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Gene: Rtraf (RNA transcription, translation and transport factor) Rattus norvegicus

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Symbol:

Rtraf

Name:

RNA transcription, translation and transport factor

RGD ID:

1304704

Description:

Predicted to enable RNA binding activity; RNA polymerase II complex binding activity; and identical protein binding activity. Predicted to be involved in negative regulation of protein kinase activity; positive regulation of transcription by RNA polymerase II; and tRNA splicing, via endonucleolytic cleavage and ligation. Predicted to be located in microtubule cytoskeleton; nucleoplasm; and perinuclear region of cytoplasm. Predicted to be part of tRNA-splicing ligase complex. Orthologous to human RTRAF (RNA transcription, translation and transport factor); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; bisphenol A; ethanol.

Type:

protein-coding

RefSeq Status:

VALIDATED

Previously known as:

hypothetical protein LOC302247; LOC302247; LRRGT00192; RGD1304704; similar to Hypothetical protein CGI-99; uncharacterized protein LOC302247; UPF0568 protein C14orf166 homolog

RGD Orthologs

Alliance Orthologs

More Info

more info ...

Related Pseudogenes:

Rtraf-ps2

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	15	4,482,699 - 4,507,115 (+)	NCBI		GRCr8
mRatBN7.2	15	4,447,243 - 4,457,973 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	15	4,442,573 - 4,457,972 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	15	4,457,639 - 4,468,370 (+)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	15	5,844,087 - 5,854,816 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	15	4,456,473 - 4,467,202 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	15	4,882,925 - 4,893,890 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	15	4,882,947 - 4,893,919 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	15	8,973,714 - 8,984,679 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	15	4,790,458 - 4,800,905 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	15	4,780,320 - 4,801,091 (+)	NCBI
Celera	15	150,595 - 161,034 (-)	NCBI		Celera
Cytogenetic Map	15	p16	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Only show annotations with direct experimental evidence (0 objects hidden)

