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Gene: Tmem39a (transmembrane protein 39a) Rattus norvegicus

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Symbol:

Tmem39a

Name:

transmembrane protein 39a

RGD ID:

1306421

Description:

Predicted to be involved in negative regulation of autophagosome assembly; negative regulation of autophagosome maturation; and positive regulation of viral genome replication. Predicted to be located in endoplasmic reticulum and membrane. Predicted to be active in endoplasmic reticulum membrane. Orthologous to human TMEM39A (transmembrane protein 39A); INTERACTS WITH 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine; bisphenol A.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Previously known as:

LOC288092; RGD1306421; similar to RIKEN cDNA 2610033C09

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):	TMEM39A (transmembrane protein 39A)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoMCL, Panther, PhylomeDB, Treefam
Mus musculus (house mouse):	Tmem39a (transmembrane protein 39a)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Tmem39a (transmembrane protein 39A)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	TMEM39A (transmembrane protein 39A)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	TMEM39A (transmembrane protein 39A)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Tmem39a (transmembrane protein 39A)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	TMEM39A (transmembrane protein 39A)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	TMEM39A (transmembrane protein 39A)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Tmem39a (transmembrane protein 39A)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Rattus rattus (black rat):	Tmem39a (transmembrane protein 39A)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Other homologs ²
Homo sapiens (human):	P2RX4 (purinergic receptor P2X 4)	HGNC	OMA
Alliance orthologs ³
Homo sapiens (human):	TMEM39A (transmembrane protein 39A)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Tmem39a (transmembrane protein 39a)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	tmem39a (transmembrane protein 39A)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Drosophila melanogaster (fruit fly):	CG13016	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Caenorhabditis elegans (roundworm):	D1007.5	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Xenopus tropicalis (tropical clawed frog):	tmem39a	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	11	75,666,154 - 75,695,486 (-)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	11	75,666,154 - 75,695,486 (-)	Ensembl				GRCr8
mRatBN7.2	11	62,160,631 - 62,189,964 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	11	62,160,631 - 62,189,964 (-)	Ensembl				mRatBN7.2
UTH_Rnor_SHR_Utx	11	70,973,153 - 71,002,485 (-)	NCBI	UTH_Rnor_SHR_Utx	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	11	63,635,410 - 63,664,742 (-)	NCBI	UTH_Rnor_SHRSP_BbbUtx_1.0	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	11	62,686,586 - 62,715,917 (-)	NCBI	UTH_Rnor_WKY_Bbb_1.0	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	11	64,723,181 - 64,752,514 (-)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	11	64,723,186 - 64,752,544 (-)	Ensembl			rn6	Rnor6.0
Rnor_5.0	11	67,357,137 - 67,386,470 (+)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	11	63,938,077 - 63,967,213 (-)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	11	61,663,433 - 61,692,755 (-)	NCBI		Celera
RGSC_v3.1	11	63,995,665 - 64,024,802 (-)	NCBI
Cytogenetic Map	11	q21	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)

17alpha-ethynylestradiol (EXP,ISO)

17beta-estradiol (ISO)

17beta-hydroxy-5alpha-androstan-3-one (ISO)

2,2',4,4'-Tetrabromodiphenyl ether (ISO)

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

4,4'-sulfonyldiphenol (ISO)

aflatoxin B1 (ISO)

Aroclor 1254 (ISO)

atrazine (ISO)

benzene (ISO)

beta-lapachone (ISO)

bis(2-ethylhexyl) phthalate (ISO)

bisphenol A (EXP,ISO)

carbon nanotube (ISO)

choline (ISO)

ciguatoxin CTX1B (ISO)

copper atom (ISO)

copper(0) (ISO)

copper(II) sulfate (ISO)

cyclosporin A (ISO)

DDE (ISO)

DDT (EXP)

dibenz[a,h]anthracene (ISO)

dibutyl phthalate (EXP,ISO)

