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Gene: Vapa (VAMP associated protein A) Chinchilla lanigera

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Symbol:

Vapa

Name:

VAMP associated protein A

RGD ID:

8971040

Description:

ENCODES a protein that exhibits FFAT motif binding (ortholog); identical protein binding (ortholog); microtubule binding (ortholog); INVOLVED IN ceramide transport (ortholog); cholesterol transport (ortholog); COPII-coated vesicle budding (ortholog); ASSOCIATED WITH chromosome 18p deletion syndrome (ortholog); dystonia (ortholog); intellectual disability (ortholog); FOUND IN bicellular tight junction (ortholog); endoplasmic reticulum (ortholog); endoplasmic reticulum exit site (ortholog)

Type:

protein-coding

RefSeq Status:

MODEL

Previously known as:

VAMP (vesicle-associated membrane protein)-associated protein A, 33kDa; vesicle-associated membrane protein-associated protein A

RGD Orthologs

Alliance Orthologs

More Info

more info ...

Latest Assembly:

ChiLan1.0 - Chinchilla ChiLan1.0 Assembly

NCBI Annotation Information:

Annotation category: partial on reference assembly

Position:

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0 Ensembl	NW_004955402	2,270,850 - 2,298,227 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955402	2,274,248 - 2,309,461 (-)	NCBI	ChiLan1.0	ChiLan1.0

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

chromosome 18p deletion syndrome (ISO)

dystonia (ISO)

intellectual disability (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

ceramide transport (ISO)

cholesterol transport (ISO)

COPII-coated vesicle budding (ISO)

endoplasmic reticulum organization (ISO)

endoplasmic reticulum to Golgi vesicle-mediated transport (ISO)

endoplasmic reticulum-plasma membrane tethering (ISO)

negative regulation by host of viral genome replication (ISO)

neuron projection development (ISO)

phospholipid transport (ISO)

positive regulation by host of viral genome replication (ISO)

positive regulation of canonical NF-kappaB signal transduction (ISO)

protein folding in endoplasmic reticulum (ISO)

protein localization to endoplasmic reticulum (ISO)

sphingomyelin biosynthetic process (ISO)

sterol transport (ISO)

viral release from host cell (ISO)

Cellular Component

bicellular tight junction (ISO)

endoplasmic reticulum (ISO)

endoplasmic reticulum exit site (ISO)

endoplasmic reticulum membrane (ISO)

Golgi membrane (ISO)

membrane (ISO)

microtubule cytoskeleton (ISO)

nuclear membrane (ISO)

perinuclear region of cytoplasm (ISO)

plasma membrane (ISO)

vesicle (ISO)

Molecular Function

FFAT motif binding (ISO)

identical protein binding (ISO)

microtubule binding (ISO)

protein binding (ISO)

protein domain specific binding (ISO)

protein heterodimerization activity (ISO)

protein homodimerization activity (ISO)

protein-containing complex binding (ISO)

References

References - curated

#	Reference Title	Reference Citation
1.	Transitive Annotation Pipeline	Automated assignment of GO, PW and RDO ISO annotations across species

Additional References at PubMed

PMID:22301074	PMID:30032202

Genomics

Comparative Map Data

Vapa
(Chinchilla lanigera - long-tailed chinchilla)

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0 Ensembl	NW_004955402	2,270,850 - 2,298,227 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955402	2,274,248 - 2,309,461 (-)	NCBI	ChiLan1.0	ChiLan1.0

VAPA
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	18	9,914,016 - 9,960,021 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	18	9,914,016 - 9,960,021 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	18	9,914,013 - 9,960,018 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	18	9,903,955 - 9,950,018 (+)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	18	9,903,983 - 9,949,571	NCBI
Celera	18	9,797,515 - 9,843,493 (+)	NCBI		Celera
Cytogenetic Map	18	p11.22	NCBI
HuRef	18	9,893,891 - 9,921,843 (+)	NCBI		HuRef
CHM1_1	18	9,913,226 - 9,959,178 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	18	10,077,467 - 10,123,397 (+)	NCBI		T2T-CHM13v2.0

Vapa
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	17	65,887,048 - 65,925,441 (-)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	17	65,885,322 - 65,920,550 (-)	Ensembl		GRCm39 Ensembl
GRCm38	17	65,580,053 - 65,616,462 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	17	65,578,327 - 65,613,555 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	17	65,929,393 - 65,962,895 (-)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	17	65,479,598 - 65,513,084 (-)	NCBI		MGSCv36	mm8
Celera	17	69,883,322 - 69,916,704 (-)	NCBI		Celera
Cytogenetic Map	17	E1.1	NCBI
cM Map	17	34.9	NCBI