Object Symbol	Species	Term	Qualifier	Evidence	With	Reference	Notes	Source	Original Reference(s)
Rtraf	Rat	(+)-catechin	multiple interactions	ISO	RTRAF (Homo sapiens)	6480464	[Catechin co-treated with Grape Seed Proanthocyanidins] results in decreased expression of RTRAF mRNA	CTD	PMID:24763279
Rtraf	Rat	1,2-dimethylhydrazine	multiple interactions	ISO	Rtraf (Mus musculus)	6480464	[1 and 2-Dimethylhydrazine co-treated with Folic Acid] results in decreased expression of RTRAF mRNA	CTD	PMID:22206623
Rtraf	Rat	2,2',4,4'-Tetrabromodiphenyl ether	decreases expression	ISO	RTRAF (Homo sapiens)	6480464	2 more ...	CTD	PMID:31675489
Rtraf	Rat	2,3,7,8-tetrachlorodibenzodioxine	increases expression	EXP		6480464	Tetrachlorodibenzodioxin results in increased expression of RTRAF mRNA	CTD	PMID:33387578
Rtraf	Rat	2,4,6-tribromophenol	decreases expression	ISO	RTRAF (Homo sapiens)	6480464	2 more ...	CTD	PMID:31675489
Rtraf	Rat	3,3',5,5'-tetrabromobisphenol A	decreases expression	ISO	RTRAF (Homo sapiens)	6480464	tetrabromobisphenol A results in decreased expression of RTRAF protein	CTD	PMID:31675489
Rtraf	Rat	4,4'-sulfonyldiphenol	increases expression	ISO	Rtraf (Mus musculus)	6480464	bisphenol S results in increased expression of RTRAF mRNA	CTD	PMID:39298647
Rtraf	Rat	4-nonylphenol	multiple interactions	ISO	Rtraf (Mus musculus)	6480464	[Diethylhexyl Phthalate co-treated with Dibutyl Phthalate co-treated with butylbenzyl phthalate co-treated with 4-nonylphenol co-treated with 4-tert-octylphenol] results in increased expression of RTRAF mRNA	CTD	PMID:30698749
Rtraf	Rat	4-tert-Octylphenol	multiple interactions	ISO	Rtraf (Mus musculus)	6480464	[Diethylhexyl Phthalate co-treated with Dibutyl Phthalate co-treated with butylbenzyl phthalate co-treated with 4-nonylphenol co-treated with 4-tert-octylphenol] results in increased expression of RTRAF mRNA	CTD	PMID:30698749
Rtraf	Rat	aflatoxin B1	decreases methylation	ISO	RTRAF (Homo sapiens)	6480464	Aflatoxin B1 results in decreased methylation of RTRAF gene	CTD	PMID:27153756
Rtraf	Rat	all-trans-retinoic acid	decreases expression	ISO	RTRAF (Homo sapiens)	6480464	Tretinoin results in decreased expression of RTRAF mRNA	CTD	PMID:33167477
Rtraf	Rat	aminoglutethimide	decreases expression	ISO	RTRAF (Homo sapiens)	6480464	Aminoglutethimide results in decreased expression of RTRAF protein	CTD	PMID:26102013
Rtraf	Rat	antirheumatic drug	increases expression	ISO	RTRAF (Homo sapiens)	6480464	Antirheumatic Agents results in increased expression of RTRAF mRNA	CTD	PMID:24449571
Rtraf	Rat	arsenite(3-)	multiple interactions	ISO	RTRAF (Homo sapiens)	6480464	arsenite promotes the reaction [G3BP1 protein binds to RTRAF mRNA]	CTD	PMID:32406909
Rtraf	Rat	benzo[a]pyrene	affects methylation	ISO	RTRAF (Homo sapiens)	6480464	Benzo(a)pyrene affects the methylation of RTRAF promoter	CTD	PMID:27901495
Rtraf	Rat	bis(2-ethylhexyl) phthalate	multiple interactions	ISO	Rtraf (Mus musculus)	6480464	[Diethylhexyl Phthalate co-treated with Dibutyl Phthalate co-treated with butylbenzyl phthalate co-treated with 4-nonylphenol co-treated with 4-tert-octylphenol] results in increased expression of RTRAF mRNA	CTD	PMID:30698749
Rtraf	Rat	bisphenol A	increases expression	EXP		6480464	bisphenol A results in increased expression of RTRAF mRNA	CTD	PMID:25181051 more ...
Rtraf	Rat	bisphenol A	multiple interactions	ISO	RTRAF (Homo sapiens)	6480464	[bisphenol A co-treated with Fulvestrant] results in decreased methylation of RTRAF gene	CTD	PMID:31601247
Rtraf	Rat	bisphenol A	decreases expression	ISO	Rtraf (Mus musculus)	6480464	bisphenol A results in decreased expression of RTRAF mRNA	CTD	PMID:33221593
Rtraf	Rat	bisphenol A	decreases expression	ISO	RTRAF (Homo sapiens)	6480464	bisphenol A results in decreased expression of RTRAF mRNA and bisphenol A results in decreased expression of RTRAF protein	CTD	PMID:29275510 and PMID:31675489
