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Protein

Semaphorin-3B

Gene

SEMA3B

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

Functioni

Inhibits axonal extension by providing local signals to specify territories inaccessible for growing axons.By similarity

GO - Biological processi

  • axon guidance Source: ProtInc
  • cell-cell signaling Source: ProtInc
Complete GO annotation...

Names & Taxonomyi

Protein namesi
Recommended name:
Semaphorin-3B
Alternative name(s):
Sema A(V)
Semaphorin-V
Short name:
Sema V
Gene namesi
Name:SEMA3B
Synonyms:SEMA5, SEMAA
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640 Componenti: Chromosome 3

Organism-specific databases

HGNCiHGNC:10724. SEMA3B.

Subcellular locationi

GO - Cellular componenti

  • endoplasmic reticulum Source: ProtInc
  • extracellular exosome Source: UniProtKB
  • membrane Source: InterPro
Complete GO annotation...

Keywords - Cellular componenti

Endoplasmic reticulum, Secreted

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA35646.

Polymorphism and mutation databases

BioMutaiSEMA3B.
DMDMi8134673.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 2424Sequence AnalysisAdd
BLAST
Chaini25 – 749725Semaphorin-3BPRO_0000032309Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Glycosylationi82 – 821N-linked (GlcNAc...)Sequence Analysis
Disulfide bondi102 ↔ 113By similarity
Glycosylationi124 – 1241N-linked (GlcNAc...)Sequence Analysis
Disulfide bondi131 ↔ 140By similarity
Disulfide bondi269 ↔ 380By similarity
Disulfide bondi293 ↔ 340By similarity
Glycosylationi427 – 4271N-linked (GlcNAc...)Sequence Analysis
Disulfide bondi516 ↔ 534By similarity
Disulfide bondi644 ↔ 710By similarity

Keywords - PTMi

Disulfide bond, Glycoprotein

Proteomic databases

MaxQBiQ13214.
PaxDbiQ13214.
PRIDEiQ13214.

Expressioni

Tissue specificityi

Expressed abundantly but differentially in a variety of neural and nonneural tissues.

Gene expression databases

CleanExiHS_SEMA3B.
ExpressionAtlasiQ13214. baseline and differential.
GenevisibleiQ13214. HS.

Interactioni

Protein-protein interaction databases

BioGridi113618. 1 interaction.
IntActiQ13214. 1 interaction.

Structurei

3D structure databases

ProteinModelPortaliQ13214.
SMRiQ13214. Positions 29-649.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini30 – 513484SemaPROSITE-ProRule annotationAdd
BLAST
Domaini573 – 65987Ig-like C2-typeAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi699 – 7024Poly-Gly
Compositional biasi724 – 74421Arg-rich (basic)Add
BLAST

Sequence similaritiesi

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

Keywords - Domaini

Immunoglobulin domain, Signal

Phylogenomic databases

eggNOGiNOG293968.
GeneTreeiENSGT00760000118854.
HOVERGENiHBG055071.
InParanoidiQ13214.
KOiK06840.
OrthoDBiEOG7X6KZG.
PhylomeDBiQ13214.