Didecyldimethylammonium (ISO)

diuron (ISO)

doxorubicin (ISO)

endosulfan (EXP)

epoxiconazole (ISO)

fluoranthene (ISO)

flutamide (EXP)

folic acid (ISO)

genistein (ISO)

gentamycin (EXP)

glafenine (EXP)

L-methionine (ISO)

methylmercury chloride (ISO)

paracetamol (EXP)

perfluorooctane-1-sulfonic acid (ISO)

pinostrobin (ISO)

pirinixic acid (ISO)

potassium chromate (ISO)

propiconazole (ISO)

silicon dioxide (ISO)

sodium arsenate (ISO)

sodium arsenite (ISO)

Soman (EXP)

sulindac (ISO)

testosterone (ISO)

tetrachloromethane (ISO)

thioacetamide (EXP)

thiram (ISO)

triptonide (ISO)

tunicamycin (ISO)

valproic acid (ISO)

vinclozolin (EXP)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

autophagy (IEA)

negative regulation of autophagosome assembly (IBA,IEA,ISO,ISS)

negative regulation of autophagosome maturation (IBA,IEA,ISO,ISS)

positive regulation of viral genome replication (IEA,ISO)

Cellular Component

endoplasmic reticulum membrane (IBA,IEA,ISO,ISS)

Molecular Function

protein binding (ISO)

References

References - curated

#	Reference Title	Reference Citation
1.	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.
2.	GOA pipeline	RGD automated data pipeline
3.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions
4.	Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences.	Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.

Additional References at PubMed

PMID:31806350	PMID:31849860

Genomics

Comparative Map Data

Tmem39a
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	11	75,666,154 - 75,695,486 (-)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	11	75,666,154 - 75,695,486 (-)	Ensembl				GRCr8
mRatBN7.2	11	62,160,631 - 62,189,964 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	11	62,160,631 - 62,189,964 (-)	Ensembl				mRatBN7.2
UTH_Rnor_SHR_Utx	11	70,973,153 - 71,002,485 (-)	NCBI	UTH_Rnor_SHR_Utx	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	11	63,635,410 - 63,664,742 (-)	NCBI	UTH_Rnor_SHRSP_BbbUtx_1.0	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	11	62,686,586 - 62,715,917 (-)	NCBI	UTH_Rnor_WKY_Bbb_1.0	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	11	64,723,181 - 64,752,514 (-)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	11	64,723,186 - 64,752,544 (-)	Ensembl			rn6	Rnor6.0
Rnor_5.0	11	67,357,137 - 67,386,470 (+)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	11	63,938,077 - 63,967,213 (-)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	11	61,663,433 - 61,692,755 (-)	NCBI		Celera
RGSC_v3.1	11	63,995,665 - 64,024,802 (-)	NCBI
Cytogenetic Map	11	q21	NCBI

TMEM39A
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	3	119,428,949 - 119,463,615 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	3	119,428,949 - 119,468,854 (-)	Ensembl			hg38	GRCh38
GRCh37	3	119,147,796 - 119,182,462 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	3	120,632,391 - 120,665,161 (-)	NCBI	Build 36	Build 36	hg18	NCBI36
Build 34	3	120,632,390 - 120,665,161	NCBI
Celera	3	117,558,168 - 117,591,144 (-)	NCBI		Celera
Cytogenetic Map	3	q13.33	NCBI
HuRef	3	116,523,203 - 116,558,223 (-)	NCBI		HuRef
CHM1_1	3	119,111,286 - 119,146,016 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	3	122,148,660 - 122,183,326 (-)	NCBI		T2T-CHM13v2.0

