Ush1c (USH1 protein network component harmonin) - Rat Genome Database

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Gene: Ush1c (USH1 protein network component harmonin) Chinchilla lanigera
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Symbol: Ush1c
Name: USH1 protein network component harmonin
RGD ID: 8916038
Description: ENCODES a protein that exhibits spectrin binding (ortholog); INVOLVED IN actin filament bundle assembly (ortholog); brush border assembly (ortholog); equilibrioception (ortholog); PARTICIPATES IN auditory mechanotransduction pathway; retinitis pigmentosa pathway; ASSOCIATED WITH autosomal recessive nonsyndromic deafness (ortholog); Autosomal Recessive Nonsyndromic Deafness 18 (ortholog); autosomal recessive nonsyndromic deafness 18A (ortholog); FOUND IN apical part of cell (ortholog); brush border (ortholog); cytoplasm (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: harmonin; Usher syndrome 1C; Usher syndrome 1C (autosomal recessive, severe)
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
Position:
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541432,298,759 - 32,351,505 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495541432,303,045 - 32,351,401 (-)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   PMID:30032202  


Genomics

Comparative Map Data
Ush1c
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541432,298,759 - 32,351,505 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495541432,303,045 - 32,351,401 (-)NCBIChiLan1.0ChiLan1.0
USH1C
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381117,493,900 - 17,544,416 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1117,493,895 - 17,544,416 (-)EnsemblGRCh38hg38GRCh38
GRCh371117,515,447 - 17,565,963 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361117,472,018 - 17,522,539 (-)NCBINCBI36Build 36hg18NCBI36
Celera1117,645,289 - 17,695,946 (-)NCBICelera
Cytogenetic Map11p15.1NCBI
HuRef1117,199,243 - 17,249,828 (-)NCBIHuRef
CHM1_11117,515,265 - 17,565,784 (-)NCBICHM1_1
T2T-CHM13v2.01117,591,495 - 17,642,149 (-)NCBIT2T-CHM13v2.0
Ush1c
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39745,844,774 - 45,887,984 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl745,844,774 - 45,887,927 (-)EnsemblGRCm39 Ensembl
GRCm38746,195,350 - 46,238,490 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl746,195,350 - 46,238,503 (-)EnsemblGRCm38mm10GRCm38
MGSCv37753,450,721 - 53,493,860 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36746,063,399 - 46,106,532 (-)NCBIMGSCv36mm8
Celera741,668,925 - 41,712,073 (-)NCBICelera
Cytogenetic Map7B3NCBI
cM Map729.66NCBI
Ush1c
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81105,831,719 - 105,880,082 (-)NCBIGRCr8
mRatBN7.2196,695,303 - 96,743,671 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl196,695,307 - 96,743,671 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1102,081,448 - 102,129,809 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01110,553,421 - 110,601,783 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01103,843,796 - 103,892,162 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01102,207,096 - 102,256,779 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1102,207,096 - 102,255,459 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01103,291,318 - 103,340,928 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4196,720,185 - 96,768,550 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1196,798,295 - 96,846,661 (-)NCBI
Celera190,943,948 - 90,992,307 (-)NCBICelera
Cytogenetic Map1q22NCBI
USH1C
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2919,827,448 - 19,877,874 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11119,787,920 - 19,838,443 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01117,548,501 - 17,598,923 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11117,233,854 - 17,284,256 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1117,233,854 - 17,284,256 (-)Ensemblpanpan1.1panPan2
USH1C
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12140,055,786 - 40,100,685 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2140,055,730 - 40,101,430 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2139,555,651 - 39,600,543 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02141,161,015 - 41,205,900 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2141,160,539 - 41,205,845 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12140,173,714 - 40,218,550 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02140,380,893 - 40,425,786 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02140,719,734 - 40,764,634 (-)NCBIUU_Cfam_GSD_1.0
Ush1c
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494745,513,303 - 45,560,765 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365281,552,289 - 1,594,801 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365281,552,175 - 1,594,740 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
USH1C
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl241,593,802 - 41,647,247 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1241,593,793 - 41,646,777 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2244,613,841 - 44,706,204 (+)NCBISscrofa10.2Sscrofa10.2susScr3
USH1C
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1147,428,181 - 47,477,578 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl147,437,596 - 47,477,834 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666038144,848,688 - 144,898,245 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Ush1c
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247669,105,990 - 9,153,663 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247669,097,466 - 9,153,602 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2


