1 hit.
PROSITEiPS50835. IG_LIKE. 1 hit.
PS51004. SEMA. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

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

Isoform 1 (identifier: Q13275-1) [UniParc]FASTAAdd to basket

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
MLVAGLLLWA SLLTGAWPSF PTQDHLPATP RVRLSFKELK ATGTAHFFNF
60 70 80 90 100
LLNTTDYRIL LKDEDHDRMY VGSKDYVLSL DLHDINREPL IIHWAASPQR
110 120 130 140 150
IEECVLSGKD VNGECGNFVR LIQPWNRTHL YVCGTGAYNP MCTYVNRGRR
160 170 180 190 200
AQATPWTQTQ AVRGRGSRAT DGALRPMPTA PRQDYIFYLE PERLESGKGK
210 220 230 240 250
CPYDPKLDTA SALINEELYA GVYIDFMGTD AAIFRTLGKQ TAMRTDQYNS
260 270 280 290 300
RWLNDPSFIH AELIPDSAER NDDKLYFFFR ERSAEAPQSP AVYARIGRIC
310 320 330 340 350
LNDDGGHCCL VNKWSTFLKA RLVCSVPGED GIETHFDELQ DVFVQQTQDV
360 370 380 390 400
RNPVIYAVFT SSGSVFRGSA VCVYSMADIR MVFNGPFAHK EGPNYQWMPF
410 420 430 440 450
SGKMPYPRPG TCPGGTFTPS MKSTKDYPDE VINFMRSHPL MYQAVYPLQR
460 470 480 490 500
RPLVVRTGAP YRLTTIAVDQ VDAADGRYEV LFLGTDRGTV QKVIVLPKDD
510 520 530 540 550
QELEELMLEE VEVFKDPAPV KTMTISSKRQ QLYVASAVGV THLSLHRCQA
560 570 580 590 600
YGAACADCCL ARDPYCAWDG QACSRYTASS KRRSRRQDVR HGNPIRQCRG
610 620 630 640 650
FNSNANKNAV ESVQYGVAGS AAFLECQPRS PQATVKWLFQ RDPGDRRREI
660 670 680 690 700
RAEDRFLRTE QGLLLRALQL SDRGLYSCTA TENNFKHVVT RVQLHVLGRD
710 720 730 740 750
AVHAALFPPL SMSAPPPPGA GPPTPPYQEL AQLLAQPEVG LIHQYCQGYW
760 770 780
RHVPPSPREA PGAPRSPEPQ DQKKPRNRRH HPPDT
Length:785
Mass (Da):88,381
Last modified:January 1, 1998 - v2
Checksum:iFE3FC796EEC1608E
GO
Isoform 2 (identifier: Q13275-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     153-183: Missing.

Show »
Length:754
Mass (Da):85,064
Checksum:iAF4203BD1D2F2665
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti270 – 2701Missing in AAB18276 (PubMed:8786119).Curated
Sequence conflicti473 – 4731A → S in AAB18276 (PubMed:8786119).Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti474 – 4741A → G.
Corresponds to variant rs1046955 [ dbSNP | Ensembl ].
VAR_011820
Natural varianti503 – 5031L → M.2 Publications
Corresponds to variant rs1046956 [ dbSNP | Ensembl ].
VAR_008855

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei153 – 18331Missing in isoform 2. 1 PublicationVSP_053417Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U33920 mRNA. Translation: AAC50568.1.
U38276 mRNA. Translation: AAB18276.1.
AC000063 Genomic DNA. Translation: AAB46344.1.
AC104450 Genomic DNA. No translation available.
BC042914 mRNA. Translation: AAH42914.1.
U32171 mRNA. Translation: AAB06011.1.
U32172 mRNA. Translation: AAB06012.1.
CCDSiCCDS2811.1. [Q13275-1]
PIRiG02173.
RefSeqiNP_004177.3. NM_004186.3. [Q13275-1]
XP_005265438.1. XM_005265381.3. [Q13275-1]
XP_005265439.1. XM_005265382.3. [Q13275-2]
UniGeneiHs.32981.