Tmem39a
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	16	38,379,060 - 38,412,524 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	16	38,379,060 - 38,412,524 (+)	Ensembl		GRCm39 Ensembl		GRCm39
GRCm38	16	38,558,698 - 38,592,162 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	16	38,558,698 - 38,592,162 (+)	Ensembl			mm10	GRCm38
MGSCv37	16	38,562,972 - 38,591,497 (+)	NCBI	MGSCv37	MGSCv37	mm9	NCBIm37
MGSCv36	16	38,482,191 - 38,510,716 (+)	NCBI		MGSCv36	mm8
Celera	16	38,974,323 - 39,003,458 (+)	NCBI		Celera
Cytogenetic Map	16	B4	NCBI
cM Map	16	26.87	NCBI

Tmem39a
(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_004955427	19,133,434 - 19,184,344 (-)	Ensembl
ChiLan1.0	NW_004955427	19,118,631 - 19,184,315 (-)	NCBI	ChiLan1.0	ChiLan1.0

TMEM39A
(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	2	117,405,393 - 117,442,261 (-)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	3	117,411,327 - 117,446,259 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	3	116,549,308 - 116,586,260 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	3	123,461,860 - 123,498,656 (-)	NCBI	PanPan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	3	123,461,860 - 123,498,656 (-)	Ensembl			panPan2	panpan1.1

TMEM39A
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	33	23,083,979 - 23,121,269 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	33	23,084,919 - 23,116,210 (-)	Ensembl			canFam3	CanFam3.1
Dog10K_Boxer_Tasha	33	23,115,430 - 23,152,613 (-)	NCBI	Dog10K_Boxer_Tasha	Dog10K_Boxer_Tasha
ROS_Cfam_1.0	33	23,321,967 - 23,360,033 (-)	NCBI	ROS_Cfam_1.0	ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	33	23,322,822 - 23,355,991 (-)	Ensembl				ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	33	23,124,462 - 23,162,449 (-)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	33	23,161,760 - 23,198,956 (-)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	33	23,729,476 - 23,767,547 (-)	NCBI	UU_Cfam_GSD_1.0	UU_Cfam_GSD_1.0

Tmem39a
(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_024405602	131,114,046 - 131,145,441 (+)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936536	6,376,543 - 6,403,667 (-)	Ensembl		SpeTri2.0 Ensembl
SpeTri2.0	NW_004936536	6,376,539 - 6,406,314 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

TMEM39A
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	13	140,797,205 - 140,831,277 (+)	Ensembl			susScr11	Sscrofa11.1
Sscrofa11.1	13	140,797,098 - 140,830,732 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	13	150,096,887 - 150,130,520 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

TMEM39A
(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	22	61,368,680 - 61,404,115 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	22	61,368,711 - 61,406,395 (+)	Ensembl		ChlSab1.1 Ensembl	chlSab2	Vervet-AGM
Vero_WHO_p1.0	NW_023666041	104,922,416 - 104,959,159 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Tmem39a
(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_004624731	28,740,048 - 28,773,701 (+)	Ensembl		HetGla_female_1.0 Ensembl	hetGla2	HetGla_female_1.0 Ensembl
HetGla 1.0	NW_004624731	28,701,873 - 28,773,697 (+)	NCBI	HetGla 1.0	HetGla 1.0	hetGla2

Tmem39a
(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	4	23,505,452 - 23,534,744 (+)	NCBI		Rrattus_CSIRO_v1

Variants

Variants in Tmem39a
187 total Variants

miRNA Target Status (No longer updated)

