Alyref (Aly/REF export factor) - Rat Genome Database
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Gene: Alyref (Aly/REF export factor) Mus musculus
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Symbol: Alyref
Name: Aly/REF export factor
RGD ID: 1322670
MGI Page MGI
Description: Exhibits RNA binding activity and single-stranded DNA binding activity. Predicted to be involved in RNA splicing; mRNA processing; and mRNA transport. Predicted to localize to nucleus. Is expressed in several structures, including branchial arch; central nervous system; genitourinary system; hemolymphoid system gland; and sensory organ. Orthologous to human ALYREF (Aly/REF export factor); PARTICIPATES IN NXF1-NXT1 export pathway; INTERACTS WITH 1,2-dimethylhydrazine; 17beta-hydroxy-5alpha-androstan-3-one; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: ally of AML-1 and LEF-1; ALY; REF; REF1; REF1-I; Refb; Refbp1; RNA and export factor binding protein 1; RNA and export factor-binding protein 1; Tcra enhancer-binding factor interacting protein 1; THO complex 4; THO complex subunit 4; tho4; Thoc; Thoc4; transcriptional coactivator Aly/REF
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Related Pseudogenes: Gm4308   Gm4310   Gm4781   Gm4850   Gm4898   Gm5698   Gm5699   Gm6489   Gm8384   Gm8391   Gm8689   Gm8701   Gm8711   Gm8723   Gm9476  
Latest Assembly: GRCm38 - Mouse Genome Assembly GRCm38
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3911120,485,330 - 120,489,342 (-)NCBIGRCm39mm39
GRCm3811120,594,504 - 120,598,399 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl11120,592,121 - 120,598,365 (-)EnsemblGRCm38mm10GRCm38
MGSCv3711120,455,830 - 120,459,679 (-)NCBIGRCm37mm9NCBIm37
MGSCv3611120,410,606 - 120,414,455 (-)NCBImm8
Celera11132,329,807 - 132,333,656 (-)NCBICelera
Cytogenetic Map11E2NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:9119228   PMID:10349636   PMID:10786854   PMID:11042159   PMID:11076861   PMID:11217851   PMID:12093754   PMID:12477932   PMID:12809490   PMID:14610273   PMID:14681479   PMID:15520881  
PMID:16033648   PMID:16141072   PMID:16141073   PMID:16679559   PMID:16971461   PMID:18495661   PMID:18799693   PMID:20059953   PMID:21122108   PMID:21267068   PMID:22922362   PMID:23180766  
PMID:24146773   PMID:24457600   PMID:26370502   PMID:27561680   PMID:28671696   PMID:29459677   PMID:29530978   PMID:30196744   PMID:30595499   PMID:30846735   PMID:31138677   PMID:31598710  
PMID:32098917   PMID:32325033  


