XLOC_020773 (rx1)


Basic Information

Item Value
gene id XLOC_020773
gene name rx1
gene type coding
species zebrafish (Danio rerio)
category of species model fish

Chromosome Information

Item Value
chromosome id NC_007133.7
NCBI id CM002906.2
chromosome length 39133080
location 4997784 ~ 5006801 (-)
genome version GRCz11_2017_zebrafish_Genome

Sequence

>TCONS_00040963
GTAAAACAGGCCCGTTTTGGATTCCTCCAACAGACATCAAGTTGGTTTTATCAATCGGAAGGCCTTATCCCAGCAATCGAATGCATTTGTCACTGGACACCATGAACATGGTGGATGACAGCTGTCTTTCGCCCAGTAATTTCCATGATATGGTCAAAGCTGGGGGCGCAGTGGTTGGCACTCGTGTCCACAGCATAGATGTGATCCTGGGCTTCAACAAGGACCAGGATTCGTTGCTCAACCCTGGAGCCAATGCTGTAGCACACAAAGTTGGAGGGGAGAGTCTTGGAGAACCAGGAAAGCTGGACCAACGGGTTCAACCTTACGGACATCTGCCACCCCTTAGGGATGGATCGGAGCAACCTACATTTCACGATGCCGACATGTTCTCCAACAAATGTGATGGGGACCTGGGGGACCTGCGGAAAGCCATCGAGAGTGACAGCAAGTCTCCGGATTCAGCCGATGGGGAGCAGCCCAAAAAAAAGCACCGCCGCAACCGCACCACCTTCACCACATACCAGCTCCATGAGCTTGAGCGAGCCTTCGAGAAGTCACACTACCCTGACGTTTACAGTCGTGAAGAGCTAGCCATGAAAGTCAATCTTCCTGAAGTTCGAGTGCAGGTTTGGTTCCAGAATCGCAGAGCCAAATGGAGGCGTCAGGAAAAAATAGACGCGAGCACCATGAAGCTCCATGACTCCCCCATGCTCTCCTTCAACCGCCCGTCCATGCACCCCACCGTGGGGCCCATGAACAACTCGCTACCCCTCGACCCTTGGCTGCCCTCGCCTCTATCCAGTGCCACTCCAGTGCACAGCATCCCAGGGTTCATGGGTCCTACACAAGGACTGCAAACGGGCTATCCCGGTCACAGTTTCCTCAGCCCACCCCAACCCATGGCACAAAGCATGCAGCCCATGGCGCCACCTCCATACCAATGCCCTCCTCCCTTCACCGACAAATACCCTCTGGAGGATGTAGATCAACGTAGTTCAAGCATTGCCGCACTGAGGATGAAAGCCAAGGAGCATATCCAGTCTATGGACAAAACCTGGCAACCCATGTGCTAAGACGTCTCTCTTTTGACTGTAAGCCTTTGTGTTTCTGTTGTCAAATCAAGAACTTGCATCGGACGGTTCACTTGTTCTCTGGGTCAGAATATTTTGGGGCAGCAAAAACAAGTTGTGCCATTATATTTATTCTTTCTGCAACTGGATGCAAGCTTCCGATGAAAACTGTTGAGTCTTGAGGATGAAACATTTACAAGCAATTCTTCATATGTCTTTTACTGCGTTATCATTTTCAGTGGTGAGTTTGGAATATCTCAAGCGTGTCCCTGGAGAGAATTTTCAAAACAACTTTAGAACTTTACACTGTGTTTCGTTTTAGTTTACACGGCGACCCTTCAAGCTTCAAGAGTTGCCGGTTTAAAATTTTACATATTAAACTCTGTATTTCAAATCCCATAGATAGGACTTTACTCCTAGGAGCACAACAATTGCAATCCCACATGTAGGACCATACTACTCAAAGGGTTAAACAATTTCCGAGTGGTACCAGAGTGACTGAAATGTGAATATGAGGGTGTGTATGGCATCACACGACCTCTGTCTACAAATTCACACTTCTTCCCGAAGGCCTGCTCCTGATGTTTTGGGTTGACATACAATATAAATATGGTCATTGGTTGAAAAAAAAGGACCTCTAGGCAGCAGATTTCATGAGCAATCCCTCGGCATGGACATGGGACAGAAACGATTAGTCTGGTGGAGAAGTTTGTACGCCTCAGTGTGCATTAGAGGCGAATATTTTTGGCAGATCCATCTTCTGTACGTGCGAAGGAGCAGAAGGGGAAACTATCAGCCCCCACCCCACAATGACTTTCCCTTTGTTTAGACCAGTTGATCCAAATCGGAACTTTTTGTTTCAACTTCTTATAGGGATTGATGGTCAGAGAGTGTCACTCTAAGACACCAATCAAAATGGATGATAGATTATATTAAACATCGGCGCCGTGCTTTAGTGGCCTTTTGGATCACTAAGAGAATATTTTGCAATCAAAACAGACCGTTTCATTGTCCACAAACACGCAAGTGGGATTTGCTGCTTATTTTTTGAAAGGAAACTCACTCAGTTCATGTTGCCAGAGTTCTgtagcaaaataaaatacatatagcTGTGTTTGACTAATAATGGTTCGGACCTTTAGATACGATTTGAGGGTGTATTAAACTTTTGAGATGGTTGAATTGTTGAACAAACTATGCTTACTAATGATTGTCTTAGTTTTGTACGGATGTTGAGAACGAGAGTTTATAGATGTTATGATTTTATACAGTTGATCAAACTGTacatttcagttatttttcatttaatgtcGTTTTACACAGTTCTGATATTGAGACCTTTGGGCCATACATTAATTTACAAACTGCATCTATGATGTTTAGGTAATTTGCACAGTTTGAACAACTGAAAAGCCAAAGTAAGACAGCAATATGACAATCACGGGCAAAAAATATGCGTATATGATCTTATTtttgtcgaaaaaaaaaaaaaagaatgtggtTTTTATGTTTGTAATGTGTCCTAGACGTTTTCACAGTTgactttaaaacaaaatgttcttaaaaataaacaaatctagtTTCTCAGAGCTTGGCTGTGGACTCCTCCATTCCTGAAAATGCTGTTCGGAGGTCTGTATGTGCGGCTGAACTATAGCAGAGATTGTCTATTTGATCGGCCCTTCTGTCTCTGTTTCTCTGACTGGTGGCGCGGAGCCAGCCCGTTAGGAAGATGAGGTTCCAGTCAATCAGACCGGCCCAGGAGGGGGTTCTGGCCCTGGGGGCCGCTGTTCCCTAATTGCCTCCTGACGCTGCTGTTCAGGCACATGTTCAGAGGGCCTGGTGCTCTGTTGTATTCATGATGTGTGAGCAATGCTCTCGGACAGATGGGACACTGCAGGGGCCATCTGGGGCCCccataaaaacatgtgctgggaaAAGAGCAAAGGGTGTGAACATGGTTCTTTCCTGTTGCACAGTTTAACATGATCTTCACAACATTCTTATGTTGGTCCTgatttttacattcatatttcatATGTCAATTCAGGAGAGAAATGCAGTCAAAAGCACTCTGACCAACTGCACAAGAAAGTGCTTAAACATTCCCAATGCCTTTGCTAATGGATagcaacatttattaattttcttgtcttttcttagtccctttattaatccggggtcgccacagaggaatgaaccgccaacttatccagcatgtttttacgcagcggatgcccttccagccgcaacccatccctgtgaaacatctacacacatacacacacatacactacggacaatttggcctttggactgtgggggaaaccggagcacctggaggaaacccacgcaaacgcagggagaacatgcaaactctgcacagaaatgccaactgagccgaggttcgaaccagtgacccagcaaacCTTCTTGCCTGCTTTGCCTGGATAGCAACAAcatggcaaaaacaaataacctaGAACTGTTGAGCACAACACCCAAGGATACACTCTTTAAAAAGAGATTCCAAAAATGGGGTTCTTGCACTGAAGGAACCAGTTTGGTTCCTCAAAGAATCTTTTCCTCAAAGTTACTCAAAGAGACATTTGTGAAGaacatgttttaataaatctAGCGAACACTTTTCACCGTAACGATCCTTTTCAAGGGTTTTTCCTGaaacaatgtcaataaagaatGTAAATCAACTTATTGGCAACCACCAACAACCTAATATCCCATATTATTTCTGCTAACACATATCAACATCCTCCTAACTGGATAGCAATGAGCTATATGTTTAAGGGTAAATTTGTATGACACCCTTTTAGGAAGCTAAAAACAGGTACCAAAGTGCAAGTTTTTGAAAGCAGTACCATTACTTAATACTTATTAGCCACGTGTGTATTATGTTCAGCCTATAGGAGTATGTGTTCAATTTATTGACAACCAAAAACAGGCAAATGTGGCATTTCTTTGCCAAGTGATGTCTCCACCTACTGGCCTAACATGCATAATGTAGTGCTTTGGCCATTTTTGTAAATCTTTGTTAATTGgg
