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Protein

Semaphorin-3D

Gene

Sema3d

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

Induces the collapse and paralysis of neuronal growth cones. Could potentially act as repulsive cues toward specific neuronal populations. Binds to neuropilin (By similarity).By similarity

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Developmental protein

Keywords - Biological processi

Differentiation, Neurogenesis

Names & Taxonomyi

Protein namesi
Recommended name:
Semaphorin-3D
Gene namesi
Name:Sema3d
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
ProteomesiUP000000589 Componenti: Chromosome 5

Organism-specific databases

MGIiMGI:1860118. Sema3d.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Secreted

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 3737Sequence AnalysisAdd
BLAST
Chaini38 – 777740Semaphorin-3DPRO_0000042161Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi117 ↔ 128By similarity
Glycosylationi139 – 1391N-linked (GlcNAc...)Sequence Analysis
Disulfide bondi146 ↔ 155By similarity
Disulfide bondi286 ↔ 398By similarity
Disulfide bondi310 ↔ 358By similarity
Disulfide bondi534 ↔ 552By similarity
Glycosylationi607 – 6071N-linked (GlcNAc...)Sequence Analysis
Disulfide bondi665 ↔ 731By similarity
Glycosylationi724 – 7241N-linked (GlcNAc...)Sequence Analysis

Keywords - PTMi

Disulfide bond, Glycoprotein

Proteomic databases

PRIDEiQ8BH34.

PTM databases

PhosphoSiteiQ8BH34.

Expressioni

Gene expression databases

BgeeiQ8BH34.
ExpressionAtlasiQ8BH34. baseline and differential.
GenevestigatoriQ8BH34.

Structurei

3D structure databases

ProteinModelPortaliQ8BH34.
SMRiQ8BH34. Positions 39-683.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini44 – 531488SemaPROSITE-ProRule annotationAdd
BLAST
Domaini533 – 58553PSIAdd
BLAST
Domaini592 – 68089Ig-like C2-typeAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi739 – 77335Arg/Lys-rich (basic)Add
BLAST

Domaini

Strong binding to neuropilin is mediated by the carboxy third of the protein.

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

eggNOGiNOG247995.
GeneTreeiENSGT00760000118854.
HOGENOMiHOG000039964.
HOVERGENiHBG055071.
InParanoidiQ8BH34.
KOiK06840.
OMAiQNIPRLK.
OrthoDBiEOG76QFGN.
PhylomeDBiQ8BH34.
TreeFamiTF316102.

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.
IPR013106. Ig_V-set.
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.
PF07686. V-set. 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]

Sequencei

Sequence statusi: Complete.

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

Q8BH34-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MNVTKDENPR SRSQDLHLFH AWMMLIMTVL FLPVTETSKQ NIPRLKLTYK
60 70 80 90 100
DLLLSNTCIP FLGSSEGLDF QTLLLDEERG ILLLGAKDHV FLLSLVDLNK
110 120 130 140 150
NFKKIYWPAA KERVELCKLA GKDANAECAN FIRVLQPYNK THVYVCGTGA
160 170 180 190 200
FHPLCGYIDL GANKEELIFK LDTHNLESGR LKCPFDPQQP FASVMTDEHL
210 220 230 240 250
YSGTASDFLG KDTAFTRSLG LMQDHHSIRT DISEHHWLNG AKFIGTFPIP
260 270 280 290 300
DTYNPDDDKI YFFFRESSQE GSTSDRSILS RVGRVCKNDV GGQRSLINKW
310 320 330 340 350
TTFLKARLIC SIPGSDGADT HFDELQDIYL LPTRDERNPV VYGVFTTTSS
360 370 380 390 400
IFKGSAVCVY SMADIRAVFN GPYAHKESAD HRWVQYDGRI PYPRPGTCPS
410 420 430 440 450
KTYDPLIKST RDFPDDVISF IRRHPVMYKS VYPVAGAPTF KRINVDYRLT
460 470 480 490 500
QIVVDHVVAE DGQYDVMFLG TDIGTVLKVV SISKEKWNME EVVLEELQVF
510 520 530 540 550
KHPTAILNME LSLKQQQLYV GSWDGLVQLS LHRCDTYGKA CADCCLARDP
560 570 580 590 600
YCAWDGNACS RYAPTSKRRA RRQDVKYGDP ITQCWDIEDS ISHETADEKV
610 620 630 640 650
IFGIEFNSTF LECIPKSQQA SVEWYIQRSG DEHREELKPD ERIIKTDYGL
660 670 680 690 700
LIRSLQKKDS GMYYCKAQEH TFIHTIVKLT LNVIENEQME NTQRAEYQEG
710 720 730 740 750
QVKDLLAESR LRYKDYIQIL SSPNFSLDQY CEQMWYKEKR RQRNKGSPKW
760 770
KHMQEMKKKR NRRHHRDLDE LQRSVAT
Length:777
Mass (Da):89,549
Last modified:March 1, 2003 - v1
Checksum:i5450D8D45D1BDABF
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK028900 mRNA. Translation: BAC26185.1.
AK052671 mRNA. Translation: BAC35092.1.
CCDSiCCDS39013.1.
RefSeqiNP_083158.3. NM_028882.4.
UniGeneiMm.89313.

