Cell atlas - SEMA6D - The Human Protein Atlas

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SEMA6D

TISSUE

CELL

CANCER

CELL ATLAS RNA EXPRESSION HUMAN CELLS

GENE/PROTEIN

Antibody validation

Dictionary
	Golgi apparatus
	Plasma membrane

Human cell
	Golgi Apparatus
	Plasma Membrane

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GENERAL INFORMATION
Gene name	SEMA6D
Gene description	Sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D
Protein class	Plasma proteins Predicted intracellular proteins Predicted membrane proteins Predicted secreted proteins
Predicted localization	Intracellular,Membrane,Secreted
Number of transcripts	16
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HUMAN PROTEIN ATLAS INFORMATION
Summary	Mainly localized to the plasma membrane. In addition localized to the Golgi apparatus.
RNA cell category	Cell line enhanced (SCLC-21H, SH-SY5Y, BJ hTERT+)
Protein evidence	Evidence at protein level
Main location	Localized to the Plasma membrane (approved)
Additional location	In addition localized to the Golgi apparatus (uncertain)

DATA RELIABILITY
Reliability score	Approved based on 1 antibody. HPA043109
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ASSAYS

RNA EXPRESSION OVERVIEW
RNA cell line category: Cell line enhanced (SCLC-21H, SH-SY5Y, BJ hTERT+) Organ Origin Category Expression Alphabetical Cell lines sorted after organ of phenotypic resemblance. Cell lines sorted after biological source for establishment. Cell lines sorted after the cell line category according to Cellosaurus. Cell lines sorted on descending RNA expression. Cell lines sorted alphabetically.

HUMAN CELLS

Summary

Mainly localized to the plasma membrane. In addition localized to the Golgi apparatus.

Main location

Plasma membrane (approved)

Additional location

Golgi apparatus (uncertain)


	Toggle channels	Low High G1 S G2 M N/A

Thumbnail	Antibody	Cell line	Location	Single-cell variation	Cell cycle dependent variation
	HPA043109	A-431	Golgi apparatus
	HPA043109	A-431	Plasma membrane
	HPA043109	U-2 OS	No staining

GENE INFORMATION
Gene name	SEMA6D (HGNC Symbol)
Synonyms	FLJ11598, KIAA1479
Description	Sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D (HGNC Symbol)
Entrez gene summary	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]
Chromosome	15
Cytoband	q21.1
Chromosome location (bp)	47184101 - 47774223
Protein evidence	Evidence at protein level (all genes)
Ensembl	ENSG00000137872 (version 83.38)
Entrez gene	80031
UniProt	Q8NFY4 (UniProt - Evidence at transcript level)
neXtProt	NX_Q8NFY4
Antibodypedia	SEMA6D antibodies

PROTEIN BROWSER

SEMA6D-001	SEMA6D-002	SEMA6D-003	SEMA6D-004	SEMA6D-005	SEMA6D-006	SEMA6D-007	SEMA6D-008	SEMA6D-009	SEMA6D-010	SEMA6D-012	SEMA6D-013	SEMA6D-015	SEMA6D-016	SEMA6D-201	SEMA6D-202

