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Gene: Vps29 (VPS29 retromer complex component) Rattus norvegicus

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Symbol:

Vps29

Name:

VPS29 retromer complex component

RGD ID:

1308332

Description:

Predicted to enable metal ion binding activity. Predicted to be involved in endocytic recycling; intracellular protein transport; and retrograde transport, endosome to Golgi. Predicted to be located in cytosol. Predicted to be part of retromer, cargo-selective complex. Predicted to be active in endosome. Orthologous to human VPS29 (VPS29 retromer complex component); PARTICIPATES IN retromer-mediated pathway; INTERACTS WITH 1,3,5-trinitro-1,3,5-triazinane; 2,3,7,8-tetrachlorodibenzodioxine; 3,4-methylenedioxymethamphetamine.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Previously known as:

LOC288666; vacuolar protein sorting 29; vacuolar protein sorting 29 (S. pombe); vacuolar protein sorting 29 homolog; vacuolar protein sorting 29 homolog (S. cerevisiae); Vacuolar protein sorting-associated protein 29; Vesicle protein sorting 29

RGD Orthologs

Alliance Orthologs

More Info

more info ...

More Info

Species	Gene symbol and name	Data Source	Assertion derived from	less info ...
Orthologs ¹				less info ...
Homo sapiens (human):	VPS29 (VPS29 retromer complex component)	HGNC	Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, PhylomeDB
Mus musculus (house mouse):	Vps29 (VPS29 retromer complex component)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Vps29 (VPS29 retromer complex component)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	VPS29 (VPS29 retromer complex component)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	VPS29 (VPS29 retromer complex component)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Vps29 (VPS29 retromer complex component)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	VPS29 (VPS29 retromer complex component)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	VPS29 (VPS29 retromer complex component)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Vps29 (VPS29 retromer complex component)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Rattus rattus (black rat):	Vps29 (VPS29 retromer complex component)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	VPS29 (VPS29 retromer complex component)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Homo sapiens (human):	VPS29 (VPS29 retromer complex component)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|SonicParanoid)
Mus musculus (house mouse):	Vps29 (VPS29 retromer complex component)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Vps29 (VPS29 retromer complex component)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|SonicParanoid)
Danio rerio (zebrafish):	vps29 (VPS29 retromer complex component)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Saccharomyces cerevisiae (baker's yeast):	VPS29	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Drosophila melanogaster (fruit fly):	Vps29	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Caenorhabditis elegans (roundworm):	vps-29	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Xenopus tropicalis (tropical clawed frog):	vps29	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)

Latest Assembly:

GRCr8 - GRCr8 Assembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	12	39,869,688 - 39,878,732 (-)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	12	39,869,688 - 39,878,848 (-)	Ensembl				GRCr8
mRatBN7.2	12	34,208,911 - 34,217,977 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	12	34,207,263 - 34,217,964 (-)	Ensembl				mRatBN7.2
UTH_Rnor_SHR_Utx	12	35,381,318 - 35,390,362 (-)	NCBI	UTH_Rnor_SHR_Utx	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	12	35,992,730 - 36,001,774 (-)	NCBI	UTH_Rnor_SHRSP_BbbUtx_1.0	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	12	35,045,052 - 35,054,096 (-)	NCBI	UTH_Rnor_WKY_Bbb_1.0	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	12	39,690,069 - 39,699,114 (-)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	12	39,690,069 - 39,699,113 (-)	Ensembl			rn6	Rnor6.0
Rnor_5.0	12	41,570,698 - 41,579,742 (-)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	12	35,403,351 - 35,412,395 (-)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	12	35,879,772 - 35,888,815 (-)	NCBI		Celera
RGSC_v3.1	12	35,266,872 - 35,275,774 (-)	NCBI
Cytogenetic Map	12	q16	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Annotation Click to see Annotation Detail View

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(1->4)-beta-D-glucan (ISO)

1,2-dimethylhydrazine (ISO)

1,3,5-trinitro-1,3,5-triazinane (EXP)

1-chloro-2,4-dinitrobenzene (ISO)

17alpha-ethynylestradiol (ISO)

2,3,7,8-tetrachlorodibenzodioxine (EXP,ISO)

