Tmem39a (transmembrane protein 39a)

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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 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
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:

mRatBN7.2 - mRatBN7.2 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
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 Ensembl
UTH_Rnor_SHR_Utx	11	70,973,153 - 71,002,485 (-)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	11	63,635,410 - 63,664,742 (-)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	11	62,686,586 - 62,715,917 (-)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	11	64,723,181 - 64,752,514 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	11	64,723,186 - 64,752,544 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	11	67,357,137 - 67,386,470 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	11	63,938,077 - 63,967,213 (-)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	11	63,995,665 - 64,024,802 (-)	NCBI
Celera	11	61,663,433 - 61,692,755 (-)	NCBI		Celera
Cytogenetic Map	11	q21	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

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

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

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

aflatoxin B1 (ISO)

Aroclor 1254 (ISO)

atrazine (ISO)

benzene (ISO)

beta-lapachone (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)

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 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,ISO,ISS)

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

positive regulation of viral genome replication (ISO)

Cellular Component

endoplasmic reticulum membrane (IBA,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
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 Ensembl
UTH_Rnor_SHR_Utx	11	70,973,153 - 71,002,485 (-)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	11	63,635,410 - 63,664,742 (-)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	11	62,686,586 - 62,715,917 (-)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	11	64,723,181 - 64,752,514 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	11	64,723,186 - 64,752,544 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	11	67,357,137 - 67,386,470 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	11	63,938,077 - 63,967,213 (-)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	11	63,995,665 - 64,024,802 (-)	NCBI
Celera	11	61,663,433 - 61,692,755 (-)	NCBI		Celera
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 - 119,468,830 (-)	Ensembl	GRCh38		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	NCBI36	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
GRCm38	16	38,558,698 - 38,592,162 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	16	38,558,698 - 38,592,162 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	16	38,562,972 - 38,591,497 (+)	NCBI	GRCm37	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
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	panpan1.1		panPan2

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	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	33	23,115,430 - 23,152,613 (-)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	33	23,321,967 - 23,360,033 (-)	NCBI		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

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	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	Sscrofa11.1		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	ChlSab1.1 Ensembl	chlSab2
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	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624731	28,701,873 - 28,773,697 (+)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Variants

Variants in Tmem39a
83 total Variants

miRNA Target Status

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 (mRatBN7.2)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
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	1	69446234	Rat
70208	Niddm22	Non-insulin dependent diabetes mellitus QTL 22	3.61		blood glucose amount (VT:0000188)	plasma glucose level (CMO:0000042)	11	59802794	82566553	Rat
724554	Iddm17	Insulin dependent diabetes mellitus QTL 17		0.001	blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	11	18976208	86241447	Rat
70180	BpQTLcluster10	Blood pressure QTL cluster 10	3.19		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	11	34918041	79918041	Rat
1581565	Pur10	Proteinuria QTL 10		0.0001	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	11	44803318	82846466	Rat
4889859	Pur28	Proteinuria QTL 28	19.5	0.001	urine total protein amount (VT:0000032)	urine total protein excretion rate (CMO:0000756)	11	45459323	75190161	Rat
8694376	Bw156	Body weight QTL 156	2.25	0.001	body lean mass (VT:0010483)	lean tissue morphological measurement (CMO:0002184)	11	23280456	68280456	Rat
10755497	Bp388	Blood pressure QTL 388	2.76		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	11	19456205	76331918	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	22959403	67959403	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	60346590	86241447	Rat
2298551	Neuinf10	Neuroinflammation QTL 10	3.7		nervous system integrity trait (VT:0010566)	spinal cord beta-2 microglobulin mRNA level (CMO:0002125)	11	31239134	78851519	Rat
1300135	Rf19	Renal function QTL 19	3.38		blood creatinine amount (VT:0005328)	creatinine clearance (CMO:0000765)	11	40946188	82566702	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	1041931	66113562	Rat
2312566	Glom20	Glomerulus QTL 20	3.6	0.001	kidney glomerulus morphology trait (VT:0005325)	index of glomerular damage (CMO:0001135)	11	44285759	82566702	Rat
724563	Uae10	Urinary albumin excretion QTL 10	6		urine albumin amount (VT:0002871)	urine albumin level (CMO:0000130)	11	27672410	82846715	Rat
724561	Plsm4	Polydactyly-luxate syndrome (PLS) morphotypes QTL 4		0.0003	forelimb integrity trait (VT:0010562)	front foot phalanges count (CMO:0001947)	11	54457534	86241447	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	23280456	68280456	Rat
631506	Bp104	Blood pressure QTL 104	2.8		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	11	59802794	82566545	Rat
4889521	Gluco62	Glucose level QTL 62	2.82	0.001	blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	11	55136729	82993457	Rat
9590313	Scort20	Serum corticosterone level QTL 20	6.51	0.001	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	11	23280456	68280456	Rat
7411658	Foco27	Food consumption QTL 27	16.2	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	11	56351424	86241447	Rat
1581572	Uae35	Urinary albumin excretion QTL 35		0.0001	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	11	44803318	82846466	Rat
8694424	Bw162	Body weight QTL 162	3.8	0.001	body lean mass (VT:0010483)	lean tissue morphological measurement (CMO:0002184)	11	23280456	68280456	Rat
1300110	Stl7	Serum triglyceride level QTL 7	4.64		blood triglyceride amount (VT:0002644)	plasma triglyceride level (CMO:0000548)	11	29528418	82566702	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	nervous system	renal system	reproductive system	respiratory system
9	11	49	113	91	90	59	25	59	6	218	97	93	45	60	31

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
mRatBN7.2 Ensembl	11	62,160,631 - 62,189,964 (-)	Ensembl
Rnor_6.0 Ensembl	11	64,723,186 - 64,752,544 (-)	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	ENSRNOP00000049087.3
	ENSRNOP00055021853
	ENSRNOP00060009802
	ENSRNOP00065025605
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

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, UniProtKB/Swiss-Prot
	ENSRNOG00055015922	UniProtKB/Swiss-Prot
	ENSRNOG00060007839	UniProtKB/Swiss-Prot
	ENSRNOG00065019086	UniProtKB/Swiss-Prot
Ensembl Transcript	ENSRNOT00000048738.5	UniProtKB/Swiss-Prot
	ENSRNOT00055027075	UniProtKB/Swiss-Prot
	ENSRNOT00060012926	UniProtKB/Swiss-Prot
	ENSRNOT00065032091	UniProtKB/Swiss-Prot
IMAGE_CLONE	IMAGE:7188963	IMAGE-MGC_LOAD
InterPro	Uncharacterised_TMEM39	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report	rno:288092	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGC_CLONE	MGC:94539	IMAGE-MGC_LOAD
NCBI Gene	288092	ENTREZGENE
PANTHER	PTHR12995	UniProtKB/Swiss-Prot
	TRANSMEMBRANE PROTEIN 39A	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	UNCHARACTERIZED	UniProtKB/TrEMBL
Pfam	Tmp39	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen	Tmem39a	PhenoGen
PROSITE	PROKAR_LIPOPROTEIN	UniProtKB/TrEMBL
RatGTEx	ENSRNOG00000003075	RatGTEx
	ENSRNOG00055015922	RatGTEx
	ENSRNOG00060007839	RatGTEx
	ENSRNOG00065019086	RatGTEx
UniProt	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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