Genomics

Comparative Map Data
Alyref
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3911120,485,330 - 120,489,342 (-)NCBIGRCm39mm39
GRCm3811120,594,504 - 120,598,399 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl11120,592,121 - 120,598,365 (-)EnsemblGRCm38mm10GRCm38
MGSCv3711120,455,830 - 120,459,679 (-)NCBIGRCm37mm9NCBIm37
MGSCv3611120,410,606 - 120,414,455 (-)NCBImm8
Celera11132,329,807 - 132,333,656 (-)NCBICelera
Cytogenetic Map11E2NCBI
ALYREF
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1781,887,835 - 81,891,586 (-)EnsemblGRCh38hg38GRCh38
GRCh381781,887,835 - 81,891,587 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371779,845,711 - 79,849,464 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361777,439,016 - 77,442,758 (-)NCBINCBI36hg18NCBI36
Build 341777,439,016 - 77,442,758NCBI
Celera1776,449,564 - 76,453,306 (-)NCBI
Cytogenetic Map17q25.3NCBI
HuRef1775,247,636 - 75,251,146 (-)NCBIHuRef
CHM1_11779,931,915 - 79,935,666 (-)NCBICHM1_1
Alyref
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.010109,768,593 - 109,774,639 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl10109,770,876 - 109,774,639 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.010109,363,929 - 109,367,692 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.410109,984,500 - 109,988,263 (-)NCBIRGSC3.4rn4RGSC3.4
Celera10104,414,714 - 104,418,477 (-)NCBICelera
Cytogenetic Map10q32.3NCBI
Alyref
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555061,278,471 - 1,281,772 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555061,278,230 - 1,282,064 (+)NCBIChiLan1.0ChiLan1.0
ALYREF
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11781,995,578 - 82,000,836 (-)NCBIpanpan1.1PanPan1.1panPan2
Mhudiblu_PPA_v01776,293,410 - 76,297,171 (-)NCBIMhudiblu_PPA_v0panPan3
ALYREF
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl9399,072 - 402,721 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.19398,207 - 402,787 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Alyref
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049365945,398,973 - 5,402,846 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ALYREF
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl121,091,976 - 1,103,054 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1121,099,239 - 1,103,058 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
ALYREF
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11673,761,763 - 73,765,560 (-)NCBI
ChlSab1.1 Ensembl1673,757,072 - 73,765,531 (-)Ensembl
Alyref
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462480110,734,392 - 10,738,191 (-)NCBI

Position Markers
Refbp2  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm381171,503,667 - 171,504,310UniSTSGRCm38
MGSCv371173,433,798 - 173,434,441UniSTSGRCm37
Celera1173,946,173 - 173,946,816UniSTS
Cytogenetic Map11E2UniSTS
Cytogenetic Map1H3UniSTS
cM Map1 UniSTS
cM Map179.48UniSTS
Thoc4  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm381171,503,900 - 171,504,298UniSTSGRCm38
MGSCv371173,434,031 - 173,434,429UniSTSGRCm37
Celera1173,946,406 - 173,946,804UniSTS
Cytogenetic Map11E2UniSTS
Cytogenetic Map1H3UniSTS
cM Map11 UniSTS
cM Map1184.31UniSTS
UniSTS:236797  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm3811120,592,193 - 120,592,443UniSTSGRCm38
MGSCv3711120,453,507 - 120,453,757UniSTSGRCm37
Celera11132,327,484 - 132,327,734UniSTS
Cytogenetic Map11E2UniSTS


QTLs in Region (GRCm38)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
15039374Adip29_madiposity 29 (mouse)1186717494120717494Mouse
15039376Bw42_mbody weight QTL 42 (mouse)1186717494120717494Mouse
15014785Mvlq1_mmacrovesicular liver lesion QTL 1 (mouse)1186717494120717494Mouse
27226789Feml16_mfemur length 16, 10 week (mouse)1187600000126900000Mouse
10044007Hbnr14_mHeligmosomoides bakeri nematode resistance 14 (mouse)Not determined1187611774121611872Mouse
11251723Ewc5_methanol withdrawal and consumption 5 (mouse)1189978425122082543Mouse
1302034Pkccl_mprotein kinase C content in lungs (mouse)Not determined1191713782122082543Mouse
1558753Ath19_matherosclerosis 19 (mouse)Not determined1191713782122082543Mouse
1301095El6_mepilepsy 6 (mouse)Not determined1193338357122082543Mouse
1300944Alcp20_malcohol preference locus 20 (mouse)Not determined1195513139122082543Mouse
1301958Alcp18_malcohol preference locus 18 (mouse)Not determined1195513139122082543Mouse
1300962Cd8mts4_mCD8 memory T cell subset 4 (mouse)Not determined1196246848122082543Mouse
1301057Nidd4_mnon-insulin-dependent diabetes mellitus 4 (mouse)Not determined1196919310122082543Mouse
1301983Berr2_mberghei resistance locus 2 (mouse)Not determined1198461783122082543Mouse
10043976Obq33_mobesity QTL 33 (mouse)Not determined1198609643122082543Mouse
10044001Alcw8_malcohol withdrawal 8 (mouse)Not determined1199363361122082543Mouse
11553867Stmm5_mskin tumor modifier of MSM 5 (mouse)11100167277122082543Mouse
11341721Rvfs2_mRift Valley fever susceptibility 2 (mouse)11100363360120996339Mouse
1301012Vispl_mvisual placing (mouse)Not determined11101131764122082543Mouse

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:1296
Count of miRNA genes:622
Interacting mature miRNAs:791
Transcripts:ENSMUST00000026125, ENSMUST00000155325, ENSMUST00000156685
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.


