O95025 (SEM3D_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Semaphorin-3D

Gene names

Name:	SEMA3D
ORF Names:	UNQ760/PRO1491

Organism

Homo sapiens (Human) [Reference proteome]

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Euarchontoglires › Primates › Haplorrhini › Simiiformes › Catarrhini › Hominoidea › Hominidae › Homininae › Homo

Protein attributes

Sequence length	777 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at transcript level

General annotation (Comments)

Function	Induces the collapse and paralysis of neuronal growth cones. Could potentially act as repulsive cues toward specific neuronal populations. Binds to neuropilin By similarity.
Subcellular location	Secreted By similarity.
Domain	Strong binding to neuropilin is mediated by the carboxy third of the protein.
Sequence similarities	Belongs to the semaphorin family. Contains 1 Ig-like C2-type (immunoglobulin-like) domain. Contains 1 PSI domain. Contains 1 Sema domain.
Sequence caution	The sequence AAH29590.1 differs from that shown. Reason: Erroneous initiation.

Ontologies

Keywords
Biological process	Differentiation Neurogenesis
Cellular component	Secreted
Coding sequence diversity	Polymorphism
Domain	Immunoglobulin domain Signal
Molecular function	Developmental protein
PTM	Disulfide bond Glycoprotein
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	cell differentiation Inferred from electronic annotation. Source: UniProtKB-KW nervous system development Inferred from electronic annotation. Source: UniProtKB-KW
Cellular_component	extracellular region Inferred from electronic annotation. Source: UniProtKB-SubCell membrane Inferred from electronic annotation. Source: InterPro
Molecular_function	receptor activity Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Signal peptide	1 – 36	36	Potential
	Chain	37 – 777	741	Semaphorin-3D		PRO_0000032314
Regions
	Domain	44 – 531	488	Sema
	Domain	533 – 585	53	PSI
	Domain	592 – 680	89	Ig-like C2-type
	Compositional bias	739 – 773	35	Arg/Lys-rich (basic)
Amino acid modifications
	Glycosylation	139	1	N-linked (GlcNAc...) Potential
	Glycosylation	607	1	N-linked (GlcNAc...) Potential
	Glycosylation	724	1	N-linked (GlcNAc...) Potential
	Disulfide bond	117 ↔ 128		By similarity
	Disulfide bond	146 ↔ 155		By similarity
	Disulfide bond	286 ↔ 398		By similarity
	Disulfide bond	310 ↔ 358		By similarity
	Disulfide bond	534 ↔ 552		By similarity
	Disulfide bond	665 ↔ 731		By similarity
Natural variations
	Natural variant	701	1	K → Q. Ref.1 Corresponds to variant rs7800072 [ dbSNP | Ensembl ].		VAR_021513

Sequences

	Sequence		Length	Mass (Da)
	O95025 [UniParc]. Last modified May 30, 2000. Version 2. Checksum: 3F7B0D7AF50F53BD	FASTA	777	89,651
	10 20 30 40 50 60 MNANKDERLK ARSQDFHLFP ALMMLSMTML FLPVTGTLKQ NIPRLKLTYK DLLLSNSCIP 70 80 90 100 110 120 FLGSSEGLDF QTLLLDEERG RLLLGAKDHI FLLSLVDLNK NFKKIYWPAA KERVELCKLA 130 140 150 160 170 180 GKDANTECAN FIRVLQPYNK THIYVCGTGA FHPICGYIDL GVYKEDIIFK LDTHNLESGR 190 200 210 220 230 240 LKCPFDPQQP FASVMTDEYL YSGTASDFLG KDTAFTRSLG PTHDHHYIRT DISEHYWLNG 250 260 270 280 290 300 AKFIGTFFIP DTYNPDDDKI YFFFRESSQE GSTSDKTILS RVGRVCKNDV GGQRSLINKW 310 320 330 340 350 360 TTFLKARLIC SIPGSDGADT YFDELQDIYL LPTRDERNPV VYGVFTTTSS IFKGSAVCVY 370 380 390 400 410 420 SMADIRAVFN GPYAHKESAD HRWVQYDGRI PYPRPGTCPS KTYDPLIKST RDFPDDVISF 430 440 450 460 470 480 IKRHSVMYKS VYPVAGGPTF KRINVDYRLT QIVVDHVIAE DGQYDVMFLG TDIGTVLKVV 490 500 510 520 530 540 SISKEKWNME EVVLEELQIF KHSSIILNME LSLKQQQLYI GSRDGLVQLS LHRCDTYGKA 550 560 570 580 590 600 CADCCLARDP YCAWDGNACS RYAPTSKRRA RRQDVKYGDP ITQCWDIEDS ISHETADEKV 610 620 630 640 650 660 IFGIEFNSTF LECIPKSQQA TIKWYIQRSG DEHREELKPD ERIIKTEYGL LIRSLQKKDS 670 680 690 700 710 720 GMYYCKAQEH TFIHTIVKLT LNVIENEQME NTQRAEHEEG KVKDLLAESR LRYKDYIQIL 730 740 750 760 770 SSPNFSLDQY CEQMWHREKR RQRNKGGPKW KHMQEMKKKR NRRHHRDLDE LPRAVAT