Predicted Target Of

	Summary Value
Count of predictions:	121
Count of miRNA genes:	92
Interacting mature miRNAs:	105
Transcripts:	ENSRNOT00000048738
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
70208	Niddm22	Non-insulin dependent diabetes mellitus QTL 22	3.61		blood glucose amount (VT:0000188)	plasma glucose level (CMO:0000042)	11	73308487	96070872	Rat
724554	Iddm17	Insulin dependent diabetes mellitus QTL 17		0.001	blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	11	46443168	91443168	Rat
1598811	Bp291	Blood pressure QTL 291	1.9		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	11	33306008	78306008	Rat
4889859	Pur28	Proteinuria QTL 28	19.5	0.001	urine total protein amount (VT:0000032)	urine total protein excretion rate (CMO:0000756)	11	58928336	99753367	Rat
10755497	Bp388	Blood pressure QTL 388	2.76		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	11	32943067	89836615	Rat
10058952	Gmadr6	Adrenal mass QTL 6	2.29	0.0072	adrenal gland mass (VT:0010420)	both adrenal glands wet weight to body weight ratio (CMO:0002411)	11	36428416	81428416	Rat
10058954	Gmadr7	Adrenal mass QTL 7	2.49	0.0049	adrenal gland mass (VT:0010420)	both adrenal glands wet weight to body weight ratio (CMO:0002411)	11	73850894	99753367	Rat
2298551	Neuinf10	Neuroinflammation QTL 10	3.7		nervous system integrity trait (VT:0010566)	spinal cord beta-2 microglobulin mRNA level (CMO:0002125)	11	58931822	92356038	Rat
1558659	Tescar1	Testicular tumor resistance QTL 1	3.9		testis integrity trait (VT:0010572)	percentage of study population developing testis tumors during a period of time (CMO:0001261)	11	34618760	79618760	Rat
2312566	Glom20	Glomerulus QTL 20	3.6	0.001	kidney glomerulus morphology trait (VT:0005325)	index of glomerular damage (CMO:0001135)	11	57754837	96071021	Rat
724563	Uae10	Urinary albumin excretion QTL 10	6		urine albumin amount (VT:0002871)	urine albumin level (CMO:0000130)	11	20193549	96351019	Rat
724561	Plsm4	Polydactyly-luxate syndrome (PLS) morphotypes QTL 4		0.0003	forelimb integrity trait (VT:0010562)	front foot phalanges count (CMO:0001947)	11	67962184	99753367	Rat
631506	Bp104	Blood pressure QTL 104	2.8		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	11	73308315	99753367	Rat
1581572	Uae35	Urinary albumin excretion QTL 35		0.0001	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	11	58272363	96350770	Rat
8694424	Bw162	Body weight QTL 162	3.8	0.001	body lean mass (VT:0010483)	lean tissue morphological measurement (CMO:0002184)	11	36749459	81749459	Rat
1300110	Stl7	Serum triglyceride level QTL 7	4.64		blood triglyceride amount (VT:0002644)	plasma triglyceride level (CMO:0000548)	11	51071021	96071021	Rat
1300147	Bp187	Blood pressure QTL 187	3.67		arterial blood pressure trait (VT:2000000)	blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)	11	22524746	82951192	Rat
1598841	Memor7	Memory QTL 7			exploratory behavior trait (VT:0010471)	total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)	11	33306008	78306008	Rat
1581565	Pur10	Proteinuria QTL 10		0.0001	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	11	58272363	96350770	Rat
8694376	Bw156	Body weight QTL 156	2.25	0.001	body lean mass (VT:0010483)	lean tissue morphological measurement (CMO:0002184)	11	36749459	81749459	Rat
1300130	Rf20	Renal function QTL 20	4.44		kidney glomerulus integrity trait (VT:0010546)	kidney glomerulus diameter (CMO:0001166)	11	31915469	76915469	Rat
1300135	Rf19	Renal function QTL 19	3.38		blood creatinine amount (VT:0005328)	creatinine clearance (CMO:0000765)	11	54415391	96071021	Rat
9589032	Epfw10	Epididymal fat weight QTL 10	9.29	0.001	epididymal fat pad mass (VT:0010421)	epididymal fat pad weight to body weight ratio (CMO:0000658)	11	36749459	81749459	Rat
4889521	Gluco62	Glucose level QTL 62	2.82	0.001	blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	11	68599321	96497754	Rat
9590313	Scort20	Serum corticosterone level QTL 20	6.51	0.001	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	11	36749459	81749459	Rat
7411658	Foco27	Food consumption QTL 27	16.2	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	11	69855943	99753367	Rat