3,4-methylenedioxymethamphetamine (EXP)

3H-1,2-dithiole-3-thione (EXP)

4,4'-diaminodiphenylmethane (ISO)

6-propyl-2-thiouracil (EXP)

actinomycin D (ISO)

aflatoxin B1 (ISO)

amitrole (EXP)

amphetamine (EXP)

aristolochic acid A (ISO)

arsenite(3-) (ISO)

benzo[a]pyrene (EXP,ISO)

beta-lapachone (ISO)

bisphenol A (EXP,ISO)

Bisphenol B (ISO)

chloropicrin (ISO)

choline (ISO)

cyproconazole (ISO)

dicrotophos (ISO)

disodium selenite (ISO)

doxorubicin (ISO)

epoxiconazole (ISO)

finasteride (EXP)

fipronil (EXP)

flutamide (EXP)

folic acid (ISO)

gentamycin (EXP)

homocysteine (ISO)

inulin (ISO)

ivermectin (ISO)

L-methionine (ISO)

lithium atom (EXP)

lithium hydride (EXP)

Mesaconitine (EXP)

methamphetamine (ISO)

methimazole (EXP)

nefazodone (EXP)

nimesulide (EXP)

Nutlin-3 (ISO)

ozone (ISO)

perfluorooctane-1-sulfonic acid (ISO)

perfluorooctanoic acid (ISO)

pregnenolone 16alpha-carbonitrile (EXP)

propiconazole (ISO)

resveratrol (ISO)

SB 431542 (ISO)

sodium arsenite (ISO)

sodium dodecyl sulfate (ISO)

sodium fluoride (ISO)

sulfadimethoxine (EXP)

sulindac (EXP)

thapsigargin (EXP)

titanium dioxide (ISO)

triphenyl phosphate (ISO)

triptonide (ISO)

valproic acid (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

biological_process (ND)

endocytic recycling (IEA,ISO,ISS)

intracellular protein transport (IBA)

protein transport (IEA)

regulation of autophagy (ISO)

retrograde transport, endosome to Golgi (IBA,IEA)

Cellular Component

cytoplasm (IEA)

cytosol (IEA,ISO)

early endosome (IEA)

endosome (IBA,IEA,ISO)

endosome membrane (IEA)

late endosome (IEA)

membrane (IEA)

protein-containing complex (IEA,ISO)

retromer complex (IBA,IEA,ISO,ISS)

retromer, cargo-selective complex (IEA,ISO)

Molecular Function

metal ion binding (IEA)

protein binding (ISO)

Molecular Pathway Annotations Click to see Annotation Detail View

retromer-mediated pathway (ISO)

References

References - curated

#	Reference Title	Reference Citation
1.	Retromer and sorting nexins in endosomal sorting.	Gallon M and Cullen PJ, Biochem Soc Trans. 2015 Feb;43(1):33-47. doi: 10.1042/BST20140290.
2.	Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
3.	Rat ISS GO annotations from MGI mouse gene data--August 2006	MGD data from the GO Consortium
4.	GOA pipeline	RGD automated data pipeline
5.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions
6.	Comprehensive gene review and curation	RGD comprehensive gene curation

Additional References at PubMed

PMID:11102511	PMID:12477932	PMID:15489334	PMID:21040701	PMID:23106098	PMID:23376485	PMID:24603492	PMID:24856514	PMID:27385586	PMID:28131823	PMID:28892079

Genomics

Comparative Map Data

Vps29
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	12	39,869,688 - 39,878,732 (-)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	12	39,869,688 - 39,878,848 (-)	Ensembl				GRCr8
mRatBN7.2	12	34,208,911 - 34,217,977 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	12	34,207,263 - 34,217,964 (-)	Ensembl				mRatBN7.2
UTH_Rnor_SHR_Utx	12	35,381,318 - 35,390,362 (-)	NCBI	UTH_Rnor_SHR_Utx	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	12	35,992,730 - 36,001,774 (-)	NCBI	UTH_Rnor_SHRSP_BbbUtx_1.0	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	12	35,045,052 - 35,054,096 (-)	NCBI	UTH_Rnor_WKY_Bbb_1.0	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	12	39,690,069 - 39,699,114 (-)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	12	39,690,069 - 39,699,113 (-)	Ensembl			rn6	Rnor6.0
Rnor_5.0	12	41,570,698 - 41,579,742 (-)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	12	35,403,351 - 35,412,395 (-)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	12	35,879,772 - 35,888,815 (-)	NCBI		Celera
RGSC_v3.1	12	35,266,872 - 35,275,774 (-)	NCBI
Cytogenetic Map	12	q16	NCBI