References

[1]	"The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment." Clark H.F., Gurney A.L., Abaya E., Baker K., Baldwin D.T., Brush J., Chen J., Chow B., Chui C., Crowley C., Currell B., Deuel B., Dowd P., Eaton D., Foster J.S., Grimaldi C., Gu Q., Hass P.E. , Heldens S., Huang A., Kim H.S., Klimowski L., Jin Y., Johnson S., Lee J., Lewis L., Liao D., Mark M.R., Robbie E., Sanchez C., Schoenfeld J., Seshagiri S., Simmons L., Singh J., Smith V., Stinson J., Vagts A., Vandlen R.L., Watanabe C., Wieand D., Woods K., Xie M.-H., Yansura D.G., Yi S., Yu G., Yuan J., Zhang M., Zhang Z., Goddard A.D., Wood W.I., Godowski P.J., Gray A.M. Genome Res. 13:2265-2270(2003) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA], VARIANT GLN-701.
[2]	"The DNA sequence of human chromosome 7." Hillier L.W., Fulton R.S., Fulton L.A., Graves T.A., Pepin K.H., Wagner-McPherson C., Layman D., Maas J., Jaeger S., Walker R., Wylie K., Sekhon M., Becker M.C., O'Laughlin M.D., Schaller M.E., Fewell G.A., Delehaunty K.D., Miner T.L. , Nash W.E., Cordes M., Du H., Sun H., Edwards J., Bradshaw-Cordum H., Ali J., Andrews S., Isak A., Vanbrunt A., Nguyen C., Du F., Lamar B., Courtney L., Kalicki J., Ozersky P., Bielicki L., Scott K., Holmes A., Harkins R., Harris A., Strong C.M., Hou S., Tomlinson C., Dauphin-Kohlberg S., Kozlowicz-Reilly A., Leonard S., Rohlfing T., Rock S.M., Tin-Wollam A.-M., Abbott A., Minx P., Maupin R., Strowmatt C., Latreille P., Miller N., Johnson D., Murray J., Woessner J.P., Wendl M.C., Yang S.-P., Schultz B.R., Wallis J.W., Spieth J., Bieri T.A., Nelson J.O., Berkowicz N., Wohldmann P.E., Cook L.L., Hickenbotham M.T., Eldred J., Williams D., Bedell J.A., Mardis E.R., Clifton S.W., Chissoe S.L., Marra M.A., Raymond C., Haugen E., Gillett W., Zhou Y., James R., Phelps K., Iadanoto S., Bubb K., Simms E., Levy R., Clendenning J., Kaul R., Kent W.J., Furey T.S., Baertsch R.A., Brent M.R., Keibler E., Flicek P., Bork P., Suyama M., Bailey J.A., Portnoy M.E., Torrents D., Chinwalla A.T., Gish W.R., Eddy S.R., McPherson J.D., Olson M.V., Eichler E.E., Green E.D., Waterston R.H., Wilson R.K. Nature 424:157-164(2003) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[3]	"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] OF 327-777. Tissue: Testis.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AY358937 mRNA. Translation: AAQ89296.1. AC004957 Genomic DNA. No translation available. BC029590 mRNA. Translation: AAH29590.1. Different initiation.
IPI	IPI00028213.
RefSeq	NP_689967.2. NM_152754.2.
UniGene	Hs.201340.
3D structure databases
ProteinModelPortal	O95025.
ModBase	Search...
Protein-protein interaction databases
STRING	9606.ENSP00000284136.
PTM databases
PhosphoSite	O95025.
Proteomic databases
PaxDb	O95025.
PRIDE	O95025.
Protocols and materials databases
DNASU	223117.
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
Ensembl	ENST00000284136; ENSP00000284136; ENSG00000153993.
GeneID	223117.
KEGG	hsa:223117.
UCSC	uc003uib.3. human.
Organism-specific databases
CTD	223117.
GeneCards	GC07M084624.
H-InvDB	HIX0006812.
HGNC	HGNC:10726. SEMA3D.
HPA	HPA037522.
MIM	609907. gene.
neXtProt	NX_O95025.
PharmGKB	PA35648.
GenAtlas	Search...
Phylogenomic databases
eggNOG	NOG247995.
HOGENOM	HOG000039964.
HOVERGEN	HBG055071.
InParanoid	O95025.
KO	K06840.
OMA	ERVELCK.
OrthoDB	EOG4SQWW5.
Gene expression databases
ArrayExpress	O95025.
Bgee	O95025.
CleanEx	HS_SEMA3D.
Genevestigator	O95025.
GermOnline	ENSG00000153993. Homo sapiens.
Family and domain databases
Gene3D	2.130.10.10. 1 hit. 2.60.40.10. 1 hit.
InterPro	IPR007110. Ig-like_dom. IPR013783. Ig-like_fold. IPR003599. Ig_sub. IPR013106. Ig_V-set. IPR003659. Plexin-like. IPR016201. Plexin-like_fold. IPR027231. Semaphorin. IPR001627. Semaphorin/CD100_Ag. IPR015943. WD40/YVTN_repeat-like_dom. [Graphical view]
PANTHER	PTHR11036. PTHR11036. 1 hit.
Pfam	PF01403. Sema. 1 hit. PF07686. V-set. 1 hit. [Graphical view]
SMART	SM00409. IG. 1 hit. SM00423. PSI. 1 hit. SM00630. Sema. 1 hit. [Graphical view]
SUPFAM	SSF103575. Plexin-like_fold. 1 hit. SSF101912. Sema. 1 hit.
PROSITE	PS50835. IG_LIKE. 1 hit. PS51004. SEMA. 1 hit. [Graphical view]
ProtoNet	Search...
Other
ChiTaRS	SEMA3D. human.
GenomeRNAi	223117.
NextBio	91714.
SOURCE	Search...

Entry information

Entry name

SEM3D_HUMAN

Accession

Primary (citable) accession number: O95025
Secondary accession number(s): A6NK46, Q6UW77, Q8NCQ1

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 30, 2000
Last sequence update:	May 30, 2000
Last modified:	May 1, 2013
This is version 115 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program

Disclaimer

Any 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.