Rtraf	Rat	Butylbenzyl phthalate	multiple interactions	ISO	Rtraf (Mus musculus)	6480464	[Diethylhexyl Phthalate co-treated with Dibutyl Phthalate co-treated with butylbenzyl phthalate co-treated with 4-nonylphenol co-treated with 4-tert-octylphenol] results in increased expression of RTRAF mRNA	CTD	PMID:30698749
Rtraf	Rat	chloropicrin	increases expression	ISO	RTRAF (Homo sapiens)	6480464	chloropicrin results in increased expression of RTRAF mRNA	CTD	PMID:26352163
Rtraf	Rat	cisplatin	increases expression	ISO	RTRAF (Homo sapiens)	6480464	Cisplatin results in increased expression of RTRAF mRNA	CTD	PMID:27392435
Rtraf	Rat	copper(II) sulfate	decreases expression	ISO	RTRAF (Homo sapiens)	6480464	Copper Sulfate results in decreased expression of RTRAF mRNA	CTD	PMID:19549813
Rtraf	Rat	cyclosporin A	increases expression	ISO	RTRAF (Homo sapiens)	6480464	Cyclosporine results in increased expression of RTRAF mRNA	CTD	PMID:20106945 and PMID:25562108
Rtraf	Rat	dibutyl phthalate	multiple interactions	ISO	Rtraf (Mus musculus)	6480464	[Diethylhexyl Phthalate co-treated with Dibutyl Phthalate co-treated with butylbenzyl phthalate co-treated with 4-nonylphenol co-treated with 4-tert-octylphenol] results in increased expression of RTRAF mRNA	CTD	PMID:30698749
Rtraf	Rat	disodium selenite	increases expression	ISO	RTRAF (Homo sapiens)	6480464	Sodium Selenite results in increased expression of RTRAF mRNA	CTD	PMID:18175754
Rtraf	Rat	doxorubicin	decreases expression	ISO	RTRAF (Homo sapiens)	6480464	Doxorubicin results in decreased expression of RTRAF mRNA	CTD	PMID:29803840
Rtraf	Rat	enzyme inhibitor	multiple interactions	ISO	RTRAF (Homo sapiens)	6480464	[Enzyme Inhibitors results in decreased activity of OGA protein] which results in increased O-linked glycosylation of RTRAF protein	CTD	PMID:23301498
Rtraf	Rat	epoxiconazole	increases expression	ISO	Rtraf (Mus musculus)	6480464	epoxiconazole results in increased expression of RTRAF mRNA	CTD	PMID:35436446
Rtraf	Rat	ethanol	increases expression	EXP		6480464	Ethanol results in increased expression of RTRAF protein	CTD	PMID:23702218
Rtraf	Rat	flutamide	increases expression	EXP		6480464	Flutamide results in increased expression of RTRAF mRNA	CTD	PMID:24136188
Rtraf	Rat	folic acid	multiple interactions	ISO	Rtraf (Mus musculus)	6480464	[1 and 2-Dimethylhydrazine co-treated with Folic Acid] results in decreased expression of RTRAF mRNA	CTD	PMID:22206623
Rtraf	Rat	fulvestrant	multiple interactions	ISO	RTRAF (Homo sapiens)	6480464	[bisphenol A co-treated with Fulvestrant] results in decreased methylation of RTRAF gene	CTD	PMID:31601247
Rtraf	Rat	gentamycin	increases expression	EXP		6480464	Gentamicins results in increased expression of RTRAF protein	CTD	PMID:22061828
Rtraf	Rat	ivermectin	decreases expression	ISO	RTRAF (Homo sapiens)	6480464	Ivermectin results in decreased expression of RTRAF protein	CTD	PMID:32959892
Rtraf	Rat	josamycin	affects response to substance	ISO	RTRAF (Homo sapiens)	6480464	RTRAF protein affects the susceptibility to Josamycin	CTD	PMID:31915244
Rtraf	Rat	lead(0)	affects expression	ISO	RTRAF (Homo sapiens)	6480464	Lead affects the expression of RTRAF mRNA	CTD	PMID:28903495
Rtraf	Rat	nitrates	multiple interactions	ISO	Rtraf (Mus musculus)	6480464	[Particulate Matter results in increased abundance of Nitrates] which results in increased expression of RTRAF mRNA	CTD	PMID:35964746
Rtraf	Rat	p-tert-Amylphenol	multiple interactions	ISO	Rtraf (Mus musculus)	6480464	[Diethylhexyl Phthalate co-treated with Dibutyl Phthalate co-treated with butylbenzyl phthalate co-treated with 4-nonylphenol co-treated with 4-tert-octylphenol] results in increased expression of RTRAF mRNA	CTD	PMID:30698749
Rtraf	Rat	resveratrol	multiple interactions	ISO	RTRAF (Homo sapiens)	6480464	[Plant Extracts co-treated with Resveratrol] results in increased expression of RTRAF mRNA	CTD	PMID:23557933
Rtraf	Rat	tributylstannane	increases expression	EXP		6480464	tributyltin results in increased expression of RTRAF mRNA	CTD	PMID:31129395
Rtraf	Rat	vinclozolin	increases methylation	EXP		6480464	vinclozolin results in increased methylation of RTRAF gene	CTD	PMID:31682807

