Alyref (Aly/REF export factor) - Rat Genome Database

Name: Alyref
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

	Submit Data \| Help \| Video Tutorials \| News \| Publications \| Download \| REST API \| Citing RGD \| Contact
	Search RGD Grant Resources Citing RGD About Us Contact Us Genes QTLs Strains Markers Community Projects Genome Information Ontologies Cell Lines References Download Submit Data OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) (beta) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer) Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease COVID-19 Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease Find Models new Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes GERRC (Gene Editing Rat Resource Center) Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive Pathways Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
	Advanced Search (OLGA)

Gene: Alyref (Aly/REF export factor) Rattus norvegicus

Analyze

Symbol:

Alyref

Name:

Aly/REF export factor

RGD ID:

1594679

Description:

Predicted to enable C5-methylcytidine-containing RNA reader activity; RNA folding chaperone; and nucleic acid binding activity. Predicted to be involved in several processes, including mRNA export from nucleus; regulation of nucleobase-containing compound metabolic process; and viral mRNA export from host cell nucleus. Predicted to be located in cytoplasm and nuclear speck. Predicted to be part of catalytic step 2 spliceosome; exon-exon junction complex; and transcription export complex. Predicted to be active in nucleus. Predicted to colocalize with chromosome, telomeric region. Orthologous to human ALYREF (Aly/REF export factor); PARTICIPATES IN NXF1-NXT1 export pathway; mRNA decay pathway; RNA transport pathway; INTERACTS WITH (+)-schisandrin B; 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine.

Type:

protein-coding

RefSeq Status:

VALIDATED

Previously known as:

LOC690585; similar to THO complex subunit 4 (Tho4) (RNA and export factor binding protein 1) (REF1-I) (Ally of AML-1 and LEF-1) (Aly/REF); THO complex 4; THO complex subunit 4; Thoc4

RGD Orthologs

Alliance Genes

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):	ALYREF (Aly/REF export factor)	HGNC	Ensembl, HomoloGene, NCBI, OMA, OrthoDB, Panther
Mus musculus (house mouse):	Alyref (Aly/REF export factor)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Alyref (Aly/REF export factor)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	ALYREF (Aly/REF export factor)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	ALYREF (Aly/REF export factor)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Alyref (Aly/REF export factor)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	ALYREF (Aly/REF export factor)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	ALYREF (Aly/REF export factor)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Alyref (Aly/REF export factor)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Other homologs ²
Homo sapiens (human):	YDJC (YdjC chitooligosaccharide deacetylase homolog)	HGNC	OMA
Alliance orthologs ³
Homo sapiens (human):	ALYREF (Aly/REF export factor)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Alyref (Aly/REF export factor)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	4931428L18Rik (RIKEN cDNA 4931428L18 gene)	Alliance	DIOPT (Ensembl Compara\|OrthoFinder\|PANTHER)
Mus musculus (house mouse):	Gm5698 (predicted gene 5698)	Alliance	DIOPT (Ensembl Compara\|OrthoFinder\|PANTHER)
Mus musculus (house mouse):	Alyref2 (Aly/REF export factor 2)	Alliance	DIOPT (Hieranoid\|InParanoid\|OrthoFinder\|PANTHER\|SonicParanoid)
Mus musculus (house mouse):	Gm4302 (predicted gene 4302)	Alliance	DIOPT (Ensembl Compara\|OrthoFinder\|PANTHER)
Mus musculus (house mouse):	Gm4340 (predicted gene 4340)	Alliance	DIOPT (Ensembl Compara\|OrthoFinder\|PANTHER)
Mus musculus (house mouse):	Gm4312 (predicted gene 4312)	Alliance	DIOPT (Ensembl Compara\|OrthoFinder\|PANTHER)
Mus musculus (house mouse):	Gm4307 (predicted gene 4307)	Alliance	DIOPT (Ensembl Compara\|OrthoFinder\|PANTHER)
Mus musculus (house mouse):	Gm4305 (predicted gene 4305)	Alliance	DIOPT (Ensembl Compara\|OrthoFinder\|PANTHER)
Mus musculus (house mouse):	Gm4303 (predicted gene 4303)	Alliance	DIOPT (Ensembl Compara\|OrthoFinder\|PANTHER)
Mus musculus (house mouse):	Gm4301 (predicted gene 4301)	Alliance	DIOPT (Ensembl Compara\|OrthoFinder\|PANTHER)
Mus musculus (house mouse):	Gm21293 (predicted gene, 21293)	Alliance	DIOPT (Ensembl Compara\|OrthoFinder\|PANTHER)
Danio rerio (zebrafish):	alyref (Aly/REF export factor)	Alliance	DIOPT (Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Drosophila melanogaster (fruit fly):	Ref1	Alliance	DIOPT (Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Saccharomyces cerevisiae (baker's yeast):	YRA1	Alliance	DIOPT (InParanoid\|OrthoFinder\|PhylomeDB)
Caenorhabditis elegans (roundworm):	aly-1	Alliance	DIOPT (Hieranoid\|InParanoid\|OrthoFinder\|PANTHER)
Caenorhabditis elegans (roundworm):	aly-2	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OrthoFinder\|PANTHER)
Caenorhabditis elegans (roundworm):	aly-3	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OrthoFinder\|PANTHER)
Xenopus tropicalis (tropical clawed frog):	alyref	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
mRatBN7.2	10	105,871,424 - 105,875,076 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	10	105,871,306 - 105,875,069 (-)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	10	110,975,253 - 110,978,898 (-)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	10	110,438,281 - 110,441,926 (-)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	10	105,791,877 - 105,795,522 (-)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	10	109,768,593 - 109,774,639 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	10	109,770,876 - 109,774,639 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	10	109,363,929 - 109,367,692 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	10	109,984,500 - 109,988,263 (-)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
Celera	10	104,414,714 - 104,418,477 (-)	NCBI		Celera
Cytogenetic Map	10	q32.3	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