PROTEIN INFORMATION
Splice variant	UniProt	Protein class	Gene ontology	Length & mass	Signal peptide (predicted)	Transmembrane regions (predicted)
SEMA6D-001 ENSP00000452815 ENST00000558014	Q8NFY4 [Direct mapping] Semaphorin-6D Show all	Predicted membrane proteins Prediction method-based Membrane proteins predicted by MDM MEMSAT3 predicted membrane proteins MEMSAT-SVM predicted membrane proteins Phobius predicted membrane proteins SCAMPI predicted membrane proteins SPOCTOPUS predicted membrane proteins THUMBUP predicted membrane proteins TMHMM predicted membrane proteins # TM segments-based 1TM proteins predicted by MDM Plasma proteins Protein evidence (Kim et al 2014) Show all	GO:0001755 [neural crest cell migration] GO:0005515 [protein binding] GO:0005737 [cytoplasm] GO:0005886 [plasma membrane] GO:0005887 [integral component of plasma membrane] GO:0007411 [axon guidance] GO:0016020 [membrane] GO:0030215 [semaphorin receptor binding] GO:0030335 [positive regulation of cell migration] GO:0045499 [chemorepellent activity] GO:0048843 [negative regulation of axon extension involved in axon guidance] GO:0050919 [negative chemotaxis] GO:0071526 [semaphorin-plexin signaling pathway] Show all	1011 aa 113.3 kDa	Yes	1
SEMA6D-002 ENSP00000446152 ENST00000536845	Q8NFY4 [Direct mapping] Semaphorin-6D Show all	Predicted membrane proteins Prediction method-based Membrane proteins predicted by MDM MEMSAT3 predicted membrane proteins MEMSAT-SVM predicted membrane proteins Phobius predicted membrane proteins SCAMPI predicted membrane proteins SPOCTOPUS predicted membrane proteins THUMBUP predicted membrane proteins TMHMM predicted membrane proteins # TM segments-based 1TM proteins predicted by MDM Plasma proteins Show all	GO:0001755 [neural crest cell migration] GO:0005515 [protein binding] GO:0005737 [cytoplasm] GO:0005886 [plasma membrane] GO:0005887 [integral component of plasma membrane] GO:0007411 [axon guidance] GO:0016020 [membrane] GO:0030215 [semaphorin receptor binding] GO:0030335 [positive regulation of cell migration] GO:0045499 [chemorepellent activity] GO:0048843 [negative regulation of axon extension involved in axon guidance] GO:0050919 [negative chemotaxis] GO:0071526 [semaphorin-plexin signaling pathway] Show all	1073 aa 119.9 kDa	Yes	1
SEMA6D-003 ENSP00000374076 ENST00000389425	Q8NFY4 [Direct mapping] Semaphorin-6D Show all	Predicted secreted proteins Secreted proteins predicted by MDSEC SignalP predicted secreted proteins Phobius predicted secreted proteins SPOCTOPUS predicted secreted proteins Plasma proteins Show all	GO:0001755 [neural crest cell migration] GO:0005515 [protein binding] GO:0005737 [cytoplasm] GO:0005886 [plasma membrane] GO:0005887 [integral component of plasma membrane] GO:0007411 [axon guidance] GO:0030215 [semaphorin receptor binding] GO:0030335 [positive regulation of cell migration] GO:0045499 [chemorepellent activity] GO:0048843 [negative regulation of axon extension involved in axon guidance] GO:0050919 [negative chemotaxis] GO:0071526 [semaphorin-plexin signaling pathway] Show all	476 aa 54.2 kDa	Yes	0
SEMA6D-004 ENSP00000324857 ENST00000316364	Q8NFY4 [Direct mapping] Semaphorin-6D Show all	Predicted membrane proteins Prediction method-based Membrane proteins predicted by MDM MEMSAT3 predicted membrane proteins MEMSAT-SVM predicted membrane proteins Phobius predicted membrane proteins SCAMPI predicted membrane proteins SPOCTOPUS predicted membrane proteins THUMBUP predicted membrane proteins TMHMM predicted membrane proteins # TM segments-based 1TM proteins predicted by MDM Plasma proteins Protein evidence (Kim et al 2014) Show all	GO:0001755 [neural crest cell migration] GO:0005515 [protein binding] GO:0005737 [cytoplasm] GO:0005886 [plasma membrane] GO:0005887 [integral component of plasma membrane] GO:0007411 [axon guidance] GO:0014911 [positive regulation of smooth muscle cell migration] GO:0014912 [negative regulation of smooth muscle cell migration] GO:0016020 [membrane] GO:0030215 [semaphorin receptor binding] GO:0030335 [positive regulation of cell migration] GO:0045499 [chemorepellent activity] GO:0048843 [negative regulation of axon extension involved in axon guidance] GO:0050919 [negative chemotaxis] GO:0071526 [semaphorin-plexin signaling pathway] Show all	1073 aa 119.9 kDa	Yes	1