Biological Process

Only show annotations with direct experimental evidence (0 objects hidden)

Object Symbol	Species	Term	Qualifier	Evidence	With	Reference	Notes	Source	Original Reference(s)
Rtraf	Rat	negative regulation of protein kinase activity	involved_in	ISO	RTRAF (Homo sapiens)	1624291	PMID:15147888	RGD	PMID:15147888
Rtraf	Rat	positive regulation of transcription by RNA polymerase II	involved_in	ISO	RTRAF (Homo sapiens)	1624291	PMID:16950395	RGD	PMID:16950395
Rtraf	Rat	tRNA splicing, via endonucleolytic cleavage and ligation	involved_in	ISO	RTRAF (Homo sapiens)	1624291	PMID:24870230	RGD	PMID:24870230
Rtraf	Rat	tRNA splicing, via endonucleolytic cleavage and ligation	involved_in	IBA	PANTHER:PTN000408710 and UniProtKB:Q9Y224	1600115	GO_REF:0000033	GO_Central	GO_REF:0000033

Cellular Component

Only show annotations with direct experimental evidence (0 objects hidden)

Object Symbol	Species	Term	Qualifier	Evidence	With	Reference	Notes	Source	Original Reference(s)
Rtraf	Rat	centrosome	located_in	ISO	RTRAF (Homo sapiens)	1624291	PMID:15147888	RGD	PMID:15147888
Rtraf	Rat	cytoplasm	located_in	ISO	RTRAF (Homo sapiens)	1624291	PMID:24608264	RGD	PMID:24608264
Rtraf	Rat	mitotic spindle	located_in	ISO	RTRAF (Homo sapiens)	1624291	PMID:15147888	RGD	PMID:15147888
Rtraf	Rat	nucleoplasm	located_in	ISO	RTRAF (Homo sapiens)	1624291		RGD	GO_REF:0000052
Rtraf	Rat	nucleus	located_in	ISO	RTRAF (Homo sapiens)	1624291	PMID:15147888 and PMID:24608264	RGD	PMID:15147888 and PMID:24608264
Rtraf	Rat	perinuclear region of cytoplasm	located_in	ISO	RTRAF (Homo sapiens)	1624291	PMID:15147888	RGD	PMID:15147888
Rtraf	Rat	tRNA-splicing ligase complex	part_of	ISO	RTRAF (Homo sapiens)	1624291	PMID:21311021 and PMID:24870230	RGD	PMID:21311021 and PMID:24870230
Rtraf	Rat	tRNA-splicing ligase complex	part_of	IBA	PANTHER:PTN000408710 and UniProtKB:Q9Y224	1600115	GO_REF:0000033	GO_Central	GO_REF:0000033

Molecular Function

Only show annotations with direct experimental evidence (0 objects hidden)

Object Symbol	Species	Term	Qualifier	Evidence	With	Reference	Notes	Source	Original Reference(s)
Rtraf	Rat	identical protein binding	enables	ISO	RTRAF (Homo sapiens)	1624291	UniProtKB:Q9Y224 more ...	RGD	PMID:15147888 and PMID:24608264
Rtraf	Rat	protein binding		IPI	Hnrnpk (Rattus norvegicus)	10054427		RGD
Rtraf	Rat	protein binding	enables	ISO	RTRAF (Homo sapiens)	1624291	UniProtKB:P31343 more ...	RGD	PMID:11507205 more ...
Rtraf	Rat	RNA binding	enables	ISO	RTRAF (Homo sapiens)	1624291	PMID:24608264	RGD	PMID:24608264
Rtraf	Rat	RNA binding	enables	IBA	PANTHER:PTN000408710 and UniProtKB:Q9Y224	1600115	GO_REF:0000033	GO_Central	GO_REF:0000033
Rtraf	Rat	RNA polymerase II complex binding	enables	ISO	RTRAF (Homo sapiens)	1624291	PMID:16950395	RGD	PMID:16950395