genetic disease (ISO)

human immunodeficiency virus infectious disease (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(+)-schisandrin B (EXP)

1,2-dimethylhydrazine (ISO)

17beta-estradiol (EXP)

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

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

3,4-methylenedioxymethamphetamine (ISO)

3-isobutyl-1-methyl-7H-xanthine (ISO)

4,4'-sulfonyldiphenol (ISO)

6-propyl-2-thiouracil (EXP)

acrylamide (EXP)

atrazine (ISO)

benzo[a]pyrene (ISO)

bis(2-chloroethyl) sulfide (ISO)

bisphenol A (EXP,ISO)

Bisphenol B (ISO)

bisphenol F (ISO)

caffeine (ISO)

carbon nanotube (ISO)

CGP 52608 (ISO)

chromium(6+) (ISO)

clozapine (ISO)

coumarin (ISO)

coumestrol (ISO)

cyclophosphamide (ISO)

cyclosporin A (ISO)

DDT (EXP)

dexamethasone (ISO)

diethylstilbestrol (ISO)

dioxygen (ISO)

folic acid (ISO)

gentamycin (EXP)

indometacin (ISO)

ivermectin (ISO)

lipopolysaccharide (ISO)

menadione (ISO)

methapyrilene (EXP)

methidathion (ISO)

microcystin-LR (ISO)

nickel atom (ISO)

nickel sulfate (ISO)

oxaliplatin (EXP)

paracetamol (ISO)

perfluorooctane-1-sulfonic acid (ISO)

quercetin (ISO)

resveratrol (ISO)

sodium arsenite (ISO)

sunitinib (ISO)

tetrachloromethane (EXP,ISO)

thioacetamide (EXP)

topotecan (EXP)

trimellitic anhydride (ISO)

triticonazole (EXP)

troglitazone (ISO)

valproic acid (ISO)

versicolorin A (ISO)

vinclozolin (EXP)

Yessotoxin (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

biological_process (ND)

mRNA export from nucleus (IBA,ISO)

positive regulation of DNA-templated transcription, elongation (ISO)

regulation of DNA recombination (ISO)

replication fork processing (ISO)

RNA export from nucleus (ISO)

RNA folding (IEA)

viral mRNA export from host cell nucleus (ISO)

Cellular Component

catalytic step 2 spliceosome (ISO)

chromosome, telomeric region (ISO)

cytoplasm (ISO)

exon-exon junction complex (ISO)

nuclear speck (IEA,ISO)

nucleus (IBA,ISO)

transcription export complex (ISO)

Molecular Function

C5-methylcytidine-containing RNA reader activity (ISO)

molecular adaptor activity (ISO)

mRNA binding (IBA)

protein binding (ISO)

RNA binding (ISO)

