clrn1 (clrn1)


Basic Information

Item Value
gene id clrn1
gene name clrn1
gene type coding
species mexican tetra (Astyanax mexicanus)
category of species ornamental fish

Chromosome Information

Item Value
chromosome id NC_035898.1
NCBI id CM008301.1
chromosome length 34292151
location 25801597 ~ 25808492 (+)
genome version Astyanax_mexicanus-2.0_2017_mexican_tetra_Genome

Sequence

>XM_007236771.3
GCGGGGAAACTGAGAAACTGACCCGGGGCGCTGTAACTTTACCCGTGGAGGACATGATGCACCGCGGCCCGTATCGGTAAACAGCCAGCAGTGTGATCCGTGTATTATACTCGCTTTATTTTATACAGGCTGCTGCAGTGTGTACTGAGGGCATGAGGGCCTGTGTGTTATGGACAGATAGATAGTAGCTGTAGAGACAGgagctagtgtgtgtgtgtgtgggatgcGGTGTGTGTGAGCCGGTTTCCTGCTCGTTCCGACCGGGTGAAGATCATCATGCCCAGCCTGCAGAAGAAGGTGGTGTTCTCGGTCGGTGGAGCGCTGAGCTTCGCCGCTGTGCTGCTGGTGGCGGCGGCCATGGGGACCCGCTGGTGGGTGCAGGCCAGCGTGCTGTGCCAAACCGGCGCCCAGCTGGTGAACGCCACGGGCTCAGAGCTGCACAAATTCATGGGCACGGTGAGCTACGGGCTTTTCCACGGTCAGAGGCTGAAACAGTGCGGTCTGGGGGGAAGACCACTCTCCTTCTCATTTTTTCCTGACCTGGTGGACGTGATGCCGTCTAGTCTTCATGTAAGCGTGATATTCTTCTGTGCAGTGCTCATCGTCTTCTCTTCTGTATGCTGTGCCTTCTTCATGTTCAATGCCTTTGGCAATCCATATGAAACCCTGCATGGACCACTTGGCCTGTACTTGTGGAACATGATCAGCTGTCTGTGCAGCTGTATGGTCTTAATCCTCTACGCAGCAGAGGTCAAACTGCATCGTCTGTCTGAGATCATCGCTAACTACAAAGAGGGCAACTTTGTCTACAAGACAAGCAGCGAGAAGTTCGACCGCTCCTTCTGGTTCATATTCCTTGTCTTCCTTATTCACTGCCTTAACATCCTCCTGATCCGCCTGTCGGGGGTCCAGTTTCCTTTCCagggggccaaagagtcggacgCCACCACGGGTGCAGCAGATCTCATGTACTGACCAGTCCTATTGTTCACCAGCTCTGCCACCCGGACGCGACACTCTATCGTGGCTATTAGCCCTCCTCAATAGGAGTCTTGCATCTTGCAGCATCCGTTGTTGTGGTTTGTTTACCGATGAATAGGCGAGGCACATCTGAGCCTGCTAAGCTGCATCCTTTCACTTTCAGAAGAGGCACAGGCCGCAGAGATAGCGTGCTGGCTGGGTCTGTGAGAGATAATTCGTAGCTATCTCTCTGCAGGGAGGCTAGTGGAGGCACCCAGTCTTTCAGCCAGAACTCTGATTGCGTATTCTGTTCATTGCCAACGCAATTAAGACTGAGGACTTTAAATGAATTGttgaaatgtagaaatgttttaGTCAGATCTGTTTCTCCGGTAAGGAAACTACACTACATACTAAAAGGGCttaaaatggttctttaagtgatgctacagaaaaaaaactccttTGGGTACATAAAGAAACATGcttgaaatagagagagagaataaaaagaatACATTCTAAGATCCTTGAAGAACCATTACTTGATGTGAAGGTtgtttgtaaattaatatttaatatttttcttcatacCATGACTTGCCACGGGACAggaaatattgtgtattgtgtccTATAAATTTTCCATGTCCCTACAAAATGATGCACTGACCTGTATGATATTTGCATGGGGTCTTCTGCAttgagttgcttgtctgtttgttCCAAACCattcacaagaaaacacctaaatacttatacaggtgtgggcatttccaACCCATCCCCTAAGGTAGCACATGCTATTCAGTATAACTTTTGTCATGTCTGTACCCATTTTTATGTCAGCCACTGTTCTCAAATATGGACCTTAAATCCAGTTTTCAGTATTTCCTGGAAGTGAAGTGAAAGTTAAAGGAACCAATAATCACGAAGTCAAAAGTCTGTATTGATGGTTGAGGTTTGGAGACTGGTGCTCTGTAACATTCCTCATAGAACCATCTAATAGAAGCATATTTATTTTTCCGAGTGTGTATTCTTATTCatagtgtgtatatgtattcTGGAACACTATgtttaattggatttttttaactattaatCTTGGGTATATTCTTGTTTAGACACCCAACCACAAAGTGCCAAGGATCATGACTGTTATGAATATCAAATGTACTTCAAATAATGAATGCtgaattaatttttaatgattttgtaCCCAACTGAATAAGATATTtagtaataaacattttaactattttaagaattatataATTCTTAGATGTGAtcaagtaaaaaaatgtaaaatagttaaatagttGATTGAGGCGTAACTGTggttttgtaaaagaaaagcatggtcactgtattttgtgttagtTTTCTGCAACTGGCCTACCAGATGCATCTTCATGATGGATGTAATTAGATATTAATTGTACTTAGAGAATTTGTAATTAGATGTAATTGATGATTGATTTAGTTTGTCGTAACTAATTCCATCTATTTCACTCTATACCATTTACAACGCACAAGTAATCACAAGTAATTTTTGCAAAATTTAAAATGGAACTGAATTTATGCATTGTTGGGATGCACTGTATGTTATGGGAAGAGTAATCTGTGAACAGATTTGATGAACATGTATTAACTTGAGTAAGTGTTTTGAGATTTTTAGACATCTATTTTAGACAGGTGCCTTACTTTGAAAGCACACGTGACCTAAATCTGtgattttcaaataaaattacACCTTTTCTGTA
>XM_007236772.3
GCGGGGAAACTGAGAAACTGACCCGGGGCGCTGTAACTTTACCCGTGGAGGACATGATGCACCGCGGCCCGTATCGGTAAACAGCCAGCAGTGTGATCCGTGTATTATACTCGCTTTATTTTATACAGGCTGCTGCAGTGTGTACTGAGGGCATGAGGGCCTGTGTGTTATGGACAGATAGATAGTAGCTGTAGAGACAGgagctagtgtgtgtgtgtgtgggatgcGGTGTGTGTGAGCCGGTTTCCTGCTCGTTCCGACCGGGTGAAGATCATCATGCCCAGCCTGCAGAAGAAGGTGGTGTTCTCGGTCGGTGGAGCGCTGAGCTTCGCCGCTGTGCTGCTGGTGGCGGCGGCCATGGGGACCCGCTGGTGGGTGCAGGCCAGCGTGCTGTGCCAAACCGGCGCCCAGCTGGTGAACGCCACGGGCTCAGAGCTGCACAAATTCATGGGCACGGTGAGCTACGGGCTTTTCCACGGTCAGAGGCTGAAACAGTGCGGTCTGGGGGGAAGACCACTCTCCTTCTCATTGCTCATCGTCTTCTCTTCTGTATGCTGTGCCTTCTTCATGTTCAATGCCTTTGGCAATCCATATGAAACCCTGCATGGACCACTTGGCCTGTACTTGTGGAACATGATCAGCTGTCTGTGCAGCTGTATGGTCTTAATCCTCTACGCAGCAGAGGTCAAACTGCATCGTCTGTCTGAGATCATCGCTAACTACAAAGAGGGCAACTTTGTCTACAAGACAAGCAGCGAGAAGTTCGACCGCTCCTTCTGGTTCATATTCCTTGTCTTCCTTATTCACTGCCTTAACATCCTCCTGATCCGCCTGTCGGGGGTCCAGTTTCCTTTCCagggggccaaagagtcggacgCCACCACGGGTGCAGCAGATCTCATGTACTGACCAGTCCTATTGTTCACCAGCTCTGCCACCCGGACGCGACACTCTATCGTGGCTATTAGCCCTCCTCAATAGGAGTCTTGCATCTTGCAGCATCCGTTGTTGTGGTTTGTTTACCGATGAATAGGCGAGGCACATCTGAGCCTGCTAAGCTGCATCCTTTCACTTTCAGAAGAGGC

