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Sema6d sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D [ Mus musculus (house mouse) ]

Gene ID: 214968, updated on 7-Aug-2018

Summary

Official Symbol
Sema6dprovided by MGI
Official Full Name
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6Dprovided by MGI
Primary source
MGI:MGI:2387661
See related
Ensembl:ENSMUSG00000027200 Vega:OTTMUSG00000015256
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
AA409156; mKIAA1479; D330011G23; 1110067B02Rik
Expression
Ubiquitous expression in cerebellum adult (RPKM 11.2), lung adult (RPKM 8.6) and 27 other tissues See more
Orthologs

Genomic context

See Sema6d in Genome Data Viewer
Location:
2; 2 F1
Exon count:
27
Annotation release Status Assembly Chr Location
106 current GRCm38.p4 (GCF_000001635.24) 2 NC_000068.7 (124089918..124667789)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 2 NC_000068.6 (124436032..124493506)

Chromosome 2 - NC_000068.7Genomic Context describing neighboring genes Neighboring gene predicted gene, 34430 Neighboring gene predicted gene, 39919 Neighboring gene RIKEN cDNA 4930517E11 gene Neighboring gene RIKEN cDNA 4930583P06 gene Neighboring gene predicted gene, 34484 Neighboring gene predicted gene, 39920

Genomic regions, transcripts, and products

Expression

  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Variation

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)

Pathways from BioSystems

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
chemorepellent activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
neuropilin binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
semaphorin receptor binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
semaphorin receptor binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
cell differentiation IEA
Inferred from Electronic Annotation
more info
 
multicellular organism development IEA
Inferred from Electronic Annotation
more info
 
negative chemotaxis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
negative regulation of axon extension ISO
Inferred from Sequence Orthology
more info
 
negative regulation of axon extension involved in axon guidance IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
negative regulation of smooth muscle cell migration IDA
Inferred from Direct Assay
more info
PubMed 
nervous system development IEA
Inferred from Electronic Annotation
more info
 
neural crest cell migration IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of cell migration IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of smooth muscle cell migration IDA
Inferred from Direct Assay
more info
PubMed 
semaphorin-plexin signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
ventricular system development IDA
Inferred from Direct Assay
more info
PubMed 
ventricular system development ISO
Inferred from Sequence Orthology
more info
PubMed 
Component Evidence Code Pubs
Golgi apparatus ISO
Inferred from Sequence Orthology
more info
 
cell surface ISO
Inferred from Sequence Orthology
more info
 
cytoplasm ISO
Inferred from Sequence Orthology
more info
 
extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
integral component of membrane IEA
Inferred from Electronic Annotation
more info
 
integral component of plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
membrane IEA
Inferred from Electronic Annotation
more info
 
plasma membrane ISO
Inferred from Sequence Orthology
more info
 

NCBI Reference Sequences (RefSeq)

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.

mRNA and Protein(s)

  1. NM_001290997.1NP_001277926.1  semaphorin-6D isoform Sema6D-2 precursor

    See identical proteins and their annotated locations for NP_001277926.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR, and uses an alternate in-frame splice site in the central coding region, compared to variant 1. The encoded isoform (Sema6D-2) is shorter than isoform Sema6D-1. Both variants 2 and 3 encode isoform Sema6D-2.
    Source sequence(s)
    AL833808, AL929570, AL935323, BC060680, BY242475
    Consensus CDS
    CCDS16671.1
    UniProtKB/Swiss-Prot
    Q76KF0
    Related
    ENSMUSP00000099531.1, OTTMUSP00000016237, ENSMUST00000103241.7, OTTMUST00000036143
    Conserved Domains (2) summary
    pfam01437
    Location:514569
    PSI; Plexin repeat
    cl15693
    Location:49513
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
  2. NM_001291000.1NP_001277929.1  semaphorin-6D isoform 3 precursor

