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SEMA3D semaphorin 3D [ Homo sapiens (human) ]

Gene ID: 223117, updated on 11-Jun-2021

Summary

Official Symbol
SEMA3Dprovided by HGNC
Official Full Name
semaphorin 3Dprovided by HGNC
Primary source
HGNC:HGNC:10726
See related
Ensembl:ENSG00000153993 MIM:609907
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
coll-2; Sema-Z2
Summary
This gene encodes a member of the semaphorin III family of secreted signaling proteins that are involved in axon guidance during neuronal development. The encoded protein contains an N-terminal Sema domain, an immunoglobulin like domain and a C-terminal basic domain. The protein encoded by this gene binds neuropilin and plays an important role in cardiovascular development. [provided by RefSeq, Aug 2016]
Expression
Biased expression in spleen (RPKM 23.4), thyroid (RPKM 18.9) and 13 other tissues See more
Orthologs
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Genomic context

See SEMA3D in Genome Data Viewer
Location:
7q21.11
Exon count:
25
Annotation release Status Assembly Chr Location
109.20210514 current GRCh38.p13 (GCF_000001405.39) 7 NC_000007.14 (84995192..85250243, complement)
105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (84624869..84879559, complement)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene high mobility group nucleosomal binding domain 2 pseudogene 11 Neighboring gene heterogeneous nuclear ribonucleoprotein A1 pseudogene 8 Neighboring gene heat shock protein family A (Hsp70) member 8 pseudogene 16 Neighboring gene dynein light chain LC8-type 1 pseudogene 7 Neighboring gene long intergenic non-protein coding RNA 972

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC39708

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables chemorepellent activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables semaphorin receptor binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Process Evidence Code Pubs
involved_in axon guidance IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in negative chemotaxis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in negative regulation of axon extension involved in axon guidance IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in neural crest cell migration IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in positive regulation of cell migration IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in semaphorin-plexin signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
is_active_in extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
is_active_in integral component of plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

Preferred Names
semaphorin-3D
Names
collapsin 2
sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3D

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_051329.1 RefSeqGene

    Range
    69925..196303
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001384900.1NP_001371829.1  semaphorin-3D precursor

    Status: REVIEWED

    Source sequence(s)
    AC004957, AC006151
    Related
    ENSP00000284136.6, ENST00000284136.11
    Conserved Domains (3) summary
    cd11252
    Location:61534
    Sema_3D; The Sema domain, a protein interacting module, of semaphorin 3D (Sema3D)
    smart00423
    Location:533570
    PSI; domain found in Plexins, Semaphorins and Integrins
    cd05871
    Location:595686
    Ig_Sema3; Immunoglobulin (Ig)-like domain of class III semaphorin Sema3
  2. NM_001384901.1NP_001371830.1  semaphorin-3D precursor

    Status: REVIEWED

    Source sequence(s)
    AC004957, AC006151
    Conserved Domains (3) summary
    cd11252
    Location:61534
    Sema_3D; The Sema domain, a protein interacting module, of semaphorin 3D (Sema3D)
    smart00423
    Location:533570
    PSI; domain found in Plexins, Semaphorins and Integrins
    cd05871
    Location:595686
    Ig_Sema3; Immunoglobulin (Ig)-like domain of class III semaphorin Sema3
  3. NM_001384902.1NP_001371831.1  semaphorin-3D precursor

    Status: REVIEWED

    Source sequence(s)
    AC004957, AC006151
    Conserved Domains (3) summary
    cd11252
    Location:61534
    Sema_3D; The Sema domain, a protein interacting module, of semaphorin 3D (Sema3D)
    smart00423
    Location:533570
    PSI; domain found in Plexins, Semaphorins and Integrins
    cd05871
    Location:595686
    Ig_Sema3; Immunoglobulin (Ig)-like domain of class III semaphorin Sema3
  4. NM_001384903.1NP_001371832.1  semaphorin-3D precursor

    Status: REVIEWED

    Source sequence(s)
    AC004957, AC006151
    Conserved Domains (3) summary
    cd11252
    Location:61534
    Sema_3D; The Sema domain, a protein interacting module, of semaphorin 3D (Sema3D)
    smart00423
    Location:533570
    PSI; domain found in Plexins, Semaphorins and Integrins
    cd05871
    Location:595686
    Ig_Sema3; Immunoglobulin (Ig)-like domain of class III semaphorin Sema3
  5. NM_152754.3NP_689967.2  semaphorin-3D precursor

    See identical proteins and their annotated locations for NP_689967.2

    Status: REVIEWED

    Source sequence(s)
    AC004957, AC006151
    Consensus CDS
    CCDS34676.1
    UniProtKB/Swiss-Prot
    O95025
    Conserved Domains (3) summary
    cd11252
    Location:61534
    Sema_3D; The Sema domain, a protein interacting module, of semaphorin 3D (Sema3D)
    smart00423
    Location:533570
    PSI; domain found in Plexins, Semaphorins and Integrins
    cd05871
    Location:595686
    Ig_Sema3; Immunoglobulin (Ig)-like domain of class III semaphorin Sema3

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20210514

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000007.14 Reference GRCh38.p13 Primary Assembly

    Range
    84995192..85250243 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011515961.2XP_011514263.1  semaphorin-3D isoform X2

    Conserved Domains (4) summary
    cd05871
    Location:402492
    Ig_Semaphorin_classIII; Immunoglobulin (Ig)-like domain of class III semaphorin
    smart00410
    Location:417486
    IG_like; Immunoglobulin like
    smart00423
    Location:339376
    PSI; domain found in Plexins, Semaphorins and Integrins
    cl15693
    Location:1340
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
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