VPS29
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	12	110,491,083 - 110,502,111 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	12	110,491,083 - 110,502,111 (-)	Ensembl			hg38	GRCh38
GRCh37	12	110,928,888 - 110,939,916 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	12	109,413,713 - 109,424,299 (-)	NCBI	Build 36	Build 36	hg18	NCBI36
Build 34	12	109,392,049 - 109,402,636	NCBI
Celera	12	110,556,089 - 110,566,675 (-)	NCBI		Celera
Cytogenetic Map	12	q24.11	NCBI
HuRef	12	107,947,467 - 107,958,045 (-)	NCBI		HuRef
CHM1_1	12	110,897,142 - 110,907,726 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	12	110,468,777 - 110,479,808 (-)	NCBI		T2T-CHM13v2.0

Vps29
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	5	122,492,391 - 122,503,047 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	5	122,492,432 - 122,503,047 (+)	Ensembl		GRCm39 Ensembl		GRCm39
GRCm38	5	122,354,328 - 122,364,984 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	5	122,354,369 - 122,364,984 (+)	Ensembl			mm10	GRCm38
MGSCv37	5	122,804,422 - 122,813,296 (+)	NCBI	MGSCv37	MGSCv37	mm9	NCBIm37
MGSCv36	5	122,615,030 - 122,623,904 (+)	NCBI		MGSCv36	mm8
Celera	5	119,436,876 - 119,445,731 (+)	NCBI		Celera
Cytogenetic Map	5	F	NCBI
cM Map	5	62.32	NCBI

Vps29
(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_004955482	7,397,123 - 7,405,591 (-)	Ensembl
ChiLan1.0	NW_004955482	7,397,123 - 7,405,593 (-)	NCBI	ChiLan1.0	ChiLan1.0

VPS29
(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	10	118,552,400 - 118,562,921 (-)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	12	118,548,803 - 118,559,324 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	12	108,061,372 - 108,071,994 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	12	111,457,536 - 111,467,826 (-)	NCBI	PanPan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	12	111,457,609 - 111,467,826 (-)	Ensembl			panPan2	panpan1.1

VPS29
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	26	8,301,699 - 8,309,364 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	26	8,301,699 - 8,309,364 (-)	Ensembl			canFam3	CanFam3.1
Dog10K_Boxer_Tasha	26	8,465,295 - 8,472,952 (-)	NCBI	Dog10K_Boxer_Tasha	Dog10K_Boxer_Tasha
ROS_Cfam_1.0	26	8,559,347 - 8,567,243 (-)	NCBI	ROS_Cfam_1.0	ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	26	8,559,347 - 8,567,243 (-)	Ensembl				ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	26	8,518,556 - 8,526,208 (-)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	26	8,577,344 - 8,584,999 (-)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	26	8,532,820 - 8,540,473 (-)	NCBI	UU_Cfam_GSD_1.0	UU_Cfam_GSD_1.0

Vps29
(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_024405118	156,020,374 - 156,029,329 (+)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936558	3,449,613 - 3,459,358 (-)	Ensembl		SpeTri2.0 Ensembl
SpeTri2.0	NW_004936558	3,449,993 - 3,459,008 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

VPS29
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	14	31,859,067 - 31,869,579 (-)	Ensembl			susScr11	Sscrofa11.1
Sscrofa11.1	14	31,860,661 - 31,869,614 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	14	33,782,284 - 33,791,248 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