    Status: VALIDATED

    Description
    Transcript Variant: This variant (7) uses an alternate in-frame splice site and contains two additional in-frame exons in the central coding region, compared to variant 1. The encoded isoform (3) is longer than isoform Sema6D-1.
    Source sequence(s)
    AB091532, AK031307, AL935323, BC060680
    Consensus CDS
    CCDS71132.1
    UniProtKB/Swiss-Prot
    Q76KF0
    UniProtKB/TrEMBL
    A2AW73
    Related
    ENSMUSP00000099530.2, OTTMUSP00000016238, ENSMUST00000103240.8, OTTMUST00000036146
    Conserved Domains (2) summary
    pfam01437
    Location:514569
    PSI; Plexin repeat
    cl15693
    Location:49513
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
  3. NM_172537.4NP_766125.2  semaphorin-6D isoform Sema6D-1 precursor

    See identical proteins and their annotated locations for NP_766125.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes isoform Sema6D-1.
    Source sequence(s)
    AB091532, AL935323, BC060680
    Consensus CDS
    CCDS16670.1
    UniProtKB/Swiss-Prot
    Q76KF0
    Related
    ENSMUSP00000061123.8, OTTMUSP00000016240, ENSMUST00000051419.14, OTTMUST00000036148
    Conserved Domains (2) summary
    pfam01437
    Location:514582
    PSI; Plexin repeat
    cl15693
    Location:49513
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
  4. NM_199238.3NP_954708.1  semaphorin-6D isoform Sema6D-2 precursor

    See identical proteins and their annotated locations for NP_954708.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site in the central coding region, compared to variant 1, resulting in an isoform (Sema6D-2) that is shorter than isoform Sema6D-1. Both variants 2 and 3 encode isoform Sema6D-2.
    Source sequence(s)
    AB091532, AL935323, BC060680
    Consensus CDS
    CCDS16671.1
    UniProtKB/Swiss-Prot
    Q76KF0
    Related
    ENSMUSP00000075674.5, ENSMUST00000076335.11
    Conserved Domains (2) summary
    pfam01437
    Location:514569
    PSI; Plexin repeat
    cl15693
    Location:49513
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
  5. NM_199239.3NP_954709.1  semaphorin-6D isoform Sema6D-5 precursor

    See identical proteins and their annotated locations for NP_954709.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) contains an additional in-frame exon in the central coding region, compared to variant 1, resulting in an isoform (Sema6D-5) that is longer than isoform Sema6D-1. The 5' UTR is incomplete because the evidence for this variant is for the CDS only, and multiple possible 5' UTR exon combinations exist.
    Source sequence(s)
    AB091534, AL935323, BC060680
    Consensus CDS
    CCDS38225.1
    UniProtKB/Swiss-Prot
    Q76KF0
    Conserved Domains (2) summary
    pfam01437
    Location:514582
    PSI; Plexin repeat
    cl15693
    Location:49513
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
  6. NM_199240.3NP_954710.1  semaphorin-6D isoform Sema6D-6 precursor

    See identical proteins and their annotated locations for NP_954710.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (6) uses an alternate in-frame splice site and contains an additional in-frame exon in the central coding region, compared to variant 1. The encoded isoform (Sema6D-6) is longer than isoform Sema6D-1. The 5' UTR is incomplete because the evidence for this variant is for the CDS only, and multiple possible 5' UTR exon combinations exist.
    Source sequence(s)
    AB091535, AL935323, BC060680
    Consensus CDS
    CCDS16672.1
    UniProtKB/Swiss-Prot
    Q76KF0
    Related
    ENSMUSP00000099528.1, OTTMUSP00000016241, ENSMUST00000103238.1, OTTMUST00000036149
    Conserved Domains (2) summary
    pfam01437
    Location:514569
    PSI; Plexin repeat
    cl15693
    Location:49513
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
  7. NM_199241.3NP_954711.1  semaphorin-6D isoform Sema6D-4 precursor

    See identical proteins and their annotated locations for NP_954711.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) uses an alternate in-frame splice site and contains two additional in-frame exons in the central coding region, compared to variant 1. The encoded isoform (Sema6D-4) is longer than isoform Sema6D-1. The 5' UTR is incomplete because the evidence for this variant is for the CDS only, and multiple possible 5' UTR exon combinations exist.
    Source sequence(s)
    AB091536, AL935323, BC060680
    Consensus CDS
    CCDS16673.1
    UniProtKB/Swiss-Prot
    Q76KF0
    Conserved Domains (2) summary
    pfam01437
    Location:514569
    PSI; Plexin repeat
    cl15693
    Location:49513
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