#	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.	Landscape of the hnRNP K protein-protein interactome.	Mikula M, etal., Proteomics. 2006 Apr;6(8):2395-406.
3.	ClinVar Automated Import and Annotation Pipeline	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions

PMID:15147888	PMID:16950395	PMID:21311021	PMID:22658674	PMID:24608264	PMID:24870230	PMID:25931508	PMID:35352799

Rtraf
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	15	4,482,699 - 4,507,115 (+)	NCBI		GRCr8
mRatBN7.2	15	4,447,243 - 4,457,973 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	15	4,442,573 - 4,457,972 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	15	4,457,639 - 4,468,370 (+)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	15	5,844,087 - 5,854,816 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	15	4,456,473 - 4,467,202 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	15	4,882,925 - 4,893,890 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	15	4,882,947 - 4,893,919 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	15	8,973,714 - 8,984,679 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	15	4,790,458 - 4,800,905 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	15	4,780,320 - 4,801,091 (+)	NCBI
Celera	15	150,595 - 161,034 (-)	NCBI		Celera
Cytogenetic Map	15	p16	NCBI

RTRAF
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	14	51,989,546 - 52,010,694 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	14	51,989,514 - 52,010,694 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	14	52,456,264 - 52,477,412 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	14	51,525,943 - 51,541,158 (+)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	14	51,525,942 - 51,667,191	NCBI
Celera	14	32,323,222 - 32,338,419 (+)	NCBI		Celera
Cytogenetic Map	14	q22.1	NCBI
HuRef	14	32,616,898 - 32,632,090 (+)	NCBI		HuRef
CHM1_1	14	52,394,686 - 52,409,879 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	14	46,196,590 - 46,217,738 (+)	NCBI		T2T-CHM13v2.0

Rtraf
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	14	19,861,470 - 19,873,891 (-)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	14	19,861,419 - 19,873,892 (-)	Ensembl		GRCm39 Ensembl
GRCm38	14	19,811,402 - 19,823,823 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	14	19,811,351 - 19,823,824 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	14	20,630,624 - 20,643,045 (-)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	14	18,602,098 - 18,614,519 (-)	NCBI		MGSCv36	mm8
Celera	14	16,194,399 - 16,206,819 (-)	NCBI		Celera
Cytogenetic Map	14	A3	NCBI
cM Map	14	10.95	NCBI

Rtraf
(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_004955409	11,034,815 - 11,049,878 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955409	11,034,815 - 11,049,400 (-)	NCBI	ChiLan1.0	ChiLan1.0

RTRAF
(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	15	53,123,300 - 53,138,555 (+)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	14	52,339,811 - 52,355,066 (+)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	14	32,589,078 - 32,604,286 (+)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	14	50,874,274 - 50,889,493 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	14	50,874,274 - 50,889,493 (+)	Ensembl	panpan1.1		panPan2

RTRAF
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	8	28,224,365 - 28,243,129 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
Dog10K_Boxer_Tasha	8	27,977,089 - 27,995,838 (+)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	8	28,402,398 - 28,417,391 (+)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	8	28,402,487 - 28,417,249 (+)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	8	28,071,637 - 28,086,629 (+)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	8	28,132,425 - 28,147,419 (+)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	8	28,479,155 - 28,494,152 (+)	NCBI		UU_Cfam_GSD_1.0

Rtraf
(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_024408640	60,441,127 - 60,456,119 (+)	NCBI		HiC_Itri_2
SpeTri2.0	NW_004936495	13,735,580 - 13,750,554 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

RTRAF
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	1	181,681,352 - 181,698,979 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	1	181,681,368 - 181,698,980 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	1	201,953,129 - 201,970,820 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

RTRAF
(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	24	29,091,241 - 29,106,349 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
Vero_WHO_p1.0	NW_023666053	17,381,922 - 17,397,082 (+)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Rtraf
(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 1.0	NW_004624731	17,032,638 - 17,047,165 (-)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Variants in Rtraf
48 total Variants

Predicted Target Of

	Summary Value
Count of predictions:	24
Count of miRNA genes:	20
Interacting mature miRNAs:	24
Transcripts:	ENSRNOT00000049255
Prediction methods:	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.