SEMA6D-005 ENSP00000346786 ENST00000354744	Q8NFY4 [Direct mapping] Semaphorin-6D Show all	Predicted membrane proteins Prediction method-based Membrane proteins predicted by MDM MEMSAT3 predicted membrane proteins MEMSAT-SVM predicted membrane proteins Phobius predicted membrane proteins SCAMPI predicted membrane proteins SPOCTOPUS predicted membrane proteins THUMBUP predicted membrane proteins TMHMM predicted membrane proteins # TM segments-based 1TM proteins predicted by MDM Plasma proteins Protein evidence (Kim et al 2014) Show all	GO:0001755 [neural crest cell migration] GO:0005515 [protein binding] GO:0005737 [cytoplasm] GO:0005886 [plasma membrane] GO:0005887 [integral component of plasma membrane] GO:0007411 [axon guidance] GO:0016020 [membrane] GO:0030215 [semaphorin receptor binding] GO:0030335 [positive regulation of cell migration] GO:0045499 [chemorepellent activity] GO:0048843 [negative regulation of axon extension involved in axon guidance] GO:0050919 [negative chemotaxis] GO:0071526 [semaphorin-plexin signaling pathway] Show all	1017 aa 113.7 kDa	Yes	1
SEMA6D-006 ENSP00000350770 ENST00000358066	Q8NFY4 [Direct mapping] Semaphorin-6D Show all	Predicted membrane proteins Prediction method-based Membrane proteins predicted by MDM MEMSAT3 predicted membrane proteins MEMSAT-SVM predicted membrane proteins Phobius predicted membrane proteins SCAMPI predicted membrane proteins SPOCTOPUS predicted membrane proteins THUMBUP predicted membrane proteins TMHMM predicted membrane proteins # TM segments-based 1TM proteins predicted by MDM Plasma proteins Protein evidence (Kim et al 2014) Show all	GO:0001755 [neural crest cell migration] GO:0005515 [protein binding] GO:0005737 [cytoplasm] GO:0005886 [plasma membrane] GO:0005887 [integral component of plasma membrane] GO:0007411 [axon guidance] GO:0016020 [membrane] GO:0030215 [semaphorin receptor binding] GO:0030335 [positive regulation of cell migration] GO:0045499 [chemorepellent activity] GO:0048843 [negative regulation of axon extension involved in axon guidance] GO:0050919 [negative chemotaxis] GO:0071526 [semaphorin-plexin signaling pathway] Show all	1011 aa 113.3 kDa	Yes	1
SEMA6D-007 ENSP00000374079 ENST00000389428	Q8NFY4 [Direct mapping] Semaphorin-6D Show all	Predicted membrane proteins Prediction method-based Membrane proteins predicted by MDM MEMSAT3 predicted membrane proteins MEMSAT-SVM predicted membrane proteins Phobius predicted membrane proteins SCAMPI predicted membrane proteins SPOCTOPUS predicted membrane proteins THUMBUP predicted membrane proteins TMHMM predicted membrane proteins # TM segments-based 1TM proteins predicted by MDM Plasma proteins Protein evidence (Kim et al 2014) Show all	GO:0001755 [neural crest cell migration] GO:0005515 [protein binding] GO:0005737 [cytoplasm] GO:0005886 [plasma membrane] GO:0005887 [integral component of plasma membrane] GO:0007411 [axon guidance] GO:0016020 [membrane] GO:0030215 [semaphorin receptor binding] GO:0030335 [positive regulation of cell migration] GO:0045499 [chemorepellent activity] GO:0048843 [negative regulation of axon extension involved in axon guidance] GO:0050919 [negative chemotaxis] GO:0071526 [semaphorin-plexin signaling pathway] Show all	998 aa 111.7 kDa	Yes	1
SEMA6D-008 ENSP00000453661 ENST00000558816	Q8NFY4 [Direct mapping] Semaphorin-6D Show all	Predicted secreted proteins Secreted proteins predicted by MDSEC SignalP predicted secreted proteins Phobius predicted secreted proteins SPOCTOPUS predicted secreted proteins Plasma proteins Show all	GO:0001755 [neural crest cell migration] GO:0005515 [protein binding] GO:0005737 [cytoplasm] GO:0005886 [plasma membrane] GO:0005887 [integral component of plasma membrane] GO:0007411 [axon guidance] GO:0016020 [membrane] GO:0030215 [semaphorin receptor binding] GO:0030335 [positive regulation of cell migration] GO:0045499 [chemorepellent activity] GO:0048843 [negative regulation of axon extension involved in axon guidance] GO:0050919 [negative chemotaxis] GO:0071526 [semaphorin-plexin signaling pathway] Show all	597 aa 67.5 kDa	Yes	0