RNA folding chaperone (ISO)

single-stranded DNA binding (ISO)

Molecular Pathway Annotations Click to see Annotation Detail View

mRNA decay pathway (IEA)

NXF1-NXT1 export pathway (ISO)

RNA transport pathway (IEA)

spliceosome pathway (IEA)

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.	mRNA export and the TREX complex.	Katahira J Biochim Biophys Acta. 2012 Jun;1819(6):507-13. doi: 10.1016/j.bbagrm.2011.12.001. Epub 2011 Dec 8.
3.	KEGG Annotation Import Pipeline	Pipeline to import KEGG annotations from KEGG into RGD
4.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions
5.	Comprehensive gene review and curation	RGD comprehensive gene curation

Additional References at PubMed

PMID:10786854	PMID:11991638	PMID:15833825	PMID:15998806	PMID:16210410	PMID:16314458	PMID:17190602	PMID:18974867	PMID:19056867	PMID:22144908	PMID:22658674	PMID:22681889
PMID:24270157	PMID:25662211	PMID:28418038	PMID:30361391

Genomics

Comparative Map Data

Alyref
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	10	105,871,424 - 105,875,076 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	10	105,871,306 - 105,875,069 (-)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	10	110,975,253 - 110,978,898 (-)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	10	110,438,281 - 110,441,926 (-)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	10	105,791,877 - 105,795,522 (-)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	10	109,768,593 - 109,774,639 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	10	109,770,876 - 109,774,639 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	10	109,363,929 - 109,367,692 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	10	109,984,500 - 109,988,263 (-)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
Celera	10	104,414,714 - 104,418,477 (-)	NCBI		Celera
Cytogenetic Map	10	q32.3	NCBI

ALYREF
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	17	81,887,835 - 81,891,587 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	17	81,887,835 - 81,891,586 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	17	79,845,711 - 79,849,463 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	17	77,439,016 - 77,442,758 (-)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	17	77,439,016 - 77,442,758	NCBI
Celera	17	76,449,564 - 76,453,306 (-)	NCBI		Celera
Cytogenetic Map	17	q25.3	NCBI
HuRef	17	75,247,636 - 75,251,146 (-)	NCBI		HuRef
CHM1_1	17	79,931,915 - 79,935,666 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	17	82,754,997 - 82,758,749 (-)	NCBI		T2T-CHM13v2.0

Alyref
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	11	120,485,330 - 120,489,342 (-)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	11	120,482,947 - 120,489,191 (-)	Ensembl		GRCm39 Ensembl
GRCm38	11	120,594,504 - 120,598,399 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	11	120,592,121 - 120,598,365 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	11	120,455,830 - 120,459,679 (-)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	11	120,410,606 - 120,414,455 (-)	NCBI		MGSCv36	mm8
Celera	11	132,329,807 - 132,333,656 (-)	NCBI		Celera
Cytogenetic Map	11	E2	NCBI
cM Map	11	84.31	NCBI

Alyref
(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_004955506	1,278,471 - 1,281,772 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955506	1,278,230 - 1,282,064 (+)	NCBI	ChiLan1.0	ChiLan1.0

ALYREF
(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	17	103,324,715 - 103,328,469 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	17	76,293,410 - 76,297,171 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	17	81,995,578 - 82,000,836 (-)	NCBI	panpan1.1	PanPan1.1	panPan2

ALYREF
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	9	398,207 - 402,787 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	9	399,072 - 402,721 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	9	1,001,232 - 1,004,942 (+)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	9	992,434 - 996,142 (+)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	9	992,429 - 996,076 (+)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	9	1,017,597 - 1,021,306 (+)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	9	1,144,188 - 1,147,898 (+)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	9	1,222,843 - 1,226,552 (+)	NCBI		UU_Cfam_GSD_1.0

Alyref
(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	1,009,113 - 1,017,137 (+)	NCBI		HiC_Itri_2
SpeTri2.0	NW_004936594	5,398,973 - 5,402,846 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

ALYREF
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	12	1,092,329 - 1,103,054 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	12	1,099,239 - 1,103,058 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1

ALYREF
(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	16	73,761,763 - 73,765,560 (-)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	16	73,757,072 - 73,765,531 (-)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666077	45,213,965 - 45,217,836 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Alyref
(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_004624801	10,733,907 - 10,738,124 (-)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624801	10,734,392 - 10,738,191 (-)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Variants

Variants in Alyref
15 total Variants

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	98
Count of miRNA genes:	75
Interacting mature miRNAs:	88
Transcripts:	ENSRNOT00000054955
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.