Markers in Region

RH142829

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	11	62,186,649 - 62,186,937 (+)	MAPPER	mRatBN7.2
Rnor_6.0	11	64,749,200 - 64,749,487	NCBI	Rnor6.0
Rnor_5.0	11	67,360,164 - 67,360,451	UniSTS	Rnor5.0
RGSC_v3.4	11	63,963,899 - 63,964,186	UniSTS	RGSC3.4
Celera	11	61,689,441 - 61,689,728	UniSTS
RH 3.4 Map	11	508.3	UniSTS
Cytogenetic Map	11	q21	UniSTS

BM385341

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	11	62,168,239 - 62,168,411 (+)	MAPPER	mRatBN7.2
Rnor_6.0	11	64,730,788 - 64,730,959	NCBI	Rnor6.0
Rnor_5.0	11	67,378,692 - 67,378,863	UniSTS	Rnor5.0
RGSC_v3.4	11	63,945,685 - 63,945,856	UniSTS	RGSC3.4
Celera	11	61,671,041 - 61,671,212	UniSTS
RH 3.4 Map	11	502.0	UniSTS
Cytogenetic Map	11	q21	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	164	91	90	59	92	59	6	356	192	11	143	81	92	31	17	17

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001013865	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	BC085845	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473967	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000011	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSRNOT00000048738 ⟹ ENSRNOP00000049087

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8 Ensembl	11	75,666,154 - 75,695,486 (-)	Ensembl
mRatBN7.2 Ensembl	11	62,160,631 - 62,189,964 (-)	Ensembl
Rnor_6.0 Ensembl	11	64,723,186 - 64,752,544 (-)	Ensembl

Ensembl Acc Id:

ENSRNOT00000167642 ⟹ ENSRNOP00000105775

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8 Ensembl	11	75,666,154 - 75,695,486 (-)	Ensembl

RefSeq Acc Id:

NM_001013865 ⟹ NP_001013887

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	11	75,666,154 - 75,695,486 (-)	NCBI
mRatBN7.2	11	62,160,631 - 62,189,964 (-)	NCBI
Rnor_6.0	11	64,723,181 - 64,752,514 (-)	NCBI
Rnor_5.0	11	67,357,137 - 67,386,470 (+)	NCBI
RGSC_v3.4	11	63,938,077 - 63,967,213 (-)	RGD
Celera	11	61,663,433 - 61,692,755 (-)	RGD

Sequence:

show sequence

CTGGGCGATGGAAGCTGAGGATGATGAGGCTTGGTGATGGGGTCAGGCTCTGCTTCTGACTTCA
GGTCTGGCTCTGGCACGGACTCCCGGTCGGGGTCTGGTAACGTAGAGACCCGACACGTTTCTTC
GACTGTCCTGTGGGATCCTGCCTGCGTCCGGGCAGCTGTTTTGGAGCGCTTCAAAGAAGGGAGT
GAGTTCGGGTGCCCGGTGTCGGGTCTGTGAAGCCGCCTCCTCCTCCCAGGGATCTCTCTCCGTG
GCCAGCCTGTTCCATGCAGTTGAAATAAGTTGACCTGAAATAAGTTAGCCTGGGTTGCAACTTC
GGGTGGCACTGGAAACTACCTGGTTCCTGGACATGCCCAGTAGAAGGAGGGGTCCTAGTCGGCA
GCAACTCAGCCGGTCAGCTTTACCTTCTATTCAGACTTTGGTTGGTGGCGGCTGTGGCAATGGA
ACAGGCTTGAGGAACAGGAATGGTAGTGCTATTGGCCTTCCAGTCCCACCCACCACAGCCTTAA
TTACCCCAGGTCCTGTTCGTCATTGCCAAATCCCCGACTTACCAGTAGATGGGAGCCTGTTCTT
TGAATTTCTTTTCTTCATCTACCTGCTGATTGTTCTGTTCATTCAGTATATCAACATCTATAAG
ACCGTGTGGTGGTATCCATACAATCATCCTGCATCTTGTACTTCACTGAATTTTCATCTCATTG
ATTATTACCTGGCAGCATTCATCACAGTGATGCTTGCGAGGAGGCTCGTATGGGCCCTCATTTC
CGAGGCTACTAAAGCAGGTGCAGCATCTATGGTTCACTACACAGCTCTGATACTGGCCCGCTTG
GTGCTCCTTACTCTGTGTGGATGGGTGCTTTGTTGGACCTTGGTCAATCTCTTCCGAAGCCATT
CAGTCCTCAATCTCCTCTTCCTTGGCTATCCGTTTGGTGTTTATGTACCTCTCTACTGTTTCCA
TCAAGATAGCAGAGCCCATCTTCTTCTCACAGACTATGTGGTTCAGCACCAGGCAGTAGAGGAC
GCAGCCTCAAATGTGGGCAGTTTGACCAGATCCAAAGATTTCCTGTCCTTACTGCTGGAGTCTC
TAAAAGAGCAGTTTAATAACAGCACGCCCATCCCCACCCACAGCTGCCCCCTGTCTCCTGACCT
CATTCGCAATGAGGTGGAATGTCTGAAGGCAGATTTCAACCACAGAATCAAGGACGTTCTCTTC
AATTCCCTCTTCAGCGCCTACTACGTAGCATTTCTCCCGCTGTGTTTTGTGAAGAGTACCCAGT
ATTACGACATGCGCTGGTCATGTGAGCACCTCATTATGGTGTGGATCAATGCTTTTGTCATGCT
CACCACGCAGCTGCTACCATCCAAATACTGTGACTTGCTACACAAATCAGCGGCTCACCTGGGC
AAGTGGCAGAAGTTGGAACATGGGTTCTACAGCAATGCTCCCCAGCACATTTGGTCAGAGAACA
CAATATGGCCTCAAGGGGTGTTGGTGCGGCACAGCAGATGTTTATATAGAGCCATGGGACCTTA
CAACGTAGCAGTGCCTTCTGATGGATCCCATGCCCGCTTTTATTTCCTGTTCCATCGCCCGTTA
CGAGTGTTGAACCTGCTTATCCTCATCGAGGGCAGTGTCATCATCTACCAGCTGTACTCGCTGC
TGCGCTCGGAGAAGTGGAACCACACGCTCTCCATGGCACTCGTTCTTTTCTGCAACTACTATGT
TTTATTTAAGCTCCTGCGGGACAGAATAGTCCTAGGCAGGGCATACTCCTACCCCTCAACAGCT
ACGGACTCAAGGCAGACCAAGCTGCCTCTCAGCAGTGAGGGAGAACTCAGATAAAGATATTTTC
ATACGATCTATTTTTTCTTGCGATTTTTATAAATATTTAAGATATTTTATATTTTGTATACTAT
TGTTTTGAAAGTTGGGAAGGGTAAGGGATATTAAATGTATCCATAAACAAGACGATGTTATCTT
TCATGTGTTAGTATATTTGAATATTATACATGAGAGGCTGCCCCTTCAGTAAAAGATTGACTTG
TTAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

hide sequence

Protein Sequences


Protein RefSeqs	NP_001013887	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAH85845	(Get FASTA)	NCBI Sequence Viewer
	EDM11211	(Get FASTA)	NCBI Sequence Viewer
	EDM11212	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSRNOP00000049087
	ENSRNOP00000049087.3
GenBank Protein	Q5U2V9	(Get FASTA)	NCBI Sequence Viewer

RefSeq Acc Id:

NP_001013887 ⟸ NM_001013865

- UniProtKB:

Q5U2V9 (UniProtKB/Swiss-Prot), A6IR58 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MPSRRRGPSRQQLSRSALPSIQTLVGGGCGNGTGLRNRNGSAIGLPVPPTTALITPGPVRHCQI
PDLPVDGSLFFEFLFFIYLLIVLFIQYINIYKTVWWYPYNHPASCTSLNFHLIDYYLAAFITVM
LARRLVWALISEATKAGAASMVHYTALILARLVLLTLCGWVLCWTLVNLFRSHSVLNLLFLGYP
FGVYVPLYCFHQDSRAHLLLTDYVVQHQAVEDAASNVGSLTRSKDFLSLLLESLKEQFNNSTPI
PTHSCPLSPDLIRNEVECLKADFNHRIKDVLFNSLFSAYYVAFLPLCFVKSTQYYDMRWSCEHL
IMVWINAFVMLTTQLLPSKYCDLLHKSAAHLGKWQKLEHGFYSNAPQHIWSENTIWPQGVLVRH
SRCLYRAMGPYNVAVPSDGSHARFYFLFHRPLRVLNLLILIEGSVIIYQLYSLLRSEKWNHTLS
MALVLFCNYYVLFKLLRDRIVLGRAYSYPSTATDSRQTKLPLSSEGELR

hide sequence

Ensembl Acc Id:

ENSRNOP00000049087 ⟸ ENSRNOT00000048738

Ensembl Acc Id:

ENSRNOP00000105775 ⟸ ENSRNOT00000167642

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-Q5U2V9-F1-model_v2	AlphaFold	Q5U2V9	1-497	view protein structure

Transcriptome

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

Promoters

RGD ID:

13698164

Promoter ID:

EPDNEW_R8688

Type:

multiple initiation site

Name:

Tmem39a_1

Description:

transmembrane protein 39a

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	11	64,752,519 - 64,752,579	EPDNEW

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1306421	AgrOrtholog
BioCyc Gene	G2FUF-21282	BioCyc
Ensembl Genes	ENSRNOG00000003075	Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript	ENSRNOT00000048738	ENTREZGENE
	ENSRNOT00000048738.5	UniProtKB/Swiss-Prot
IMAGE_CLONE	IMAGE:7188963	IMAGE-MGC_LOAD
InterPro	Uncharacterised_TMEM39	UniProtKB/Swiss-Prot
KEGG Report	rno:288092	UniProtKB/Swiss-Prot
MGC_CLONE	MGC:94539	IMAGE-MGC_LOAD
NCBI Gene	288092	ENTREZGENE
PANTHER	PTHR12995	UniProtKB/Swiss-Prot
	TRANSMEMBRANE PROTEIN 39A	UniProtKB/Swiss-Prot
Pfam	Tmp39	UniProtKB/Swiss-Prot
PhenoGen	Tmem39a	PhenoGen
RatGTEx	ENSRNOG00000003075	RatGTEx
UniProt	A0ABK0LU40_RAT	UniProtKB/TrEMBL
	A6IR58	ENTREZGENE, UniProtKB/TrEMBL
	A6IR59_RAT	UniProtKB/TrEMBL
	Q5U2V9	ENTREZGENE, UniProtKB/Swiss-Prot

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2006-03-30	Tmem39a	transmembrane protein 39a	RGD1306421	similar to RIKEN cDNA 2610033C09	Symbol and Name updated	1299863	APPROVED
2005-12-06	RGD1306421	similar to RIKEN cDNA 2610033C09	RGD1306421_predicted	similar to RIKEN cDNA 2610033C09 (predicted)	Symbol and Name updated	1559027	APPROVED
2005-01-20	RGD1306421_predicted	similar to RIKEN cDNA 2610033C09 (predicted)	LOC288092_predicted		Symbol and Name status set to approved	1331353	APPROVED
2005-01-12	LOC288092_predicted	similar to RIKEN cDNA 2610033C09 (predicted)			Symbol and Name status set to provisional	70820	PROVISIONAL

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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