VPS29
(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	11	105,729,112 - 105,738,592 (-)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
Vero_WHO_p1.0	NW_023666037	139,380,955 - 139,391,819 (+)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Vps29
(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_004624747	21,399,303 - 21,408,141 (+)	Ensembl		HetGla_female_1.0 Ensembl	hetGla2	HetGla_female_1.0 Ensembl
HetGla 1.0	NW_004624747	21,399,196 - 21,408,140 (+)	NCBI	HetGla 1.0	HetGla 1.0	hetGla2

Vps29
(Rattus rattus - black rat)

Black Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Black Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Rrattus_CSIRO_v1	16	31,485,932 - 31,494,833 (-)	NCBI		Rrattus_CSIRO_v1

Variants

Variants in Vps29
64 total Variants

miRNA Target Status (No longer updated)

Predicted Target Of

	Summary Value
Count of predictions:	187
Count of miRNA genes:	133
Interacting mature miRNAs:	140
Transcripts:	ENSRNOT00000001717
Prediction methods:	Microtar, Miranda, Rnahybrid, Targetscan
Result types:	miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.

QTLs in Region (GRCr8)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
631560	Apr1	Acute phase response QTL 1	6.1		orosomucoid 1 amount (VT:0010541)	plasma orosomucoid 1 level (CMO:0001467)	12	24805022	52308831	Rat
70213	Niddm27	Non-insulin dependent diabetes mellitus QTL 27	3.72		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	12	11200494	52308831	Rat
8552964	Pigfal17	Plasma insulin-like growth factor 1 level QTL 17	3.5		blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	12	11200494	52308831	Rat
8693635	Alc28	Alcohol consumption QTL 28	2.7	0.439	drinking behavior trait (VT:0001422)	calculated ethanol drink intake rate (CMO:0001615)	12	28717718	50386405	Rat
7411641	Foco19	Food consumption QTL 19	27.7	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	12	11200494	52308831	Rat
7411643	Foco20	Food consumption QTL 20		0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	12	25989355	52308831	Rat
5684888	Pia42	Pristane induced arthritis QTL 42			joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	12	3489416	48489416	Rat
1300162	Bp188	Blood pressure QTL 188	3.19		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	12	37764145	51558799	Rat
1641928	Alcrsp5	Alcohol response QTL 5			response to alcohol trait (VT:0010489)	duration of loss of righting reflex (CMO:0002289)	12	18473041	52308831	Rat
1549829	Scl48	Serum cholesterol level QTL 48	5		blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	12	15264248	52308831	Rat
8552912	Pigfal6	Plasma insulin-like growth factor 1 level QTL 6	5		blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	12	11200497	52308831	Rat
10059594	Kidm46	Kidney mass QTL 46	3.79	0.025	kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	12	11743528	52308831	Rat
8552918	Pigfal7	Plasma insulin-like growth factor 1 level QTL 7			blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	12	11200494	52308831	Rat
70169	Eae13	Experimental allergic encephalomyelitis QTL 13		0.032	nervous system integrity trait (VT:0010566)	experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)	12	29775522	42298555	Rat
1600386	Calcic2	Intracellular calcium level QTL 2		0.001	platelet physiology trait (VT:0005464)	platelet intracellular calcium level (CMO:0000922)	12	33700432	46784661	Rat
1300175	Cm5	Cardiac mass QTL 5	3.78		heart mass (VT:0007028)	heart left ventricle weight to body weight ratio (CMO:0000530)	12	33700432	51558799	Rat
1556747	Calcic1	Intracellular calcium level QTL 1		3.6	platelet calcium amount (VT:0010500)	platelet intracellular calcium level (CMO:0000922)	12	33700432	46784661	Rat
631829	Alc6	Alcohol consumption QTL 6	4.7		consumption behavior trait (VT:0002069)	ethanol drink intake rate (CMO:0001407)	12	34243475	43352593	Rat
61404	Bw120	Body weight QTL 120	5.1		body mass (VT:0001259)	body mass index (BMI) (CMO:0000105)	12	17464979	46784661	Rat
1331786	Kidm11	Kidney mass QTL 11	3.571		kidney mass (VT:0002707)	right kidney wet weight (CMO:0000082)	12	16187438	52308831	Rat
8693658	Alc33	Alcohol consumption QTL 33	2.1	0.68	drinking behavior trait (VT:0001422)	calculated ethanol drink intake rate (CMO:0001615)	12	28717718	49212240	Rat
2293699	Bss49	Bone structure and strength QTL 49	5.61	0.0001	lumbar vertebra size trait (VT:0010518)	lumbar vertebra trabecular cross-sectional area (CMO:0001692)	12	16135029	52308831	Rat
1331761	Bp218	Blood pressure QTL 218	2.973		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	12	16187438	51213550	Rat
1331763	Wbc2	White blood cell count QTL 2	3.162		leukocyte quantity (VT:0000217)	total white blood cell count (CMO:0000365)	12	11200494	52308831	Rat
7411547	Bw129	Body weight QTL 129		0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	6	11200494	52308831	Rat
7387292	Kidm42	Kidney mass QTL 42	3.03	0.0004	kidney mass (VT:0002707)	left kidney wet weight (CMO:0000083)	12	1	41361854	Rat
2303569	Gluco44	Glucose level QTL 44	2		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	12	18473041	52308831	Rat
1298081	Cia25	Collagen induced arthritis QTL 25	4.7		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	12	2747694	47747694	Rat
2303575	Insul14	Insulin level QTL 14	4		blood insulin amount (VT:0001560)	blood insulin level (CMO:0000349)	12	3087180	48087180	Rat
7411588	Foco6	Food consumption QTL 6		0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	12	11200494	52308831	Rat
7243862	Mcs30	Mammary carcinoma susceptibility QTL 30	8.62		mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	12	5633306	50633306	Rat
2300186	Bmd59	Bone mineral density QTL 59	7.1	0.0001	lumbar vertebra mineral mass (VT:0010511)	volumetric bone mineral density (CMO:0001553)	12	16135029	52308831	Rat
7411597	Foco10	Food consumption QTL 10		0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	12	11200494	52308831	Rat