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
2316949	Gluco60	Glucose level QTL 60	3.7		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	10	14487011	107057807	Rat
1331791	Cm31	Cardiac mass QTL 31	3.84606		heart mass (VT:0007028)	heart wet weight (CMO:0000069)	10	29299504	107211142	Rat
61387	Bp1	Blood pressure QTL 1	5.1		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	51770177	107211142	Rat
61387	Bp1	Blood pressure QTL 1	5.1		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	10	51770177	107211142	Rat
70171	Cari1	Carrageenan-induced inflammation QTL 1	4.9	0.0005	hypodermis integrity trait (VT:0010550)	inflammatory exudate volume (CMO:0001429)	10	53797385	107211142	Rat
2313103	Bss80	Bone structure and strength QTL 80	2	0.0001	tibia strength trait (VT:1000284)	tibia midshaft endosteal cross-sectional area (CMO:0001716)	10	62057807	107057807	Rat
2313105	Bss79	Bone structure and strength QTL 79	1.8	0.0001	tibia size trait (VT:0100001)	tibia midshaft cross-sectional area (CMO:0001717)	10	62057807	107057807	Rat
61449	Ciaa2	CIA Autoantibody QTL 2	7.1		blood autoantibody amount (VT:0003725)	calculated serum anti-type 2 collagen antibody titer (CMO:0001279)	10	63221094	107211142	Rat
2317029	Aia19	Adjuvant induced arthritis QTL 19	2.98		joint integrity trait (VT:0010548)	left rear ankle joint diameter (CMO:0002149)	10	66978955	107211142	Rat
2317039	Aia6	Adjuvant induced arthritis QTL 6	4.31		joint integrity trait (VT:0010548)	right rear ankle joint diameter (CMO:0002150)	10	66978955	107211142	Rat
10450498	Bp384	Blood pressure QTL 384		0.002	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	10	67750049	107211142	Rat
1642980	Bp300	Blood pressure QTL 300			arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	68383129	107211142	Rat
61396	Bp9	Blood pressure QTL 9	4.8	0.0001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	68420376	107211142	Rat
2300172	Bmd57	Bone mineral density QTL 57	9.8	0.0001	femur mineral mass (VT:0010011)	volumetric bone mineral density (CMO:0001553)	10	69738412	107211142	Rat
2293646	Bss25	Bone structure and strength QTL 25	10.96	0.0001	femur morphology trait (VT:0000559)	femur cross-sectional area (CMO:0001661)	10	69738412	107211142	Rat
2293663	Bss33	Bone structure and strength QTL 33	9.34	0.0001	femur strength trait (VT:0010010)	femur midshaft polar moment of inertia (CMO:0001669)	10	69738412	107211142	Rat
6893366	Bw106	Body weight QTL 106	0.3	0.47	body mass (VT:0001259)	body weight (CMO:0000012)	10	70199100	107211142	Rat
70193	Mcs7	Mammary carcinoma susceptibility QTL 7	2.38		mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	10	72224939	107211142	Rat
2298548	Neuinf7	Neuroinflammation QTL 7	3.4		nervous system integrity trait (VT:0010566)	spinal cord RT1-B protein level (CMO:0002132)	10	72224939	107211142	Rat
2292438	Bp311	Blood pressure QTL 311			arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	10	76246085	107211142	Rat
1302404	Cia27	Collagen induced arthritis QTL 27	2.6	0.0045	joint integrity trait (VT:0010548)	experimental arthritis severity measurement (CMO:0001459)	10	76452683	107211142	Rat
4889492	Pancm2	Pancreatic morphology QTL 2	3.2		pancreatic beta cell morphology trait (VT:0005217)	ratio of insulin-positive cell area to total area of splenic region of pancreas (CMO:0001814)	10	76748906	107211142	Rat
2303589	Bw87	Body weight QTL 87	2		body mass (VT:0001259)	body weight (CMO:0000012)	10	81285008	107211142	Rat
2317754	Glom25	Glomerulus QTL 25	3.5		urine protein amount (VT:0005160)	urine protein level (CMO:0000591)	10	82685200	107211142	Rat
631538	Oia5	Oil induced arthritis QTL 5			joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	87055121	107211142	Rat
61363	Oia3	Oil induced arthritis QTL 3		0.001	joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	87307617	107211142	Rat
634320	Niddm49	Non-insulin dependent diabetes mellitus QTL 49	4.41		blood glucose amount (VT:0000188)	plasma glucose level (CMO:0000042)	10	88539139	107211142	Rat
12880395	Cm109	Cardiac mass QTL 109		0.001	heart right ventricle mass (VT:0007033)	heart right ventricle weight to body weight ratio (CMO:0000914)	10	90404397	107211142	Rat
12880396	Am13	Aortic mass QTL 13		0.001	aorta mass (VT:0002845)	aorta weight to aorta length to body weight ratio (CMO:0002722)	10	90404397	107211142	Rat
12880398	Kidm67	Kidney mass QTL 67		0.001	kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	10	90404397	107211142	Rat
12880384	Cm107	Cardiac mass QTL 107		0.001	heart mass (VT:0007028)	heart wet weight to body weight ratio (CMO:0002408)		90404397	107211142	Rat
12880385	Cm108	Cardiac mass QTL 108		0.001	heart left ventricle mass (VT:0007031)	heart left ventricle weight to body weight ratio (CMO:0000530)		90404397	107211142	Rat
1579915	Bp280	Blood pressure QTL 280		0.001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	10	90404397	107211142	Rat
1300137	Bp186	Blood pressure QTL 186	3.57		arterial blood pressure trait (VT:2000000)	blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)	10	90627439	107057807	Rat
724530	Bp149	Blood pressure QTL 149		0.0001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	10	90627439	107211142	Rat
1558652	Bw57	Body weight QTL 57	4.2	0.0008	body mass (VT:0001259)	body weight (CMO:0000012)	10	90910316	107211142	Rat
1354641	Bvd2	Brain ventricular dilatation QTL 2	6.36	0.001	brain ventricle morphology trait (VT:0000822)	hydrocephalus severity score (CMO:0001881)	10	93223816	107057807	Rat
10450493	Bp382	Blood pressure QTL 382		0.002	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	10	94759759	107211142	Rat
2292436	Bp310	Blood pressure QTL 310			arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	10	94759759	107211142	Rat
1578663	Bss18	Bone structure and strength QTL 18	3.6		femur width (VT:1000666)	femoral neck width (CMO:0001695)	10	96703043	107057807	Rat
1578672	Bmd16	Bone mineral density QTL 16	6.2		femur mineral mass (VT:0010011)	compact volumetric bone mineral density (CMO:0001730)	10	96703043	107057807	Rat