Genome annotation databases

EnsembliENSMUST00000030868; ENSMUSP00000030868; ENSMUSG00000040254.
GeneIDi108151.
KEGGimmu:108151.
UCSCiuc008wlx.2. mouse.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK028900 mRNA. Translation: BAC26185.1.
AK052671 mRNA. Translation: BAC35092.1.
CCDSiCCDS39013.1.
RefSeqiNP_083158.3. NM_028882.4.
UniGeneiMm.89313.

3D structure databases

ProteinModelPortaliQ8BH34.
SMRiQ8BH34. Positions 39-683.
ModBaseiSearch...
MobiDBiSearch...

PTM databases

PhosphoSiteiQ8BH34.

Proteomic databases

PRIDEiQ8BH34.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000030868; ENSMUSP00000030868; ENSMUSG00000040254.
GeneIDi108151.
KEGGimmu:108151.
UCSCiuc008wlx.2. mouse.

Organism-specific databases

CTDi223117.
MGIiMGI:1860118. Sema3d.

Phylogenomic databases

eggNOGiNOG247995.
GeneTreeiENSGT00760000118854.
HOGENOMiHOG000039964.
HOVERGENiHBG055071.
InParanoidiQ8BH34.
KOiK06840.
OMAiQNIPRLK.
OrthoDBiEOG76QFGN.
PhylomeDBiQ8BH34.
TreeFamiTF316102.

Miscellaneous databases

ChiTaRSiSema3d. mouse.
NextBioi360170.
PROiQ8BH34.
SOURCEiSearch...

Gene expression databases

BgeeiQ8BH34.
ExpressionAtlasiQ8BH34. baseline and differential.
GenevestigatoriQ8BH34.

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.
IPR013106. Ig_V-set.
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.
PF07686. V-set. 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. "The transcriptional landscape of the mammalian genome."
    Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K., Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.
    , Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R., Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T., Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A., Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B., Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M., Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S., Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E., Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D., Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M., Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H., Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V., Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S., Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H., Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N., Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F., Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G., Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C., Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y., Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S., Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K., Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R., van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H., Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M., Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C., Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S., Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K., Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M., Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C., Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A., Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.
    Science 309:1559-1563(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: C57BL/6J.
    Tissue: Kidney and Skin.
  2. Lubec G., Sunyer B., Chen W.-Q.
    Submitted (JAN-2009) to UniProtKB
    Cited for: PROTEIN SEQUENCE OF 479-486, IDENTIFICATION BY MASS SPECTROMETRY.
    Strain: OF1.
    Tissue: Hippocampus.

Entry informationi

Entry nameiSEM3D_MOUSE
AccessioniPrimary (citable) accession number: Q8BH34
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 27, 2005
Last sequence update: March 1, 2003
Last modified: April 1, 2015
This is version 98 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. 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.