XLOC_008959 (clrn1)


Basic Information

Item Value
gene id XLOC_008959
gene name clrn1
gene type coding
species zebrafish (Danio rerio)
category of species model fish

Chromosome Information

Item Value
chromosome id NC_007126.7
NCBI id CM002899.2
chromosome length 48040578
location 3947696 ~ 3956906 (-)
genome version GRCz11_2017_zebrafish_Genome

Sequence

>TCONS_00017677
TGGGATCCAACTTTCCTCTGACAGCATGTGTTACATATCATTAGAGACCATTTTATAGCGTTCATATATTCAGGCGTGCAAAGAAACCCACAGCATGTTGGATTGCATGAAGATTGTCAGTGCGCGTCTTAGTTTGGATTTCCACTGATGAGGCTGTGCGCGTCGCCGTGTCCAAACACAATGCCTAACCGTCAAAAGCAAGTTATATTCTCCATCGCCGGGGTGCTTTGTTTTGGTTGTGTTTTAGTCGTGGCGGCTGCAATGGGCACTCAGTTTTGGGTTCAAGCGGCTGTTTTGTGTAAAACAGGAGCTCAAATTGTTAACGCGTCCGGGGCAGAGCTGGGTAAATTCATCGGAAAGGCAAACTACGGACTTTTTCACGGACATGGGATGAAACAATGTGGTCTGGGAGACAGACCCTTTTATTTTTCATTTTTTCCTGACCTGATGGATGTGGTTCCAGCCAGTCTTCACGTGAGCGTGATCTTCTTCTGCTCGGTGCTCATCGTCTTCTCCTCGGTGTGCTGTGGATTCTTCTTTTACAATGCTTTCGGGAGCCCATATGAGACGCTGCATGGACCCCAGGGCCTTTACCTCTGGAACATGATCAGCTCTTTCTGCGCCTGCTTGGTCCTCATTTTGTTCTCCTCTGAGGTCAAGCTGCACCACCTCACTGAGATCATCTTCAACTTCAACGAGGGCAGCTTCGTCTACAAGACTCACAGCGAGTGCTACGACAGGTCCTTCTGGCTCATCTTCCTCACCTTCCTCTTGCACGGCCTCAACGTCCTGCTCATCCGCCTGGCCGGGATCCAGTTCCCCTTTCAACAGGCCAAAGAGTCCGACGCCAGCACCGGAGCTGCAGATCTCATGTACTGAGCGGCTCTTTTCTTTTGTTCGTCTTCCTCCCCTGCACACGACATCCACCCGCATCGAGGAGCGCTTCTCAATAGGAGTCTTCTGGACGCCAGCATCCGCTTTGTTTACAGCGGAAAGTCAAGGCACATTTGAGCCTCTTAAGCCATTGAGAGCACGTGGTGGTGTTGAGCCTGGAGATGCTCGTGTGTCTGGAGGGAAGAACATTCAGTCTGTCAATCACTGAAACAATTAACGCTCACTGTTTCGAGCGGCTGATGAAAACAGCCTGTAGTTTCCAGTCTGCATGGGGACATCACAGTTTCCTCTGCTCGCCGAGCTTTTATTCGCACAAAAGGGATGCGACAATTGGCGATTCTCTGCGCTGACAACAAAAAGTATTTTGACCCTTAAGCCACACTTAAATATGTATGAATGTCCGCATTAGATAAGCTGACCCACCAAGCAGttttgtttaatagatgtctaaggccatgtccacacatacacaggcatTTTATAAAATGGATTTTCCCtgctttcatttaaataaaaaaaaatgtctattc

Function

symbol description
clrn1 Acts upstream of or within several processes, including plasma membrane bounded cell projection organization; sensory perception of sound; and synaptic vesicle recycling via endosome. Located in ciliary transition zone and stereocilium bundle. Is expressed in auditory epithelial support cell; brain; receptor cell (sensu Animalia); and sensory system. Used to study Usher syndrome. Human ortholog(s) of this gene implicated in Usher syndrome type 3A and retinitis pigmentosa 61. Orthologous to human CLRN1 (clarin 1).

GO:

id name namespace
GO:0060088 auditory receptor cell stereocilium organization biological_process
GO:0050957 equilibrioception biological_process
GO:0007605 sensory perception of sound biological_process
GO:0036466 synaptic vesicle recycling via endosome biological_process
GO:0035418 protein localization to synapse biological_process
GO:0060271 cilium assembly biological_process
GO:0050808 synapse organization biological_process
GO:0008104 protein localization biological_process
GO:0035869 ciliary transition zone cellular_component
GO:0032421 stereocilium bundle cellular_component
GO:0016020 membrane cellular_component
GO:0016021 integral component of membrane cellular_component
GO:0003674 molecular_function molecular_function

KEGG: NA

ZFIN:

id description
ZDB-GENE-040718-420 Acts upstream of or within several processes, including plasma membrane bounded cell projection organization; sensory perception of sound; and synaptic vesicle recycling via endosome. Located in ciliary transition zone and stereocilium bundle. Is expressed in auditory epithelial support cell; brain; receptor cell (sensu Animalia); and sensory system. Used to study Usher syndrome. Human ortholog(s) of this gene implicated in Usher syndrome type 3A and retinitis pigmentosa 61. Orthologous to human CLRN1 (clarin 1).

Ensembl:

ensembl_id ENSDARG00000102890

RNA

RNA id representative length rna type GC content exon number start site end site
TCONS_00017677 True 1424 mRNA 0.48 3 3947696 3956906

Neighbor

gene id symbol gene type direction distance location
XLOC_008958 mindy4b coding downstream 7025 3926095 ~ 3940671 (-)
XLOC_008957 NA coding downstream 186739 3754566 ~ 3760957 (-)
XLOC_008956 lpar6a coding downstream 210923 3656212 ~ 3736773 (-)
XLOC_008955 cog6 coding downstream 412991 3454529 ~ 3534705 (-)
XLOC_008954 slc25a15a coding downstream 665476 3255054 ~ 3282220 (-)
XLOC_008960 gpr171 coding upstream 970 3957876 ~ 3963649 (-)
XLOC_008961 si:ch73-309g22.1 coding upstream 13891 3970797 ~ 3976035 (-)
XLOC_008962 CR626884.4 coding upstream 52666 4009572 ~ 4011013 (-)
XLOC_008963 CR626884.6 coding upstream 61456 4018362 ~ 4027367 (-)
XLOC_008964 P2RY14 coding upstream 79803 4036709 ~ 4037626 (-)
XLOC_008952 NA non-coding downstream 785237 3160438 ~ 3162459 (-)
XLOC_008951 NA non-coding downstream 831434 3115337 ~ 3116262 (-)
XLOC_008946 CABZ01086029.1 non-coding downstream 1016675 2918257 ~ 2931021 (-)
XLOC_008942 NA non-coding downstream 1131554 2813516 ~ 2816142 (-)
XLOC_008970 NA non-coding upstream 206672 4163578 ~ 4174873 (-)
XLOC_008973 CU467614.1 non-coding upstream 408252 4365158 ~ 4365272 (-)
XLOC_008997 FO704791.1 non-coding upstream 1426156 5383062 ~ 5383180 (-)
XLOC_009008 NA non-coding upstream 1941504 5898410 ~ 5901982 (-)
XLOC_009014 NA non-coding upstream 3011475 6968381 ~ 6976921 (-)

Expression


Co-expression Network

Homologous

species gene id symbol gene type chromosome NCBI id location