Expression

RNA-SEQ Expression

High: > 1000 TPM value Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM Below Cutoff: < 0.5 TPM

	alimentary part of gastrointestinal system	circulatory system	endocrine system	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	musculoskeletal system	nervous system	renal system	reproductive system	respiratory system	appendage
High
Medium	3	42	57	41	19	41	7	10	74	35	41	11	7
Low		1					1	1					1
Below cutoff

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001394394	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	NR_172126	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039086877	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC131537	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473948	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000220	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

RefSeq Acc Id:

ENSRNOT00000054955 ⟹ ENSRNOP00000051838

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	10	105,871,306 - 105,875,069 (-)	Ensembl
Rnor_6.0 Ensembl	10	109,770,876 - 109,774,639 (-)	Ensembl

RefSeq Acc Id:

ENSRNOT00000071823 ⟹ ENSRNOP00000066841

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	10	105,871,306 - 105,875,069 (-)	Ensembl

RefSeq Acc Id:

NM_001394394 ⟹ NP_001381323

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	10	105,871,424 - 105,875,069 (-)	NCBI

RefSeq Acc Id:

NR_172126

RefSeq Status:

VALIDATED

Type:

NON-CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	10	105,871,424 - 105,875,069 (-)	NCBI

RefSeq Acc Id:

XM_039086877 ⟹ XP_038942805

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	10	105,872,259 - 105,875,076 (-)	NCBI

Protein Sequences


Protein RefSeqs	NP_001381323	(Get FASTA)	NCBI Sequence Viewer
	XP_038942805	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	EDM06861	(Get FASTA)	NCBI Sequence Viewer
	EDM06862	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSRNOP00000051838
	ENSRNOP00000051838.2
	ENSRNOP00000066841
	ENSRNOP00000066841.3