SEMA6D-009 ENSP00000453097 ENST00000559184	H0YL82 [Direct mapping] Semaphorin-6D Show all	Predicted secreted proteins Secreted proteins predicted by MDSEC Phobius predicted secreted proteins SPOCTOPUS predicted secreted proteins Show all		22 aa 2.5 kDa	Yes	0
SEMA6D-010 ENSP00000453420 ENST00000560636		Predicted intracellular proteins Show all		1 aa 0.1 kDa	No	0
SEMA6D-012 ENSP00000453530 ENST00000561133	H0YMA6 [Direct mapping] Semaphorin-6D Show all	Predicted secreted proteins Secreted proteins predicted by MDSEC SignalP predicted secreted proteins Phobius predicted secreted proteins SPOCTOPUS predicted secreted proteins Show all	GO:0005515 [protein binding] Show all	148 aa 17.6 kDa	Yes	0
SEMA6D-013 ENSP00000453755 ENST00000559196	H0YMV0 [Direct mapping] Semaphorin-6D Show all	Predicted secreted proteins Secreted proteins predicted by MDSEC SignalP predicted secreted proteins Phobius predicted secreted proteins SPOCTOPUS predicted secreted proteins Show all	GO:0005515 [protein binding] Show all	219 aa 25.4 kDa	Yes	0
SEMA6D-015 ENSP00000453518 ENST00000559064	H0YM97 [Direct mapping] Semaphorin-6D Show all	Predicted intracellular proteins Show all		54 aa 5.8 kDa	No	0
SEMA6D-016 ENSP00000453689 ENST00000560006	H0YMP7 [Direct mapping] Semaphorin-6D Show all	Predicted membrane proteins Prediction method-based Membrane proteins predicted by MDM MEMSAT3 predicted membrane proteins MEMSAT-SVM predicted membrane proteins Phobius predicted membrane proteins SCAMPI predicted membrane proteins SPOCTOPUS predicted membrane proteins THUMBUP predicted membrane proteins TMHMM predicted membrane proteins # TM segments-based 1TM proteins predicted by MDM Show all	GO:0016021 [integral component of membrane] Show all	198 aa 21.8 kDa	No	1
SEMA6D-201 ENSP00000348276 ENST00000355997	Q8NFY4 [Direct mapping] Semaphorin-6D Show all	Predicted secreted proteins Secreted proteins predicted by MDSEC SignalP predicted secreted proteins Phobius predicted secreted proteins SPOCTOPUS predicted secreted proteins Plasma proteins Show all	GO:0001755 [neural crest cell migration] GO:0005515 [protein binding] GO:0005737 [cytoplasm] GO:0005886 [plasma membrane] GO:0005887 [integral component of plasma membrane] GO:0007411 [axon guidance] GO:0016020 [membrane] GO:0030215 [semaphorin receptor binding] GO:0030335 [positive regulation of cell migration] GO:0045499 [chemorepellent activity] GO:0048843 [negative regulation of axon extension involved in axon guidance] GO:0050919 [negative chemotaxis] GO:0071526 [semaphorin-plexin signaling pathway] Show all	597 aa 67.5 kDa	Yes	0
SEMA6D-202 ENSP00000442040 ENST00000537942	Q8NFY4 [Direct mapping] Semaphorin-6D Show all	Predicted membrane proteins Prediction method-based Membrane proteins predicted by MDM MEMSAT3 predicted membrane proteins MEMSAT-SVM predicted membrane proteins Phobius predicted membrane proteins SCAMPI predicted membrane proteins SPOCTOPUS predicted membrane proteins THUMBUP predicted membrane proteins TMHMM predicted membrane proteins # TM segments-based 1TM proteins predicted by MDM Plasma proteins Show all	GO:0001755 [neural crest cell migration] GO:0005515 [protein binding] GO:0005737 [cytoplasm] GO:0005886 [plasma membrane] GO:0005887 [integral component of plasma membrane] GO:0007411 [axon guidance] GO:0016020 [membrane] GO:0030215 [semaphorin receptor binding] GO:0030335 [positive regulation of cell migration] GO:0045499 [chemorepellent activity] GO:0048843 [negative regulation of axon extension involved in axon guidance] GO:0050919 [negative chemotaxis] GO:0071526 [semaphorin-plexin signaling pathway] Show all	1011 aa 113.3 kDa	Yes	1

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The Project

The Human Protein Atlas

The Human Protein Atlas project is funded
by the Knut & Alice Wallenberg foundation.