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
1641913	Colcr2	Colorectal carcinoma resistance QTL 2	6.57	0.0197	intestine integrity trait (VT:0010554)	poorly differentiated malignant colorectal tumor number (CMO:0002076)	15	2266368	22711984	Rat
10401805	Kidm51	Kidney mass QTL 51			kidney mass (VT:0002707)	both kidneys wet weight (CMO:0000085)	15	306329	45306329	Rat
5684946	Bss98	Bone structure and strength QTL 98	3.9	0.0026	tibia strength trait (VT:1000284)	tibia ultimate force (CMO:0001734)	15	1058250	14481294	Rat
1354657	Despr13	Despair related QTL 13		0.0022	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	15	1	29912054	Rat
1641887	Alcrsp14	Alcohol response QTL 14			response to alcohol trait (VT:0010489)	brain neurotensin receptor 1 density (CMO:0002068)	15	1	42356671	Rat
2298549	Neuinf12	Neuroinflammation QTL 12	3.5		nervous system integrity trait (VT:0010566)	spinal cord beta-2 microglobulin mRNA level (CMO:0002125)	15	1	55302115	Rat
731170	Pur3	Proteinuria QTL 3	2.3	0.0005	urine protein amount (VT:0005160)	urine protein excretion rate (CMO:0000759)	15	1	41686771	Rat
8552920	Pigfal8	Plasma insulin-like growth factor 1 level QTL 8	3		blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	15	1	34723002	Rat
738017	Hcas7	Hepatocarcinoma susceptibility QTL 7	2.91		liver integrity trait (VT:0010547)	liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)	15	2266368	46921453	Rat
8694361	Abfw6	Abdominal fat weight QTL 6	10.2	0.001	visceral adipose mass (VT:0010063)	abdominal fat pad weight to body weight ratio (CMO:0000095)	15	1	34723002	Rat
9589149	Insul29	Insulin level QTL 29	9.06	0.001	blood insulin amount (VT:0001560)	plasma insulin level (CMO:0000342)	15	1	34723002	Rat

AA945900

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	15	4,458,226 - 4,458,364 (+)	MAPPER	mRatBN7.2
Rnor_6.0	15	4,894,144 - 4,894,281	NCBI	Rnor6.0
Rnor_5.0	15	8,984,933 - 8,985,070	UniSTS	Rnor5.0
RGSC_v3.4	15	4,801,328 - 4,801,465	UniSTS	RGSC3.4
Celera	15	150,035 - 150,172	UniSTS
RH 3.4 Map	15	68.1	UniSTS
Cytogenetic Map	15	p16	UniSTS

UniSTS:235896

Rat Assembly	Chr	Position (strand)	Source	JBrowse
GRCr8	15	4,496,498 - 4,497,473 (+)	Marker Load Pipeline
mRatBN7.2	15	4,447,355 - 4,448,330 (+)	MAPPER	mRatBN7.2
Rnor_6.0	15	4,883,033 - 4,884,007	NCBI	Rnor6.0
Rnor_5.0	15	8,973,822 - 8,974,796	UniSTS	Rnor5.0
RGSC_v3.4	15	4,790,458 - 4,791,432	UniSTS	RGSC3.4
Celera	15	160,060 - 161,034	UniSTS
Cytogenetic Map	15	p16	UniSTS

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

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


RefSeq Transcripts	NM_001395114	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_006251636	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_006251638	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_063274191	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AY539943	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH474061	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ215371	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ220810	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ221847	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ224955	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ229372	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ229497	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000015	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSRNOT00000049255 ⟹ ENSRNOP00000049155

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	15	4,442,573 - 4,457,970 (+)	Ensembl
Rnor_6.0 Ensembl	15	4,882,947 - 4,893,919 (+)	Ensembl

