Ush2a (usherin) - Rat Genome Database

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Gene: Ush2a (usherin) Chinchilla lanigera
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Symbol: Ush2a
Name: usherin
RGD ID: 8773079
Description: ENCODES a protein that exhibits collagen binding (ortholog); identical protein binding (ortholog); myosin binding (ortholog); INVOLVED IN establishment of localization in cell (ortholog); establishment of protein localization (ortholog); hair cell differentiation (ortholog); PARTICIPATES IN auditory mechanotransduction pathway; retinitis pigmentosa pathway; ASSOCIATED WITH autism spectrum disorder (ortholog); autosomal dominant nonsyndromic deafness 36 (ortholog); autosomal recessive nonsyndromic deafness (ortholog); FOUND IN apical plasma membrane (ortholog); basement membrane (ortholog); ciliary basal body (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: Usher syndrome 2A (autosomal recessive, mild)
RGD Orthologs
Human
Mouse
Rat
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: ChiLan1.0 - Chinchilla ChiLan1.0 Assembly
NCBI Annotation Information: Annotation category: partial on reference assembly
Position:
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554061,838,885 - 2,496,980 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554061,837,831 - 2,499,664 (+)NCBIChiLan1.0ChiLan1.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Transitive Annotation Pipeline Automated assignment of GO, PW and RDO ISO annotations across species
2. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
Additional References at PubMed
PMID:22301074  


Genomics

Comparative Map Data
Ush2a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554061,838,885 - 2,496,980 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554061,837,831 - 2,499,664 (+)NCBIChiLan1.0ChiLan1.0
USH2A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381215,622,891 - 216,423,448 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1215,622,891 - 216,423,448 (-)EnsemblGRCh38hg38GRCh38
GRCh371215,796,233 - 216,596,790 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361213,862,859 - 214,663,361 (-)NCBINCBI36Build 36hg18NCBI36
Build 341212,735,682 - 212,985,133NCBI
Celera1189,020,056 - 189,820,422 (-)NCBICelera
Cytogenetic Map1q41NCBI
HuRef1186,470,498 - 187,272,188 (-)NCBIHuRef
CHM1_11217,068,567 - 217,869,890 (-)NCBICHM1_1
T2T-CHM13v2.01214,863,291 - 215,663,779 (-)NCBIT2T-CHM13v2.0
Ush2a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391187,995,035 - 188,697,694 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1187,994,220 - 188,697,238 (+)EnsemblGRCm39 Ensembl
GRCm381188,262,838 - 188,965,497 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1188,262,023 - 188,965,041 (+)EnsemblGRCm38mm10GRCm38
MGSCv371190,086,717 - 190,788,920 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361189,963,822 - 190,665,716 (+)NCBIMGSCv36mm8
Celera1195,189,439 - 195,876,703 (+)NCBICelera
Cytogenetic Map1H6NCBI
cM Map192.29NCBI
Ush2a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr813102,368,783 - 103,035,230 (+)NCBIGRCr8
mRatBN7.21399,837,445 - 100,503,935 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1399,837,445 - 100,503,922 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx13102,352,932 - 103,019,370 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.013103,742,004 - 104,408,169 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.013100,938,790 - 101,610,718 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.013106,750,738 - 107,434,195 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl13106,751,625 - 107,427,329 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.013111,395,505 - 112,057,548 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.413104,481,807 - 104,606,485 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.113104,670,849 - 104,795,529 (+)NCBI
Celera1399,331,812 - 99,994,577 (+)NCBICelera
Cytogenetic Map13q26NCBI
USH2A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2132,981,404 - 33,782,083 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1132,939,322 - 33,739,723 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01191,193,130 - 191,994,664 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11196,048,086 - 196,850,216 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1196,048,086 - 196,850,216 (-)Ensemblpanpan1.1panPan2
USH2A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13811,063,221 - 11,750,444 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3811,063,817 - 11,750,444 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3811,100,934 - 11,787,913 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.03811,089,431 - 11,776,697 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl3811,089,576 - 11,776,697 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.13811,101,486 - 11,789,687 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.03811,453,699 - 12,141,739 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.03811,739,438 - 12,442,329 (-)NCBIUU_Cfam_GSD_1.0
Ush2a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934460,113,945 - 60,848,953 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366282,123,957 - 2,858,872 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049366282,123,917 - 2,859,958 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
USH2A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1105,825,591 - 6,662,733 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2107,790,789 - 8,411,655 (-)NCBISscrofa10.2Sscrofa10.2susScr3
USH2A
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12513,171,499 - 13,950,553 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2513,173,576 - 13,947,724 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605513,613,553 - 14,394,397 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Ush2a
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462483549,877 - 758,640 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462483548,213 - 758,640 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2