Vapa
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	9	112,624,791 - 112,654,731 (-)	NCBI		GRCr8
mRatBN7.2	9	105,177,904 - 105,208,400 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	9	105,177,907 - 105,207,847 (-)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	9	113,588,500 - 113,618,316 (-)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	9	118,698,807 - 118,728,640 (-)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	9	117,054,450 - 117,084,266 (-)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	9	113,300,831 - 113,331,872 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	9	113,300,832 - 113,331,319 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	9	112,833,701 - 112,864,112 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	9	104,339,039 - 104,368,908 (-)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	9	104,548,519 - 104,578,388 (-)	NCBI
Celera	9	102,564,697 - 102,594,412 (-)	NCBI		Celera
Cytogenetic Map	9	q37	NCBI

VAPA
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
NHGRI_mPanPan1-v2	17	28,496,390 - 28,537,484 (-)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	18	14,188,987 - 14,230,079 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	18	4,329,479 - 4,373,047 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	18	6,613,042 - 6,642,425 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	18	6,612,105 - 6,637,829 (-)	Ensembl	panpan1.1		panPan2

VAPA
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	7	75,844,927 - 75,891,811 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	7	75,845,000 - 75,889,076 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	7	75,242,387 - 75,289,206 (+)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	7	75,905,356 - 75,948,878 (+)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	7	75,905,322 - 75,949,488 (+)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	7	75,603,405 - 75,650,255 (+)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	7	75,621,438 - 75,668,178 (+)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	7	75,930,605 - 75,977,554 (+)	NCBI		UU_Cfam_GSD_1.0

Vapa
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024404944	2,321,989 - 2,357,518 (-)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936626	1,548,139 - 1,568,656 (-)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936626	1,550,305 - 1,585,783 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

VAPA
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	6	98,210,053 - 98,254,226 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	6	98,212,335 - 98,254,272 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1

VAPA
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	18	68,784,786 - 68,825,333 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	18	68,784,799 - 68,827,581 (+)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666050	43,739,425 - 43,782,261 (+)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Vapa
(Heterocephalus glaber - naked mole-rat)

Naked Mole-Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Naked Mole-Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla_female_1.0 Ensembl	NW_004624770	18,411,789 - 18,447,009 (+)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624770	18,411,921 - 18,447,004 (+)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Expression

RNA-SEQ Expression

Click on a value in the shaded box below the category label to view a detailed expression data table for that system.

Sequence

Nucleotide Sequences


RefSeq Transcripts	XM_013514923	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AGCD01000072	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AGCD01000073	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AGCD01000074	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	GBCB01006390	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	GBDK01015995	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSCLAT00000009602 ⟹ ENSCLAP00000009473

Type:

CODING

Position:

Chinchilla Assembly	Chr	Position (strand)	Source
ChiLan1.0 Ensembl	NW_004955402	2,270,850 - 2,298,227 (-)	Ensembl

RefSeq Acc Id:

XM_013514923 ⟹ XP_013370377

Type:

CODING

Position:

Chinchilla Assembly	Chr	Position (strand)	Source
ChiLan1.0	NW_004955402	2,274,248 - 2,309,461 (-)	NCBI

Sequence:

show sequence

CGCAGGGCATGCTGGGAGTCGGGCGCGGCGCTCCTGGACTGGCAGACGCGAGGCATCAGTGTCG
CAGGCTCTTGGCGACGTCTTCGGAGCTCGTCGTGACGGAGGGCCGCGCCCTTGTCCTGCGCTGC
GCTCTGCGTCGGCCTCACGGGCCCCGTCACGCCCTTTTCCTTGACAGCTGCGCCGAACCGGGAG
CGGCGGCTAGCGGGGGCGCGCAAGCGCAGCAGCTCGCGTCGCAGAGGCCGGCCGGGGGGCGGGG
CGGACGTGAGCGGCTGGCGGCGTCGGGGACGCGCACGTAGCCACGCAGAGGCCGTCACGTGGGG
CACCGAGGATCGCAGTGCGCGTGGCCGCGGCGGCTGTGTGAGGTTGAGTCAGTTGTGAGAGTCG
GAGCTGCTGACCCCGCGGCGGCCCCGCGAACCCGCGACCGAGCGACAGGCGTTGAGGCCCGAGG
CCGGAGCCTGGCCCCGTGCTAGAGCTCGGCCGAGCCGGGCCGCGCCCCCGCCCAGCCCGCAGAC
CGCCGCCGCGGGCGCGCCCCCGCTCTGCGCTGCCTCCGATGGCGTCCGCCTCCGGGGCCATGGC
GAAACACGAGCAGATCTTGGTCCTCGACCCGCCCACAGACCTCAAATTCAAAGGCCCCTTCACA
GATGTAGTCACTACAAATCTTAAATTGAGAAATCCGTCAGATAGAAAAGTATGTTTCAAAGTGA
AGACTACAGCACCTCGCCGGTACTGTGTGAGGCCCAATAGTGGAATTATTGACCCAGGGTCGAC
AGTGACTGTTTCAGTAATGCTACAGCCTTTTGACTATGATCCAAATGAAAAGAGCAAACACAAG
TTTATGGTACAGACAATTTTTGCTCCACCAAACACTTCAGATATGGAAGCAGTGTGGAAAGAGG
CAAAACCTGATGAACTAATGGATTCTAAATTGAGATGTGTATTTGAAATGCCAAATGAAAATGA
TAAATTGGGTGTAACTCCACCAGGGACAGCTCCACTCGCCACCTCAGTGAGCAGCGTCAGCAAC
ACAGCTGCAGCACCCGCCACTTACCCCAGGACGAGTGATCCCAGGAGAATCAGTGTGTTGACAC
AGGAGAAGCAGAAGAACGATATGGAACCTAGCAAAGCTGTTCCACTGAATGCGTCTAAACAAGA
TGGACCCATGCCAAAACCGCACAGTGTTTCACTCAATGATACTGAGACACGGAAGCTCATGGAG
GAGTGTAAAAGACTTCAGGGAGAAATGATGAAGCTGTCAGAAGAAAATCGGCACCTGAGAGAGG
AAGGCTTAAGGCTCAGGAAGGTAGCACATTCGGAGAAGCCTGGGTCGGCCTCGGCTGCGTCCTT
CAGAGACAACGTCACCAGTCCTCTCCCCTCACTCCTTGTTGTGATTGCAGCCATCTTCATCGGG
TTCTTTCTAGGGAAGTTCATCTTGTAGAGTGAAGCATGCAGAGTGCTATTTCTTTTTTTTTTTT
TTTTTTCTCTTGACCAGAAAAAGATTTGTTTACCTACCATTTCACTGGTAGTGTGGCCCGCAGT
GACCATTTTTTTTGTGTGTACAGCGTCAATACAGGCTTTGCCTCTAATGATCTCTTATGGTTAG
AAAACACAGTAAAAACTGTCGGCTGCTGGACAGGTTGTCTATCACCAGGTCATCATTAGCAGGT
GTCAGTGGCACACAGTCTGTCATGAAATTCATAATAAGGAGTTGTTTTCTTTGTGGTTTTAATA
AGAGTTCAACAATTGTTCAGAGTCTTGTAAATGTTATTTTAATAATCCCTTTAAATTTTATCTG
TTGCTGTTACCTCTTGAAATATGATTTATTTAGATTGCTAATATCACTCATTCAGGAAATGCCA
AGAGGTGTTCTGTGGGGAAATGGTGCCTCTTACCATGTACATTTTCTCCTTTACCTTTGCTAAT
ATCATGGCGGAATTTTTCTTACCCTTGTGAGGCAACTGTTCACTGAGTTTTTCATCCTTACGGT
CCTGTCCCATGGTATTTAACATAAAAAAATAAAACTGTTAACAGATTCTTGCTCGATAG

hide sequence

Protein Sequences


Protein RefSeqs	XP_013370377	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSCLAP00000009473
	ENSCLAP00000009473.1

RefSeq Acc Id:

XP_013370377 ⟸ XM_013514923

- Sequence:

show sequence

MASASGAMAKHEQILVLDPPTDLKFKGPFTDVVTTNLKLRNPSDRKVCFKVKTTAPRRYCVRPN
SGIIDPGSTVTVSVMLQPFDYDPNEKSKHKFMVQTIFAPPNTSDMEAVWKEAKPDELMDSKLRC
VFEMPNENDKLGVTPPGTAPLATSVSSVSNTAAAPATYPRTSDPRRISVLTQEKQKNDMEPSKA
VPLNASKQDGPMPKPHSVSLNDTETRKLMEECKRLQGEMMKLSEENRHLREEGLRLRKVAHSEK
PGSASAASFRDNVTSPLPSLLVVIAAIFIGFFLGKFIL

hide sequence

Ensembl Acc Id:

ENSCLAP00000009473 ⟸ ENSCLAT00000009602

Protein Domains

MSP

Additional Information

External Database Links

Database	Acc Id	Source(s)
Ensembl Genes	ENSCLAG00000006573	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSCLAT00000009602	ENTREZGENE
	ENSCLAT00000009602.1	UniProtKB/TrEMBL
Gene3D-CATH	2.60.40.10	UniProtKB/TrEMBL
InterPro	Ig-like_fold	UniProtKB/TrEMBL
	MSP_dom	UniProtKB/TrEMBL
	PapD-like_sf	UniProtKB/TrEMBL
	VAP	UniProtKB/TrEMBL
NCBI Gene	Vapa	ENTREZGENE
PANTHER	PTHR10809	UniProtKB/TrEMBL
	VESICLE-ASSOCIATED MEMBRANE PROTEIN-ASSOCIATED PROTEIN A	UniProtKB/TrEMBL
Pfam	Motile_Sperm	UniProtKB/TrEMBL
PIRSF	VAMP-associated	UniProtKB/TrEMBL
PROSITE	MSP	UniProtKB/TrEMBL
Superfamily-SCOP	SSF49354	UniProtKB/TrEMBL
UniProt	A0A8C2V6D1_CHILA	UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2016-08-16	Vapa	VAMP associated protein A		VAMP (vesicle-associated membrane protein)-associated protein A, 33kDa	Symbol and/or name change	5135510	APPROVED

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

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