RefSeqs of Annotated Genomes: Mus musculus Annotation Release 106

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

Reference GRCm38.p4 C57BL/6J

Genomic

  1. NC_000068.7 Reference GRCm38.p4 C57BL/6J

    Range
    124089918..124667789
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011239427.2XP_011237729.1  semaphorin-6D isoform X5

    See identical proteins and their annotated locations for XP_011237729.1

    UniProtKB/Swiss-Prot
    Q76KF0
    Conserved Domains (2) summary
    pfam01437
    Location:514569
    PSI; Plexin repeat
    cl15693
    Location:49513
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
  2. XM_006499112.3XP_006499175.1  semaphorin-6D isoform X1

    See identical proteins and their annotated locations for XP_006499175.1

    Conserved Domains (2) summary
    pfam01437
    Location:514582
    PSI; Plexin repeat
    cl15693
    Location:49513
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
  3. XM_006499113.3XP_006499176.1  semaphorin-6D isoform X1

    See identical proteins and their annotated locations for XP_006499176.1

    Conserved Domains (2) summary
    pfam01437
    Location:514582
    PSI; Plexin repeat
    cl15693
    Location:49513
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
  4. XM_006499111.3XP_006499174.1  semaphorin-6D isoform X1

    See identical proteins and their annotated locations for XP_006499174.1

    Conserved Domains (2) summary
    pfam01437
    Location:514582
    PSI; Plexin repeat
    cl15693
    Location:49513
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
  5. XM_017316995.1XP_017172484.1  semaphorin-6D isoform X2

    Conserved Domains (2) summary
    pfam01437
    Location:514582
    PSI; Plexin repeat
    cl15693
    Location:49513
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
  6. XM_017317019.1XP_017172508.1  semaphorin-6D isoform X7

    UniProtKB/Swiss-Prot
    Q76KF0
    Related
    ENSMUSP00000077691.5, ENSMUST00000078621.11
    Conserved Domains (2) summary
    pfam01437
    Location:514582
    PSI; Plexin repeat
    cl15693
    Location:49513
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
  7. XM_017317010.1XP_017172499.1  semaphorin-6D isoform X4

    Conserved Domains (2) summary
    pfam01437
    Location:514582
    PSI; Plexin repeat
    cl15693
    Location:49513
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
  8. XM_017317001.1XP_017172490.1  semaphorin-6D isoform X3

    UniProtKB/Swiss-Prot
    Q76KF0
    Related
    ENSMUSP00000099529.3, OTTMUSP00000016242, ENSMUST00000103239.9, OTTMUST00000036150
    Conserved Domains (2) summary
    pfam01437
    Location:514569
    PSI; Plexin repeat
    cl15693
    Location:49513
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
  9. XM_017317021.1XP_017172510.1  semaphorin-6D isoform X8

    UniProtKB/Swiss-Prot
    Q76KF0
    Conserved Domains (2) summary
    pfam01437
    Location:514569
    PSI; Plexin repeat
    cl15693
    Location:49513
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
  10. XM_017317012.1XP_017172501.1  semaphorin-6D isoform X5

    UniProtKB/Swiss-Prot
    Q76KF0
    Related
    ENSMUSP00000077014.5, ENSMUST00000077847.11
    Conserved Domains (2) summary
    pfam01437
    Location:514569
    PSI; Plexin repeat
    cl15693
    Location:49513
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
  11. XM_017317014.1XP_017172503.1  semaphorin-6D isoform X6

  12. XM_017317026.1XP_017172515.1  semaphorin-6D isoform X9

    Conserved Domains (2) summary
    pfam01437
    Location:514582
    PSI; Plexin repeat
    cl15693
    Location:49513
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
  13. XM_017317028.1XP_017172517.1  semaphorin-6D isoform X10

    Conserved Domains (2) summary
    pfam01437
    Location:514582
    PSI; Plexin repeat
    cl15693
    Location:49513
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
  14. XM_006499114.3XP_006499177.1  semaphorin-6D isoform X1

    See identical proteins and their annotated locations for XP_006499177.1

    Conserved Domains (2) summary
    pfam01437
    Location:514582
    PSI; Plexin repeat
    cl15693
    Location:49513
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
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