Ensembl Acc Id:

ENSRNOT00000092002 ⟹ ENSRNOP00000070052

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	15	4,447,356 - 4,457,972 (+)	Ensembl
Rnor_6.0 Ensembl	15	4,883,033 - 4,893,721 (+)	Ensembl

Ensembl Acc Id:

ENSRNOT00000101009 ⟹ ENSRNOP00000084953

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	15	4,447,270 - 4,457,970 (+)	Ensembl

Ensembl Acc Id:

ENSRNOT00000120090 ⟹ ENSRNOP00000089550

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	15	4,447,272 - 4,457,970 (+)	Ensembl

RefSeq Acc Id:

NM_001395114 ⟹ NP_001382043

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	15	4,496,394 - 4,507,115 (+)	NCBI
mRatBN7.2	15	4,447,251 - 4,457,973 (+)	NCBI

RefSeq Acc Id:

XM_006251638 ⟹ XP_006251700

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	15	4,496,383 - 4,507,112 (+)	NCBI
mRatBN7.2	15	4,447,243 - 4,457,973 (+)	NCBI
Rnor_6.0	15	4,882,925 - 4,893,890 (+)	NCBI
Rnor_5.0	15	8,973,714 - 8,984,679 (+)	NCBI

Sequence:

show sequence

GTCATCGCCCCGCCCCCTCGCCGCGTCGCCGGTGCCTGCGCCGCCCGCCTCACCTCGCTTCTCCTGTCCCGGCGGAGGCCCGGGCGGCCAGCGCGAGCAGCGGGGACCATGTTCCGACGCAAGCTCAC
GGCCCTGGATTACCACAACCCCACAGGCTTCAACTGCAAAGATGAAACAGAGTTTAGAAACTTTATCGTTTGGCTTGAAGACCAGAAGATCAGACACTACAAGATTGAAGACAGAGGTAACTTGAGAA
ACATCCACAGCAGTGACTGGCCCAAGTTCTTTGAAAAGTATCTCAGAGATGTTAACTGTCCTTTCAAGATCCAGGACCGGCAAGAAGCCATTGACTGGCTCCTTGGCTTAGCTGTTAGGCTTGAATAT
GGAGACAACGCTGAAAAGTACAAGGACTCAGTGCCTGACAACAGGAAAAACGCTGACAACGCAGCTAAAAACTCGGAGCCATTGATCAACCTGGACGTAAACAATCCTGATTTTAAGGCGGGTGTCAT
GGCTCTGGCTAACCTCCTTCAGATTCAGCGTCACGATGACTACTTGGTAATGCTGAAGGGCTTACCTGTTGCTTTAGACAAACATATTCTTGGCTTTGACACAGGCGATGCAGTTCTTAATGAAGCTG
CTCAGATCCTGCGGTTGCTACACATAGAAGAGCTCAGAGAGCTACAGACGAAAATTAATGAAGCCATAGTAGCCGTTCAGGCCATCATTGCTGATCCAAAGACAGACCACAGACTGGGGAAAGTTGGG
AGATGAGCACATGAGGGTTTCAGCTTCTCACCTTAGTGATGGGAACTGTCACACCAGCATGTGCTTGGAAATCAAATGTCACACTTTGAAGGGAGGAGTCCCAGGAGATTGACCATGTCCTAGAGATT
TACCACCACTGCTTTTTTTCTTTAATAAAGTTGGGGAAGTAAAAGGC

hide sequence

RefSeq Acc Id:

XM_063274191 ⟹ XP_063130261

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	15	4,482,699 - 4,507,112 (+)	NCBI