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSMUST00000026125   ⟹   ENSMUSP00000026125
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl11120,592,121 - 120,598,365 (-)Ensembl
RefSeq Acc Id: ENSMUST00000155325
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl11120,594,509 - 120,595,657 (-)Ensembl
RefSeq Acc Id: ENSMUST00000156685
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl11120,595,616 - 120,598,231 (-)Ensembl
RefSeq Acc Id: NM_011568   ⟹   NP_035698
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm3911120,485,342 - 120,489,191 (-)NCBI
GRCm3811120,594,516 - 120,598,365 (-)NCBI
MGSCv3711120,455,830 - 120,459,679 (-)RGD
Celera11132,329,807 - 132,333,656 (-)RGD
cM Map11 ENTREZGENE
Sequence:
RefSeq Acc Id: XR_001779950
RefSeq Status:
Type: NON-CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm3911120,485,330 - 120,489,342 (-)NCBI
GRCm3811120,594,504 - 120,598,399 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_035698   ⟸   NM_011568
- UniProtKB: O08583 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSMUSP00000026125   ⟸   ENSMUST00000026125
Protein Domains
RRM

Promoters
RGD ID:6820395
Promoter ID:MM_KWN:10938
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:3T3L1_Day0,   3T3L1_Day1,   BoneMarrow_0Hour,   BoneMarrow_2Hour,   BoneMarrow_4Hour,   Brain,   ES_Cell,   Kidney,   Liver,   Lung,   MEF_B4,   MEF_B6,   Spleen
Transcripts:NM_001038230,   NM_025389,   OTTMUST00000009196,   OTTMUST00000009198,   OTTMUST00000061821
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv3611120,458,941 - 120,460,062 (+)MPROMDB
RGD ID:8677698
Promoter ID:EPDNEW_M16880
Type:initiation region
Name:Alyref_1
Description:Mus musculus Aly/REF export factor , mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm3811120,598,353 - 120,598,413EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:1341044 AgrOrtholog
Ensembl Genes ENSMUSG00000025134 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSMUSP00000026125 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSMUST00000026125 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 3.30.70.330 UniProtKB/Swiss-Prot
InterPro FoP_C UniProtKB/Swiss-Prot
  Nucleotide-bd_a/b_plait_sf UniProtKB/Swiss-Prot
  RBD_domain_sf UniProtKB/Swiss-Prot
  RRM_dom UniProtKB/Swiss-Prot
KEGG Report mmu:21681 UniProtKB/Swiss-Prot
MGD MGI:1341044 ENTREZGENE
NCBI Gene 21681 ENTREZGENE
Pfam FoP_duplication UniProtKB/Swiss-Prot
  RRM_1 UniProtKB/Swiss-Prot
PhenoGen Alyref PhenoGen
PROSITE RRM UniProtKB/Swiss-Prot
SMART FoP_duplication UniProtKB/Swiss-Prot
  RRM UniProtKB/Swiss-Prot
Superfamily-SCOP SSF54928 UniProtKB/Swiss-Prot
UniGene Mm.1886 ENTREZGENE
UniProt O08583 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary Q0VBL5 UniProtKB/Swiss-Prot
  Q8CBM4 UniProtKB/Swiss-Prot
  Q9JJW7 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2011-12-20 Alyref  Aly/REF export factor  Thoc4  THO complex 4  Symbol and/or name change 5135510 APPROVED