Family and domain databases

Gene3Di2.130.10.10. 1 hit.
2.60.40.10. 1 hit.
InterProiIPR007110. Ig-like_dom.
IPR013783. Ig-like_fold.
IPR003599. Ig_sub.
IPR016201. Plexin-like_fold.
IPR002165. Plexin_repeat.
IPR001627. Semap_dom.
IPR027231. Semaphorin.
IPR015943. WD40/YVTN_repeat-like_dom.
[Graphical view]
PANTHERiPTHR11036. PTHR11036. 1 hit.
PfamiPF01437. PSI. 1 hit.
PF01403. Sema. 1 hit.
[Graphical view]
SMARTiSM00409. IG. 1 hit.
SM00423. PSI. 1 hit.
SM00630. Sema. 1 hit.
[Graphical view]
SUPFAMiSSF101912. SSF101912. 1 hit.
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: Q13214-1) [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
MGRAGAAAVI PGLALLWAVG LGSAAPSPPR LRLSFQELQA WHGLQTFSLE
60 70 80 90 100
RTCCYQALLV DEERGRLFVG AENHVASLNL DNISKRAKKL AWPAPVEWRE
110 120 130 140 150
ECNWAGKDIG TECMNFVKLL HAYNRTHLLA CGTGAFHPTC AFVEVGHRAE
160 170 180 190 200
EPVLRLDPGR IEDGKGKSPY DPRHRAASVL VGEELYSGVA ADLMGRDFTI
210 220 230 240 250
FRSLGQRPSL RTEPHDSRWL NEPKFVKVFW IPESENPDDD KIYFFFRETA
260 270 280 290 300
VEAAPALGRL SVSRVGQICR NDVGGQRSLV NKWTTFLKAR LVCSVPGVEG
310 320 330 340 350
DTHFDQLQDV FLLSSRDHRT PLLYAVFSTS SSIFQGSAVC VYSMNDVRRA
360 370 380 390 400
FLGPFAHKEG PMHQWVSYQG RVPYPRPGMC PSKTFGTFSS TKDFPDDVIQ
410 420 430 440 450
FARNHPLMYN SVLPTGGRPL FLQVGANYTF TQIAADRVAA ADGHYDVLFI
460 470 480 490 500
GTDVGTVLKV ISVPKGSRPS AEGLLLEELH VFEDSAAVTS MQISSKRHQL
510 520 530 540 550
YVASRSAVAQ IALHRCAAHG RVCTECCLAR DPYCAWDGVA CTRFQPSAKR
560 570 580 590 600
RFRRQDVRNG DPSTLCSGDS SRPALLEHKV FGVEGSSAFL ECEPRSLQAR
610 620 630 640 650
VEWTFQRAGV TAHTQVLAEE RTERTARGLL LRRLRRRDSG VYLCAAVEQG
660 670 680 690 700
FTQPLRRLSL HVLSATQAER LARAEEAAPA APPGPKLWYR DFLQLVEPGG
710 720 730 740
GGSANSLRMC RPQPALQSLP LESRRKGRNR RTHAPEPRAE RGPRSATHW
Length:749
Mass (Da):83,122
Last modified:November 1, 1996 - v1
Checksum:i1F3B8F63F59444F3
GO
Isoform 2 (identifier: Q13214-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     332-332: Missing.

Note: No experimental confirmation available.
Show »
Length:748
Mass (Da):83,035
Checksum:i587C53CB65AB4656
GO

Sequence cautioni

The sequence AAC02731.1 differs from that shown. Reason: Erroneous gene model prediction. Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti29 – 368PRLRLSFQ → HAFGSPSKV in AAC02731 (PubMed:16641997).Curated
Sequence conflicti308 – 3081Q → RPFPAE in BAB88870 (Ref. 2) Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti348 – 3481R → C in a non-small cell lung cancer cell line. 1 Publication
VAR_014221
Natural varianti397 – 3971D → H in a non-small cell lung cancer cell line. 1 Publication
VAR_014222
Natural varianti415 – 4151T → I in a non-small cell lung cancer cell line. 1 Publication
Corresponds to variant rs2071203 [ dbSNP | Ensembl ].
VAR_014223

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei332 – 3321Missing in isoform 2. 1 PublicationVSP_023032

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U28369 mRNA. Translation: AAD09138.1.
AB083186 mRNA. Translation: BAB88870.1.
U73167 Genomic DNA. Translation: AAC02731.1. Sequence problems.
BC009113 mRNA. Translation: AAH09113.1.
BC013975 mRNA. Translation: AAH13975.1.
BC024220 mRNA. Translation: AAH24220.1.
CCDSiCCDS74941.1. [Q13214-1]
PIRiG01856.
RefSeqiNP_001005914.1. NM_001005914.2. [Q13214-2]
NP_001276989.1. NM_001290060.1. [Q13214-1]
NP_001276990.1. NM_001290061.1.
NP_001276991.1. NM_001290062.1.
NP_001276992.1. NM_001290063.1.
NP_004627.1. NM_004636.3. [Q13214-1]
UniGeneiHs.82222.

