Seroatlas · Human Serome Atlas

SEMA6D

Semaphorin-6D

Also known as: FLJ11598, KIAA1479, SEM6D_HUMAN

Cross-references: UniProt · Ensembl · Human Protein Atlas · GeneCards · NCBI Gene

Protein identityUniProt · HPA

UniProt accession
Q8NFY4
Gene
SEMA6D
Ensembl
ENSG00000137872
Chromosome
15
Canonical length
1073 aa
Protein class
Plasma proteins, Predicted intracellular proteins, Predicted membrane proteins
Subcellular location
Golgi apparatus,Plasma membrane
Secretome location
Intracellular and membrane

OverviewNCBI Gene

Semaphorins are a large family, including both secreted and membrane associated proteins, many of which have been implicated as inhibitors or chemorepellents in axon pathfinding, fasciculation and branching, and target selection. All semaphorins possess a semaphorin (Sema) domain and a PSI domain (found in plexins, semaphorins and integrins) in the N-terminal extracellular portion. Additional sequence motifs C-terminal to the semaphorin domain allow classification into distinct subfamilies. Results demonstrate that transmembrane semaphorins, like the secreted ones, can act as repulsive axon guidance cues. This gene encodes a class 6 vertebrate transmembrane semaphorin that demonstrates alternative splicing. Several transcript variants have been identified and expression of the distinct encoded isoforms is thought to be regulated in a tissue- and development-dependent manner. [provided by RefSeq, Nov 2010]

Canonical amino-acid sequenceUniProt

1073 residues, UniProt reviewed canonical sequence.

>Q8NFY4|SEMA6D
     1  MRVFLLCAYI LLLMVSQLRA VSFPEDDEPL NTVDYHYSRQ YPVFRGRPSG NESQHRLDFQ
    61  LMLKIRDTLY IAGRDQVYTV NLNEMPKTEV IPNKKLTWRS RQQDRENCAM KGKHKDECHN
   121  FIKVFVPRND EMVFVCGTNA FNPMCRYYRL STLEYDGEEI SGLARCPFDA RQTNVALFAD
   181  GKLYSATVAD FLASDAVIYR SMGDGSALRT IKYDSKWIKE PHFLHAIEYG NYVYFFFREI
   241  AVEHNNLGKA VYSRVARICK NDMGGSQRVL EKHWTSFLKA RLNCSVPGDS FFYFDVLQSI
   301  TDIIQINGIP TVVGVFTTQL NSIPGSAVCA FSMDDIEKVF KGRFKEQKTP DSVWTAVPED
   361  KVPKPRPGCC AKHGLAEAYK TSIDFPDETL SFIKSHPLMD SAVPPIADEP WFTKTRVRYR
   421  LTAISVDHSA GPYQNYTVIF VGSEAGMVLK VLAKTSPFSL NDSVLLEEIE AYNHAKCSAE
   481  NEEDKKVISL QLDKDHHALY VAFSSCIIRI PLSRCERYGS CKKSCIASRD PYCGWLSQGS
   541  CGRVTPGMLA EGYEQDTEFG NTAHLGDCHE ILPTSTTPDY KIFGGPTSDM EVSSSSVTTM
   601  ASIPEITPKV IDTWRPKLTS SRKFVVQDDP NTSDFTDPLS GIPKGVRWEV QSGESNQMVH
   661  MNVLITCVFA AFVLGAFIAG VAVYCYRDMF VRKNRKIHKD AESAQSCTDS SGSFAKLNGL
   721  FDSPVKEYQQ NIDSPKLYSN LLTSRKELPP NGDTKSMVMD HRGQPPELAA LPTPESTPVL
   781  HQKTLQAMKS HSEKAHGHGA SRKETPQFFP SSPPPHSPLS HGHIPSAIVL PNATHDYNTS
   841  FSNSNAHKAE KKLQNIDHPL TKSSSKRDHR RSVDSRNTLN DLLKHLNDPN SNPKAIMGDI
   901  QMAHQNLMLD PMGSMSEVPP KVPNREASLY SPPSTLPRNS PTKRVDVPTT PGVPMTSLER
   961  QRGYHKNSSQ RHSISAMPKN LNSPNGVLLS RQPSMNRGGY MPTPTGAKVD YIQGTPVSVH
  1021  LQPSLSRQSS YTSNGTLPRT GLKRTPSLKP DVPPKPSFVP QTPSVRPLNK YTY

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against SEMA6D can act on the native protein depends on physical access: surface and secreted proteins are reachable by circulating antibodies, intracellular proteins usually are not.

Antibody reachability
Cell surface
Secreted
No
Transmembrane segments
1
Mean surface accessibility (rSASA)
0.46
Highest tissue expression
40 nTPM

Expression across tissuesHPA

Tissue

  • placenta: 40 nTPM
  • small intestine: 36 nTPM
  • duodenum: 21 nTPM
  • ovary: 21 nTPM
  • skeletal muscle: 20 nTPM
  • pancreas: 15 nTPM

Single-cell type

  • bergmann glia: 1,265 nCPM
  • cone photoreceptor cells: 888 nCPM
  • cytotrophoblasts: 530 nCPM
  • brain inhibitory neurons: 502 nCPM
  • other brain neurons: 350 nCPM
  • distal convoluted tubule cells: 246 nCPM

Immune cell

  • neutrophil: 0.2 nTPM
  • memory CD8 T-cell: 0.1 nTPM
  • basophil: 0 nTPM
  • classical monocyte: 0 nTPM
  • eosinophil: 0 nTPM
  • gdT-cell: 0 nTPM

Brain region

  • midbrain: 101 nTPM
  • white matter: 93 nTPM
  • cerebral cortex: 91 nTPM
  • basal ganglia: 83 nTPM
  • pons: 82 nTPM
  • thalamus: 77 nTPM

Genetic constraint and essentialitygnomAD · DepMap

Does the body need this protein intact? Low LOEUF or a strong DepMap dependency means loss or blockade of the protein is likely to be felt.

gnomAD LOEUF (loss-of-function intolerance)
0.32
gnomAD pLI
0.94
gnomAD missense Z
1.08
DepMap mean gene effect
0.01
DepMap dependency class
selective

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 4% of surveyed tumor types (aggregate summary; per-cohort expression, alteration, and survival load in the interactive view).

OntologyGO

Biological processes

Molecular functions

Cellular components

Protein domainsUniProt · Pfam · InterPro

KeywordsUniProt

Antibody and autoantibody relevanceSeroatlas analysis

Seroatlas reads SEMA6D as an antibody target. Whether an autoantibody or antibody against SEMA6D could matter depends on whether native SEMA6D is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

SEMA6D is annotated at the cell surface, where native SEMA6D is exposed to circulating antibodies and is a prime autoantibody target that could block, deplete, or overstimulate it.

Annotation status

The present source text does not explicitly label SEMA6D as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

Canonical record: https://seroatlas.com/gene/SEMA6D. Study-independent annotations aggregated from UniProt, Human Protein Atlas, PubMed, IEDB, Pfam, InterPro, Gene Ontology, AlphaFold, gnomAD, DepMap, ClinVar, TCGA. Catalog release seroatlas-reviewed-human-uniprot-20260313.

Seroatlas is the reference for exploring autoantibody and antibody serology at the human-protein level: the autoreactome and human serome, multiplex serology (HuProt, HuScan, VirScan, PhIP-Seq).

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