Expression

RNA-SEQ Expression


Sequence


Ensembl Acc Id: ENSCLAT00000025109   ⟹   ENSCLAP00000024869
Type: CODING
Position:
Chinchilla AssemblyChrPosition (strand)Source
ChiLan1.0 EnsemblNW_00495541432,298,759 - 32,351,505 (-)Ensembl
Ensembl Acc Id: ENSCLAT00000025110   ⟹   ENSCLAP00000024870
Type: CODING
Position:
Chinchilla AssemblyChrPosition (strand)Source
ChiLan1.0 EnsemblNW_00495541432,303,465 - 32,340,145 (-)Ensembl
Ensembl Acc Id: ENSCLAT00000025111   ⟹   ENSCLAP00000024871
Type: CODING
Position:
Chinchilla AssemblyChrPosition (strand)Source
ChiLan1.0 EnsemblNW_00495541432,303,497 - 32,351,299 (-)Ensembl
Ensembl Acc Id: ENSCLAT00000025112   ⟹   ENSCLAP00000024872
Type: CODING
Position:
Chinchilla AssemblyChrPosition (strand)Source
ChiLan1.0 EnsemblNW_00495541432,303,497 - 32,351,299 (-)Ensembl
RefSeq Acc Id: XM_005380388   ⟹   XP_005380445
Type: CODING
Position:
Chinchilla AssemblyChrPosition (strand)Source
ChiLan1.0NW_00495541432,303,045 - 32,351,401 (-)NCBI
Sequence:
RefSeq Acc Id: XM_005380389   ⟹   XP_005380446
Type: CODING
Position:
Chinchilla AssemblyChrPosition (strand)Source
ChiLan1.0NW_00495541432,303,045 - 32,351,401 (-)NCBI
Sequence:
RefSeq Acc Id: XM_013512089   ⟹   XP_013367543
Type: CODING
Position:
Chinchilla AssemblyChrPosition (strand)Source
ChiLan1.0NW_00495541432,303,045 - 32,351,401 (-)NCBI
Sequence:
RefSeq Acc Id: XR_260217
Type: NON-CODING
Position:
Chinchilla AssemblyChrPosition (strand)Source
ChiLan1.0NW_00495541432,303,045 - 32,351,401 (-)NCBI
Sequence:
RefSeq Acc Id: XP_005380445   ⟸   XM_005380388
- Peptide Label: isoform X3
- UniProtKB: A0A8C2W4Q2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_005380446   ⟸   XM_005380389
- Peptide Label: isoform X2
- UniProtKB: A0A8C2W402 (UniProtKB/TrEMBL),   A0A8C2YUS7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_013367543   ⟸   XM_013512089
- Peptide Label: isoform X1
- UniProtKB: A0A8C2YUS7 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSCLAP00000024869   ⟸   ENSCLAT00000025109
Ensembl Acc Id: ENSCLAP00000024870   ⟸   ENSCLAT00000025110
Ensembl Acc Id: ENSCLAP00000024872   ⟸   ENSCLAT00000025112
Ensembl Acc Id: ENSCLAP00000024871   ⟸   ENSCLAT00000025111
Protein Domains
PDZ


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCLAG00000017070 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSCLAT00000025109 ENTREZGENE
  ENSCLAT00000025109.1 UniProtKB/TrEMBL
  ENSCLAT00000025110.1 UniProtKB/TrEMBL
  ENSCLAT00000025111 ENTREZGENE
  ENSCLAT00000025111.1 UniProtKB/TrEMBL
  ENSCLAT00000025112.1 UniProtKB/TrEMBL
Gene3D-CATH 1.20.1160.20 UniProtKB/TrEMBL
  2.30.42.10 UniProtKB/TrEMBL
InterPro Harmonin UniProtKB/TrEMBL
  PDZ UniProtKB/TrEMBL
  PDZ_sf UniProtKB/TrEMBL
  USH2_Complex_Protein UniProtKB/TrEMBL
NCBI Gene Ush1c ENTREZGENE
PANTHER PDZ DOMAIN CONTAINING WHIRLIN AND HARMONIN-RELATED UniProtKB/TrEMBL
  PTHR23116:SF36 UniProtKB/TrEMBL
Pfam PDZ UniProtKB/TrEMBL
  USH1C_N UniProtKB/TrEMBL
PROSITE PDZ UniProtKB/TrEMBL
SMART PDZ UniProtKB/TrEMBL
Superfamily-SCOP SSF50156 UniProtKB/TrEMBL
UniProt A0A8C2W402 ENTREZGENE, UniProtKB/TrEMBL
  A0A8C2W4Q2 ENTREZGENE, UniProtKB/TrEMBL
  A0A8C2YUS7 ENTREZGENE, UniProtKB/TrEMBL
  A0A8C2YUT4_CHILA UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-08-03 Ush1c  USH1 protein network component harmonin    Usher syndrome 1C  Symbol and/or name change 5135510 APPROVED
2015-08-25 Ush1c  Usher syndrome 1C    Usher syndrome 1C (autosomal recessive, severe)  Symbol and/or name change 5135510 APPROVED