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).

NR:

description
clarin-1-like

GO: NA

KEGG:

id description
K23841 CLRN; clarin

RNA

RNA id representative length rna type GC content exon number start site end site
XM_007236771.3 True 2723 mRNA 0.42 3 25801597 25808492
XM_007236772.3 False 1085 mRNA 0.55 3 25801597 25806920

Neighbor

gene id symbol gene type direction distance location
LOC103023233 NA coding upstream 18550 25774795 ~ 25783047 (+)
LOC103022923 LOC103022923,LOC108426899 coding upstream 35812 25748629 ~ 25765785 (+)
LOC103031763 NA coding upstream 59934 25732877 ~ 25741663 (+)
rnf168 NA coding upstream 71928 25722719 ~ 25729669 (+)
LOC103022406 ano7 coding upstream 79930 25704994 ~ 25721667 (+)
mindy4b fam188b2,LOC107598659 coding downstream 8251 25816743 ~ 25829067 (+)
dscaml1 dscaml1,LOC107752281 coding downstream 689060 26497552 ~ 26675015 (+)
LOC103037665 NA coding downstream 893067 26701559 ~ 26708772 (+)
pgam5 pgam5 coding downstream 1150892 26959384 ~ 26964690 (+)
LOC107197223 NA coding downstream 1251653 27060145 ~ 27103854 (+)
G13612 NA non-coding upstream 25987 25727307 ~ 25775610 (+)
G13607 NA non-coding upstream 97647 25699497 ~ 25703950 (+)
G13589 NA non-coding upstream 157234 25644013 ~ 25644363 (+)
G13565 NA non-coding upstream 293148 25508205 ~ 25508449 (+)
G13545 NA non-coding upstream 398479 25401020 ~ 25403118 (+)
LOC111194239 NA non-coding downstream 99249 25907741 ~ 25908666 (+)
G13733 nars2,LOC107670421,LOC107699825 non-coding downstream 195154 26003646 ~ 26006679 (+)
G13822 NA non-coding downstream 640775 26449267 ~ 26449469 (+)
G13823 NA non-coding downstream 641029 26449521 ~ 26457756 (+)
G13828 NA non-coding downstream 649502 26457994 ~ 26468572 (+)
LOC103023549 gpr171 other upstream 6513 25788584 ~ 25795084 (+)
mfrp mfrp other upstream 128361 25660898 ~ 25673236 (+)
LOC103045399 LOC108426937,LOC108277812 other upstream 158854 25561633 ~ 25642743 (+)
LOC103040166 LOC103040166,LOC108426893 other upstream 462162 25246996 ~ 25339435 (+)
G13445 spcs2,LOC107677086 other upstream 745494 25052513 ~ 25056103 (+)
G14047 NA other downstream 1201056 27009548 ~ 27040529 (+)
LOC103031366 LOC105899914 other downstream 2241637 28050129 ~ 28077818 (+)
rbfox1 rbfox1 other downstream 2303554 28112046 ~ 28607089 (+)
G14444 NA other downstream 3320575 29129067 ~ 29129373 (+)
G14480 NA other downstream 3586668 29395160 ~ 29398166 (+)

Expression


Co-expression Network