Protein RefSeqs	NP_001382043	(Get FASTA)	NCBI Sequence Viewer
	XP_006251700	(Get FASTA)	NCBI Sequence Viewer
	XP_063130261	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAS66283	(Get FASTA)	NCBI Sequence Viewer
	EDL86202	(Get FASTA)	NCBI Sequence Viewer
	EDL86203	(Get FASTA)	NCBI Sequence Viewer
	EDL86204	(Get FASTA)	NCBI Sequence Viewer
	EDL86205	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSRNOP00000049155
	ENSRNOP00000049155.2
	ENSRNOP00000070052
	ENSRNOP00000070052.1
	ENSRNOP00000084953
	ENSRNOP00000084953.1
	ENSRNOP00000089550.1

RefSeq Acc Id:	XP_006251700 ⟸ XM_006251638
- Peptide Label:	isoform X2
- UniProtKB:	A0A8I6GBA2 (UniProtKB/TrEMBL), A0A8I6AA36 (UniProtKB/TrEMBL)
- Sequence:	show sequence MFRRKLTALDYHNPTGFNCKDETEFRNFIVWLEDQKIRHYKIEDRGNLRNIHSSDWPKFFEKYLRDVNCPFKIQDRQEAIDWLLGLAVRLEYGDNAEKYKDSVPDNRKNADNAAKNSEPLINLDVNNP DFKAGVMALANLLQIQRHDDYLVMLKGLPVALDKHILGFDTGDAVLNEAAQILRLLHIEELRELQTKINEAIVAVQAIIADPKTDHRLGKVGR hide sequence

Ensembl Acc Id:

ENSRNOP00000070052 ⟸ ENSRNOT00000092002

Ensembl Acc Id:

ENSRNOP00000049155 ⟸ ENSRNOT00000049255

Ensembl Acc Id:

ENSRNOP00000084953 ⟸ ENSRNOT00000101009

Ensembl Acc Id:

ENSRNOP00000089550 ⟸ ENSRNOT00000120090

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-Q6QI16-F1-model_v2	AlphaFold	Q6QI16	1-296	view protein structure

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

RGD ID:

13699573

Promoter ID:

EPDNEW_R10095

Type:

initiation region

Name:

Rtraf_1

Description:

RNA transcription, translation and transport factor

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	15	4,882,981 - 4,883,041	EPDNEW

Database	Acc Id	Source(s)
BioCyc Gene	G2FUF-14518	BioCyc
Ensembl Genes	ENSRNOG00000000340	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000049255	ENTREZGENE
	ENSRNOT00000049255.4	UniProtKB/TrEMBL
	ENSRNOT00000092002	ENTREZGENE
	ENSRNOT00000092002.2	UniProtKB/TrEMBL
	ENSRNOT00000101009	ENTREZGENE
	ENSRNOT00000101009.1	UniProtKB/TrEMBL
	ENSRNOT00000120090.1	UniProtKB/TrEMBL
InterPro	Putative_carnitine_def-assoc	UniProtKB/TrEMBL
NCBI Gene	302247	ENTREZGENE
PANTHER	PTHR15924	UniProtKB/TrEMBL
Pfam	RLL	UniProtKB/TrEMBL
PhenoGen	Rtraf	PhenoGen
RatGTEx	ENSRNOG00000000340	RatGTEx
UniProt	A0A8I6AA36	ENTREZGENE, UniProtKB/TrEMBL
	A0A8I6GBA2	ENTREZGENE, UniProtKB/TrEMBL
	A6KKK9	ENTREZGENE, UniProtKB/TrEMBL
	F7EMB2	ENTREZGENE, UniProtKB/TrEMBL
	Q6QI16_RAT	UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2017-09-26	Rtraf	RNA transcription, translation and transport factor	RGD1304704	similar to Hypothetical protein CGI-99	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2005-12-06	RGD1304704	similar to Hypothetical protein CGI-99	RGD1304704_predicted	similar to Hypothetical protein CGI-99 (predicted)	Symbol and Name updated	1559027	APPROVED
2005-01-20	RGD1304704_predicted	similar to Hypothetical protein CGI-99 (predicted)	LOC302247_predicted		Symbol and Name status set to approved	1331353	APPROVED
2005-01-12	LOC302247_predicted	similar to Hypothetical protein CGI-99 (predicted)			Symbol and Name status set to provisional	70820	PROVISIONAL

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


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


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