RefSeq Acc Id:

ENSRNOP00000051838 ⟸ ENSRNOT00000054955

RefSeq Acc Id:	XP_038942805 ⟸ XM_039086877
- Peptide Label:	isoform X2
- UniProtKB:	D3ZXH7 (UniProtKB/TrEMBL), A6HLF8 (UniProtKB/TrEMBL)

RefSeq Acc Id:

ENSRNOP00000066841 ⟸ ENSRNOT00000071823

RefSeq Acc Id:	NP_001381323 ⟸ NM_001394394
- UniProtKB:	M0RBB1 (UniProtKB/TrEMBL), A6HLF7 (UniProtKB/TrEMBL)

Protein Domains

RRM

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-M0RBB1-F1-model_v2	AlphaFold	M0RBB1	1-103	view protein structure
AF-D3ZXH7-F1-model_v2	AlphaFold	D3ZXH7	1-189	view protein structure

Transcriptome

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

Promoters

RGD ID:

13697966

Promoter ID:

EPDNEW_R8490

Type:

initiation region

Name:

Alyref_1

Description:

Aly/REF export 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	10	109,774,636 - 109,774,696	EPDNEW

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1594679	AgrOrtholog
BioCyc Gene	G2FUF-22406	BioCyc
Ensembl Genes	ENSRNOG00000036687	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000054955	ENTREZGENE
	ENSRNOT00000054955.3	UniProtKB/TrEMBL
	ENSRNOT00000071823	ENTREZGENE
	ENSRNOT00000071823.3	UniProtKB/TrEMBL
Gene3D-CATH	3.30.70.330	UniProtKB/TrEMBL
InterPro	FoP_C	UniProtKB/TrEMBL
	Nucleotide-bd_a/b_plait_sf	UniProtKB/TrEMBL
	RBD_domain_sf	UniProtKB/TrEMBL
	RRM_RNP1	UniProtKB/TrEMBL
KEGG Report	rno:690585	UniProtKB/TrEMBL
NCBI Gene	690585	ENTREZGENE
PANTHER	RNA AND EXPORT FACTOR BINDING PROTEIN	UniProtKB/TrEMBL
	THO COMPLEX SUBUNIT 4	UniProtKB/TrEMBL
Pfam	FoP_duplication	UniProtKB/TrEMBL
	RRM_1	UniProtKB/TrEMBL
PhenoGen	Alyref	PhenoGen
PROSITE	RRM	UniProtKB/TrEMBL
RatGTEx	ENSRNOG00000036687	RatGTEx
SMART	FoP_duplication	UniProtKB/TrEMBL
	RRM	UniProtKB/TrEMBL
Superfamily-SCOP	SSF54928	UniProtKB/TrEMBL
UniProt	A6HLF7	ENTREZGENE, UniProtKB/TrEMBL
	A6HLF8	ENTREZGENE, UniProtKB/TrEMBL
	D3ZXH7	ENTREZGENE, UniProtKB/TrEMBL
	M0RBB1	ENTREZGENE, UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2013-08-02	Alyref	Aly/REF export factor	Thoc4	THO complex 4	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2008-07-08	Thoc4	THO complex 4	LOC688305	similar to THO complex subunit 4 (Tho4) (RNA and export factor binding protein 1) (REF1-I) (Ally of AML-1 and LEF-1) (Aly/REF)	Data merged from RGD:1590065	1643240	APPROVED
2008-03-06	Thoc4	THO complex 4	LOC690585	similar to THO complex subunit 4 (Tho4) (RNA and export factor binding protein 1) (REF1-I) (Ally of AML-1 and LEF-1) (Aly/REF)	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2006-11-20	LOC690585	similar to THO complex subunit 4 (Tho4) (RNA and export factor binding protein 1) (REF1-I) (Ally of AML-1 and LEF-1) (Aly/REF)			Symbol and Name status set to provisional	70820	PROVISIONAL
2006-11-20	LOC688305	similar to THO complex subunit 4 (Tho4) (RNA and export factor binding protein 1) (REF1-I) (Ally of AML-1 and LEF-1) (Aly/REF)			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)

Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

RGD Manual Annotations

Imported Annotations - KEGG (archival)

Send us a Message

Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

RGD Manual Annotations

Imported Annotations - KEGG (archival)