Genome annotation databases

EnsembliENST00000002829; ENSP00000002829; ENSG00000001617. [Q13275-1]
ENST00000434342; ENSP00000409859; ENSG00000001617. [Q13275-2]
GeneIDi6405.
KEGGihsa:6405.
UCSCiuc003cyj.3. human. [Q13275-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Web resourcesi

Atlas of Genetics and Cytogenetics in Oncology and Haematology

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U33920 mRNA. Translation: AAC50568.1.
U38276 mRNA. Translation: AAB18276.1.
AC000063 Genomic DNA. Translation: AAB46344.1.
AC104450 Genomic DNA. No translation available.
BC042914 mRNA. Translation: AAH42914.1.
U32171 mRNA. Translation: AAB06011.1.
U32172 mRNA. Translation: AAB06012.1.
CCDSiCCDS2811.1. [Q13275-1]
PIRiG02173.
RefSeqiNP_004177.3. NM_004186.3. [Q13275-1]
XP_005265438.1. XM_005265381.3. [Q13275-1]
XP_005265439.1. XM_005265382.3. [Q13275-2]
UniGeneiHs.32981.

3D structure databases

ProteinModelPortaliQ13275.
SMRiQ13275. Positions 30-697.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi112305. 5 interactions.
IntActiQ13275. 2 interactions.
MINTiMINT-1392156.
STRINGi9606.ENSP00000002829.

PTM databases

PhosphoSiteiQ13275.

Polymorphism and mutation databases

BioMutaiSEMA3F.
DMDMi8134696.

Proteomic databases

MaxQBiQ13275.
PaxDbiQ13275.
PRIDEiQ13275.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000002829; ENSP00000002829; ENSG00000001617. [Q13275-1]
ENST00000434342; ENSP00000409859; ENSG00000001617. [Q13275-2]
GeneIDi6405.
KEGGihsa:6405.
UCSCiuc003cyj.3. human. [Q13275-1]

Organism-specific databases

CTDi6405.
GeneCardsiGC03P050167.
H-InvDBHIX0204323.
HGNCiHGNC:10728. SEMA3F.
HPAiHPA035008.
MIMi601124. gene.
neXtProtiNX_Q13275.
PharmGKBiPA35650.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiNOG320723.
GeneTreeiENSGT00760000118854.
HOGENOMiHOG000039964.
HOVERGENiHBG055071.
InParanoidiQ13275.
KOiK06840.
OMAiCAWDGQA.
PhylomeDBiQ13275.
TreeFamiTF352628.

Miscellaneous databases

ChiTaRSiSEMA3F. human.
GeneWikiiSEMA3F.
GenomeRNAii6405.
NextBioi24886.
PROiQ13275.
SOURCEiSearch...

Gene expression databases

BgeeiQ13275.
CleanExiHS_SEMA3F.
ExpressionAtlasiQ13275. baseline and differential.
GenevestigatoriQ13275.