Markers in Region

AW049835

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	12	34,209,412 - 34,209,522 (+)	MAPPER	mRatBN7.2
Rnor_6.0	12	39,690,571 - 39,690,680	NCBI	Rnor6.0
Rnor_5.0	12	41,571,200 - 41,571,309	UniSTS	Rnor5.0
RGSC_v3.4	12	35,403,853 - 35,403,962	UniSTS	RGSC3.4
Celera	12	35,880,274 - 35,880,383	UniSTS
Cytogenetic Map	12	q16	UniSTS

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.

Download All Expressed Objects for this Gene

alimentary part of gastrointestinal system	appendage	circulatory system	ectoderm	endocrine system	endoderm	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	mesenchyme	mesoderm	musculoskeletal system	nervous system	renal system	reproductive system	respiratory system	sensory system	visual system
16	12	67	165	91	90	59	92	59	6	356	192	11	144	81	92	31	17	17

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001105932	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AB578912	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AB578913	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AB578914	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AB578915	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AB578916	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AB578917	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AB578918	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AB578919	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AB578920	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AB578921	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AB578922	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AB578923	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AC104314	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC167055	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473973	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ213481	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ224287	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000012	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSRNOT00000001717 ⟹ ENSRNOP00000001717

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8 Ensembl	12	39,870,252 - 39,878,732 (-)	Ensembl
mRatBN7.2 Ensembl	12	34,209,475 - 34,217,964 (-)	Ensembl
Rnor_6.0 Ensembl	12	39,690,069 - 39,699,113 (-)	Ensembl

Ensembl Acc Id:

ENSRNOT00000078683 ⟹ ENSRNOP00000068822

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8 Ensembl	12	39,869,688 - 39,878,848 (-)	Ensembl
mRatBN7.2 Ensembl	12	34,209,077 - 34,216,202 (-)	Ensembl
Rnor_6.0 Ensembl	12	39,690,397 - 39,697,465 (-)	Ensembl

Ensembl Acc Id:

ENSRNOT00000088905 ⟹ ENSRNOP00000074640

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8 Ensembl	12	39,869,688 - 39,873,582 (-)	Ensembl
mRatBN7.2 Ensembl	12	34,209,077 - 34,217,935 (-)	Ensembl
Rnor_6.0 Ensembl	12	39,690,237 - 39,699,088 (-)	Ensembl

Ensembl Acc Id:

ENSRNOT00000099825 ⟹ ENSRNOP00000097672

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8 Ensembl	12	39,869,688 - 39,878,848 (-)	Ensembl
mRatBN7.2 Ensembl	12	34,207,263 - 34,217,947 (-)	Ensembl

Ensembl Acc Id:

ENSRNOT00000116545 ⟹ ENSRNOP00000081706

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	12	34,207,263 - 34,212,806 (-)	Ensembl

RefSeq Acc Id:

NM_001105932 ⟹ NP_001099402

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	12	39,869,688 - 39,878,732 (-)	NCBI
mRatBN7.2	12	34,208,911 - 34,217,956 (-)	NCBI
Rnor_6.0	12	39,690,069 - 39,699,113 (-)	NCBI
Rnor_5.0	12	41,570,698 - 41,579,742 (-)	NCBI
RGSC_v3.4	12	35,403,351 - 35,412,395 (-)	RGD
Celera	12	35,879,772 - 35,888,815 (-)	RGD

Sequence:

show sequence

CGGAAGAAGTGGGCGGGTCAGCGAGGTGCCTGAGGAAGAGGGCAGCGGCGTTCGTGGTGACTGA
ACGGAATCCCGGTGACAGGATGTTGGTGTTGGTATTAGGAGATCTGCACATTCCACACCGGTGC
AACAGCCTGCCGGCCAAATTTAAAAAACTCCTGGTGCCAGGAAAAATCCAGCACATTCTCTGCA
CTGGAAACCTTTGCACCAAGGAGAGCTATGACTATCTCAAGACTCTGGCTGGTGATGTCCACAT
CGTAAGAGGAGACTTCGATGAGAGTCTGAATTACCCAGAACAGAAGGTTGTGACTGTGGGGCAG
TTCAAGATCGGTCTGATCCATGGCCACCAAGTTATTCCGTGGGGAGACATGGCTAGCTTAGCCC
TGCTGCAGAGGCAGTTTGATGTGGACATTCTTATCTCAGGACACACACACAAATTCGAAGCATT
TGAGCATGAAAATAAATTCTATATTAACCCAGGTTCTGCCACTGGAGCCTATAATGCCTTGGAA
ACAAATATTATTCCGTCATTTGTGCTGATGGACATCCAGGCTTCTACCGTGGTCACTTACGTCT
ATCAGCTAATTGGAGATGACGTAAAAGTAGAACGAATTGAGTATAAAAAGTCATAAAGCCAGGC
CGGTCTCCACCACTTATTTTTTTCTCATTTCCTTGTTCAAATCAGATAATTAAACACTTAAGAG
GCACACAGTTGTATCACTTTTATAATATTTTGCACTAAAAAGTCTTCTCTGTTGATACAGTTGC
TCTAAAGCTTCTTGTAAACTCTTAAGAATATATTTAGTTTGCAGTATATGGCTTCTATAAGAAG
CAGCCCACCCCACAGTCCAGGACCATGTTAGGAAGTTTGTCCTTGTAAATAGCTTCCCAGTTGG
TTTTGGACTGCATAGAAAACTAGTGCATGAGGAGAAAGGATCCAGGCTTTGTGTGTGTTTTCTC
TTCTCTGGTAATAAATGTGTACCTTCCATTTAGACGTTCTTGAAAGCCTGTGTTTAATTTAAAA
AGCAAACGTGAAATCTCAGCACTCAAGAGGCAGAGGCGGGTGGATCTCTTCAGCATTTTTTGCC
AGTTTGGTCTACATTGTTAATGCTAGGCCAGCCAAAACTACACAGGAGACCCTGTCTCAAGAAA
ACCAAAA

hide sequence

Protein Sequences


Protein RefSeqs	NP_001099402	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAI67055	(Get FASTA)	NCBI Sequence Viewer
	B2RZ78	(Get FASTA)	NCBI Sequence Viewer
	EDM13693	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSRNOP00000074640.1
	ENSRNOP00000097672