Expression

RNA-SEQ Expression


Sequence

Nucleotide Sequences
RefSeq Transcripts XM_013519932 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_013519934 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AGCD01005636 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AGCD01005637 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AGCD01005638 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AGCD01005639 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AGCD01005640 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AGCD01005641 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AGCD01005642 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AGCD01005643 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AGCD01005644 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AGCD01005645 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AGCD01005646 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AGCD01005647 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AGCD01005648 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AGCD01005649 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AGCD01005650 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  GBCE01108384 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  GBCE01108396 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Ensembl Acc Id: ENSCLAT00000014127   ⟹   ENSCLAP00000013970
Type: CODING
Position:
Chinchilla AssemblyChrPosition (strand)Source
ChiLan1.0 EnsemblNW_0049554061,838,885 - 2,496,980 (+)Ensembl
RefSeq Acc Id: XM_013519932   ⟹   XP_013375386
Type: CODING
Position:
Chinchilla AssemblyChrPosition (strand)Source
ChiLan1.0NW_0049554061,837,831 - 2,499,664 (+)NCBI
Sequence:
RefSeq Acc Id: XM_013519934   ⟹   XP_013375388
Type: CODING
Position:
Chinchilla AssemblyChrPosition (strand)Source
ChiLan1.0NW_0049554061,837,831 - 2,499,664 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs XP_013375386 (Get FASTA)   NCBI Sequence Viewer  
  XP_013375388 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSCLAP00000013970
  ENSCLAP00000013970.1
RefSeq Acc Id: XP_013375386   ⟸   XM_013519932
- Peptide Label: isoform X1
- UniProtKB: A0A8C2YPL4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_013375388   ⟸   XM_013519934
- Peptide Label: isoform X2
- UniProtKB: A0A8C2YPL4 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSCLAP00000013970   ⟸   ENSCLAT00000014127

Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCLAG00000009662 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSCLAT00000014127 ENTREZGENE
  ENSCLAT00000014127.1 UniProtKB/TrEMBL
Gene3D-CATH 2.60.120.200 UniProtKB/TrEMBL
  2.60.40.10 UniProtKB/TrEMBL
  Galactose-binding domain-like UniProtKB/TrEMBL
  Laminin UniProtKB/TrEMBL
InterPro ConA-like_dom_sf UniProtKB/TrEMBL
  EGF-like_dom UniProtKB/TrEMBL
  FN3_dom UniProtKB/TrEMBL
  FN3_sf UniProtKB/TrEMBL
  Ig-like_fold UniProtKB/TrEMBL
  LamG-like UniProtKB/TrEMBL
  Laminin_G UniProtKB/TrEMBL
  Laminin_N UniProtKB/TrEMBL
  LE_dom UniProtKB/TrEMBL
  RTP_Phos/Ushers UniProtKB/TrEMBL
NCBI Gene Ush2a ENTREZGENE
PANTHER CYTOKINE RECEPTOR UniProtKB/TrEMBL
  USHERIN UniProtKB/TrEMBL
Pfam fn3 UniProtKB/TrEMBL
  Laminin_EGF UniProtKB/TrEMBL
  Laminin_G_2 UniProtKB/TrEMBL
  Laminin_G_3 UniProtKB/TrEMBL
  Laminin_N UniProtKB/TrEMBL
PRINTS EGFLAMININ UniProtKB/TrEMBL
PROSITE EGF_LAM_1 UniProtKB/TrEMBL
  EGF_LAM_2 UniProtKB/TrEMBL
  FN3 UniProtKB/TrEMBL
  LAM_G_DOMAIN UniProtKB/TrEMBL
  LAMININ_NTER UniProtKB/TrEMBL
SMART EGF UniProtKB/TrEMBL
  EGF_Lam UniProtKB/TrEMBL
  FN3 UniProtKB/TrEMBL
  LamG UniProtKB/TrEMBL
  LamGL UniProtKB/TrEMBL
  LamNT UniProtKB/TrEMBL
Superfamily-SCOP EGF/Laminin UniProtKB/TrEMBL
  SSF49265 UniProtKB/TrEMBL
  SSF49899 UniProtKB/TrEMBL
UniProt A0A8C2YPL4 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-08-03 Ush2a  usherin    Usher syndrome 2A (autosomal recessive, mild)  Symbol and/or name change 5135510 APPROVED