Family and domain databases

Gene3Di2.130.10.10. 2 hits.
2.60.40.10. 1 hit.
InterProiIPR007110. Ig-like_dom.
IPR013783. Ig-like_fold.
IPR003599. Ig_sub.
IPR016201. Plexin-like_fold.
IPR001627. Semap_dom.
IPR027231. Semaphorin.
IPR015943. WD40/YVTN_repeat-like_dom.
[Graphical view]
PANTHERiPTHR11036. PTHR11036. 1 hit.
PfamiPF01403. Sema. 1 hit.
[Graphical view]
SMARTiSM00409. IG. 1 hit.
SM00423. PSI. 1 hit.
SM00630. Sema. 1 hit.
[Graphical view]
SUPFAMiSSF101912. SSF101912. 2 hits.
SSF103575. SSF103575. 1 hit.
PROSITEiPS50835. IG_LIKE. 1 hit.
PS51004. SEMA. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Distinct 3p21.3 deletions in lung cancer and identification of a new human semaphorin."
    Roche J., Boldog F., Robinson M., Robinson L., Varella-Garcia M., Swanton M., Waggoner B., Fishel R., Franklin W., Gemmill R., Drabkin H.
    Oncogene 12:1289-1297(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
    Tissue: Fetal brain.
  2. "Isolation of the human semaphorin III/F gene (SEMA3F) at chromosome 3p21, a region deleted in lung cancer."
    Xiang R.-H., Hensel C.H., Garcia D.K., Carlson H.C., Kok K., Daly M.C., Kerbacher K., van den Berg A., Veldhuis P., Buys C.H.C.M., Naylor S.L.
    Genomics 32:39-48(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2), VARIANT MET-503.
    Tissue: Fetal brain.
  3. "The sequence of H. sapiens cosmid clone LUCA19."
    Nelson J., Biewald T.
    Submitted (NOV-1996) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  4. "The DNA sequence, annotation and analysis of human chromosome 3."
    Muzny D.M., Scherer S.E., Kaul R., Wang J., Yu J., Sudbrak R., Buhay C.J., Chen R., Cree A., Ding Y., Dugan-Rocha S., Gill R., Gunaratne P., Harris R.A., Hawes A.C., Hernandez J., Hodgson A.V., Hume J.
    , Jackson A., Khan Z.M., Kovar-Smith C., Lewis L.R., Lozado R.J., Metzker M.L., Milosavljevic A., Miner G.R., Morgan M.B., Nazareth L.V., Scott G., Sodergren E., Song X.-Z., Steffen D., Wei S., Wheeler D.A., Wright M.W., Worley K.C., Yuan Y., Zhang Z., Adams C.Q., Ansari-Lari M.A., Ayele M., Brown M.J., Chen G., Chen Z., Clendenning J., Clerc-Blankenburg K.P., Chen R., Chen Z., Davis C., Delgado O., Dinh H.H., Dong W., Draper H., Ernst S., Fu G., Gonzalez-Garay M.L., Garcia D.K., Gillett W., Gu J., Hao B., Haugen E., Havlak P., He X., Hennig S., Hu S., Huang W., Jackson L.R., Jacob L.S., Kelly S.H., Kube M., Levy R., Li Z., Liu B., Liu J., Liu W., Lu J., Maheshwari M., Nguyen B.-V., Okwuonu G.O., Palmeiri A., Pasternak S., Perez L.M., Phelps K.A., Plopper F.J., Qiang B., Raymond C., Rodriguez R., Saenphimmachak C., Santibanez J., Shen H., Shen Y., Subramanian S., Tabor P.E., Verduzco D., Waldron L., Wang J., Wang J., Wang Q., Williams G.A., Wong G.K.-S., Yao Z., Zhang J., Zhang X., Zhao G., Zhou J., Zhou Y., Nelson D., Lehrach H., Reinhardt R., Naylor S.L., Yang H., Olson M., Weinstock G., Gibbs R.A.
    Nature 440:1194-1198(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  5. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1), VARIANT MET-503.
    Tissue: Brain.
  6. "Human semaphorins A(V) and IV reside in the 3p21.3 small cell lung cancer deletion region and demonstrate distinct expression patterns."
    Sekido Y., Bader S., Latif F., Chen J.-Y., Duh F.-M., Wei M.-H., Albanesi J.P., Lee C.-C., Lerman M.I., Minna J.D.
    Proc. Natl. Acad. Sci. U.S.A. 93:4120-4125(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 394-436 (ISOFORM 1/2).
    Tissue: Placenta.

Entry informationi

Entry nameiSEM3F_HUMAN
AccessioniPrimary (citable) accession number: Q13275
Secondary accession number(s): C9JQ85
, Q13274, Q13372, Q15704, Q6GTR4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: January 1, 1998
Last modified: April 29, 2015
This is version 137 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Human chromosome 3
    Human chromosome 3: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.