RefSeq Acc Id:	NP_001099402 ⟸ NM_001105932
- UniProtKB:	A6J1A4 (UniProtKB/Swiss-Prot), B2RZ78 (UniProtKB/Swiss-Prot), A0A8I6AUQ8 (UniProtKB/TrEMBL)
- Sequence:	show sequence MLVLVLGDLHIPHRCNSLPAKFKKLLVPGKIQHILCTGNLCTKESYDYLKTLAGDVHIVRGDFD ESLNYPEQKVVTVGQFKIGLIHGHQVIPWGDMASLALLQRQFDVDILISGHTHKFEAFEHENKF YINPGSATGAYNALETNIIPSFVLMDIQASTVVTYVYQLIGDDVKVERIEYKKS hide sequence

Ensembl Acc Id:

ENSRNOP00000074640 ⟸ ENSRNOT00000088905

Ensembl Acc Id:

ENSRNOP00000001717 ⟸ ENSRNOT00000001717

Ensembl Acc Id:

ENSRNOP00000068822 ⟸ ENSRNOT00000078683

Ensembl Acc Id:

ENSRNOP00000097672 ⟸ ENSRNOT00000099825

Ensembl Acc Id:

ENSRNOP00000081706 ⟸ ENSRNOT00000116545

Protein Domains

Calcineurin-like phosphoesterase

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-B2RZ78-F1-model_v2	AlphaFold	B2RZ78	1-182	view protein structure

Transcriptome

eQTL		View at Phenogen
WGCNA		View at Phenogen
Tissue/Strain Expression		View at Phenogen

Promoters

RGD ID:

13698658

Promoter ID:

EPDNEW_R9172

Type:

initiation region

Name:

Vps29_1

Description:

VPS29 retromer complex component

SO ACC ID:

SO:0000170

Source:

EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)

Experiment Methods:

Single-end sequencing.

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	12	39,699,099 - 39,699,159	EPDNEW

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1308332	AgrOrtholog
BioCyc Gene	G2FUF-19244	BioCyc
Ensembl Genes	ENSRNOG00000001274	Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript	ENSRNOT00000088905.2	UniProtKB/Swiss-Prot
	ENSRNOT00000099825	ENTREZGENE
Gene3D-CATH	3.60.21.10	UniProtKB/Swiss-Prot
IMAGE_CLONE	IMAGE:7302374	IMAGE-MGC_LOAD
InterPro	Calcineurin-like_PHP_lpxH	UniProtKB/Swiss-Prot
	Metallo-depent_PP-like	UniProtKB/Swiss-Prot
	Phosphodiesterase_MJ0936/Vps29	UniProtKB/Swiss-Prot
	Vps29	UniProtKB/Swiss-Prot
KEGG Report	rno:288666	UniProtKB/Swiss-Prot
MGC_CLONE	MGC:189354	IMAGE-MGC_LOAD
NCBI Gene	288666	ENTREZGENE
PANTHER	PTHR11124	UniProtKB/Swiss-Prot
Pfam	Metallophos_2	UniProtKB/Swiss-Prot
PhenoGen	Vps29	PhenoGen
RatGTEx	ENSRNOG00000001274	RatGTEx
Superfamily-SCOP	SSF56300	UniProtKB/Swiss-Prot
UniProt	A0A0G2JTS3_RAT	UniProtKB/TrEMBL
	A0A8I6AUQ8	ENTREZGENE, UniProtKB/TrEMBL
	A0A8L2Q0U7_RAT	UniProtKB/TrEMBL
	A6J1A4	ENTREZGENE
	B2RZ78	ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary	A6J1A4	UniProtKB/Swiss-Prot

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2015-07-01	Vps29	VPS29 retromer complex component	Vps29	vacuolar protein sorting 29 homolog (S. cerevisiae)	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2008-09-25	Vps29	vacuolar protein sorting 29 homolog (S. cerevisiae)	Vps29	vacuolar protein sorting 29 (S. pombe)	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2008-04-30	Vps29	vacuolar protein sorting 29 (S. pombe)	Vps29_predicted	vacuolar protein sorting 29 (S. pombe) (predicted)	'predicted' is removed	2292626	APPROVED
2005-01-12	Vps29_predicted	vacuolar protein sorting 29 (S. pombe) (predicted)			Symbol and Name status set to approved	70820	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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