Genome annotation databases

EnsembliENST00000433753; ENSP00000485281; ENSG00000012171. [Q13214-2]
ENST00000616701; ENSP00000484146; ENSG00000012171. [Q13214-1]
ENST00000618865; ENSP00000481957; ENSG00000012171. [Q13214-1]
GeneIDi7869.
KEGGihsa:7869.
UCSCiuc003cyt.3. human. [Q13214-2]
uc003cyu.3. human. [Q13214-1]

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
U28369 mRNA. Translation: AAD09138.1.
AB083186 mRNA. Translation: BAB88870.1.
U73167 Genomic DNA. Translation: AAC02731.1. Sequence problems.
BC009113 mRNA. Translation: AAH09113.1.
BC013975 mRNA. Translation: AAH13975.1.
BC024220 mRNA. Translation: AAH24220.1.
CCDSiCCDS74941.1. [Q13214-1]
PIRiG01856.
RefSeqiNP_001005914.1. NM_001005914.2. [Q13214-2]
NP_001276989.1. NM_001290060.1. [Q13214-1]
NP_001276990.1. NM_001290061.1.
NP_001276991.1. NM_001290062.1.
NP_001276992.1. NM_001290063.1.
NP_004627.1. NM_004636.3. [Q13214-1]
UniGeneiHs.82222.

3D structure databases

ProteinModelPortaliQ13214.
SMRiQ13214. Positions 29-649.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi113618. 1 interaction.
IntActiQ13214. 1 interaction.

Polymorphism and mutation databases

BioMutaiSEMA3B.
DMDMi8134673.

Proteomic databases

MaxQBiQ13214.
PaxDbiQ13214.
PRIDEiQ13214.

Protocols and materials databases

DNASUi7869.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000433753; ENSP00000485281; ENSG00000012171. [Q13214-2]
ENST00000616701; ENSP00000484146; ENSG00000012171. [Q13214-1]
ENST00000618865; ENSP00000481957; ENSG00000012171. [Q13214-1]
GeneIDi7869.
KEGGihsa:7869.
UCSCiuc003cyt.3. human. [Q13214-2]
uc003cyu.3. human. [Q13214-1]

Organism-specific databases

CTDi7869.
GeneCardsiGC03P050304.
HGNCiHGNC:10724. SEMA3B.
MIMi601281. gene.
neXtProtiNX_Q13214.
PharmGKBiPA35646.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiNOG293968.
GeneTreeiENSGT00760000118854.
HOVERGENiHBG055071.
InParanoidiQ13214.
KOiK06840.
OrthoDBiEOG7X6KZG.
PhylomeDBiQ13214.

Miscellaneous databases

ChiTaRSiSEMA3B. human.
GeneWikiiSEMA3B.
GenomeRNAii7869.
NextBioi30317.
PROiQ13214.
SOURCEiSearch...

Gene expression databases

CleanExiHS_SEMA3B.
ExpressionAtlasiQ13214. baseline and differential.
GenevisibleiQ13214. HS.

Family and domain databases

Gene3Di2.130.10.10. 1 hit.
2.60.40.10. 1 hit.
InterProiIPR007110. Ig-like_dom.
IPR013783. Ig-like_fold.
IPR003599. Ig_sub.
IPR016201. Plexin-like_fold.
IPR002165. Plexin_repeat.
IPR001627. Semap_dom.
IPR027231. Semaphorin.
IPR015943. WD40/YVTN_repeat-like_dom.
[Graphical view]
PANTHERiPTHR11036. PTHR11036. 1 hit.
PfamiPF01437. PSI. 1 hit.
PF01403. Sema. 1 hit.
[Graphical view]
SMARTiSM00409. IG. 1 hit.
SM00423. PSI. 1 hit.
SM00630. Sema. 1 hit.
[Graphical view]
SUPFAMiSSF101912. SSF101912. 1 hit.
SSF103575. SSF103575. 1 hit.
PROSITEiPS50835. IG_LIKE. 1 hit.
PS51004. SEMA. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "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] (ISOFORM 1).
  2. "Semaphorin 3B (SEMA3B) cDNA."
    Koyama N.
    Submitted (APR-2002) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
  3. "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].
  4. "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 2).
    Tissue: Brain and Muscle.
  5. "The 630-kb lung cancer homozygous deletion region on human chromosome 3p21.3: identification and evaluation of the resident candidate tumor suppressor genes."
    The international lung cancer chromosome 3p21.3 tumor suppressor gene consortium
    Lerman M.I., Minna J.D.
    Cancer Res. 60:6116-6133(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: DISCUSSION OF SEQUENCE, VARIANTS CYS-348; HIS-397 AND ILE-415.

Entry informationi

Entry nameiSEM3B_HUMAN
AccessioniPrimary (citable) accession number: Q13214
Secondary accession number(s): Q6GU46
, Q8TB71, Q8TDV7, Q93018, Q96GX0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: November 1, 1996
Last modified: June 24, 2015
This is version 135 of the entry and version 1 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.