>TCONS_00040964
cacacacacaccagcagtcTGTCCAGCGGAATCCACTGGAGAACTTCTTCTGCGCGACTGTATATGTTTTCATGTTTAAAGTGAGAGCGGTGGAGGTCAGTCGGGAGCGTACAGTAGCAGACGGAGGCGTGCTCAACACCCGCATGTGACCCATTGCTTAGGGAGAAACAGGTGGATGCAGGTCAGATTGGAGACGGAGAGCAAACGGAGCATCTCCTGCCAGAGGTAAAACAGGCCCGTTTTGGATTCCTCCAACAGACATCAAGTTGGTTTTATCAATCGGAAGGCCTTATCCCAGCAATCGAATGCATTTGTCACTGGACACCATGAACATGGTGGATGACAGCTGTCTTTCGCCCAGTAATTTCCATGATATGGTCAAAGCTGGGGGCGCAGTGGTTGGCACTCGTGTCCACAGCATAGATGTGATCCTGGGCTTCAACAAGGACCAGGATTCGTTGCTCAACCCTGGAGCCAATGCTGTAGCACACAAAGTTGGAGGGGAGAGTCTTGGAGAACCAGGAAAGCTGGACCAACGGGTTCAACCTTACGGACATCTGCCACCCCTTAGGGATGGATCGGAGCAACCTACATTTCACGATGCCGACATGTTCTCCAACAAATGTGATGGGGACCTGGGGGACCTGCGGAAAGCCATCGAGAGTGACAGCAAGTCTCCGGATTCAGCCGATGGGGAGCAGCCCAAAAAAAAGCACCGCCGCAACCGCACCACCTTCACCACATACCAGCTCCATGAGCTTGAGCGAGCCTTCGAGAAGTCACACTACCCTGACGTTTACAGTCGTGAAGAGCTAGCCATGAAAGTCAATCTTCCTGAAGTTCGAGTGCAGGTTTGGTTCCAGAATCGCAGAGCCAAATGGAGGCGTCAGGAAAAAATAGACGCGAGCACCATGAAGCTCCATGACTCCCCCATGCTCTCCTTCAACCGCCCGTCCATGCACCCCACCGTGGGGCCCATGAACAACTCGCTACCCCTCGACCCTTGGCTGCCCTCGCCTCTATCCAGTGCCACTCCAGTGCACAGCATCCCAGGGTTCATGGGTCCTACACAAGGACTGCAAACGGGCTATCCCGGTCACAGTTTCCTCAGCCCACCCCAACCCATGGCACAAAGCATGCAGCCCATGGCGCCACCTCCATACCAATGCCCTCCTCCCTTCACCGACAAATACCCTCTGGAGGATGTAGATCAACGTAGTTCAAGCATTGCCGCACTGAGGATGAAAGCCAAGGAGCATATCCAGTCTATGGACAAAACCTGGCAACCCATGTGCTAAGACGTCTCTCTTTTGACTGTAAGCCTTTGTGTTTCTGTTGTCAAATCAAGAACTTGCATCGGACGGTTCACTTGTTCTCTGGGTCAGAATATTTTGGGGCAGCAAAAACAAGTTGTGCCATTATATTTATTCTTTCTGCAACTGGATGCAAGCTTCCGATGAAAACTGTTGAGTCTTGAGGATGAAACATTTACAAGCAATTCTTCATATGTCTTTTACTGCGTTATCATTTTCAGTGGTGAGTTTGGAATATCTCAAGCGTGTCCCTGGAGAGAATTTTCAAAACAACTTTAGAACTTTACACTGTGTTTCGTTTTAGTTTACACGGCGACCCTTCAAGCTTCAAGAGTTGCCGGTTTAAAATTTTACATATTAAACTCTGTATTTCAAATCCCATAGATAGGACTTTACTCCTAGGAGCACAACAATTGCAATCCCACATGTAGGACCATACTACTCAAAGGGTTAAACAATTTCCGAGTGGTACCAGAGTGACTGAAATGTGAATATGAGGGTGTGTATGGCATCACACGACCTCTGTCTACAAATTCACACTTCTTCCCGAAGGCCTGCTCCTGATGTTTTGGGTTGACATACAATATAAATATGGTCATTGGTTGAAAAAAAAGGACCTCTAGGCAGCAGATTTCATGAGCAATCCCTCGGCATGGACATGGGACAGAAACGATTAGTCTGGTGGAGAAGTTTGTACGCCTCAGTGTGCATTAGAGGCGAATATTTTTGGCAGATCCATCTTCTGTACGTGCGAAGGAGCAGAAGGGGAAACTATCAGCCCCCACCCCACAATGACTTTCCCTTTGTTTAGACCAGTTGATCCAAATCGGAACTTTTTGTTTCAACTTCTTATAGGGATTGATGGTCAGAGAGTGTCACTCTAAGACACCAATCAAAATGGATGATAGATTATATTAAACATCGGCGCCGTGCTTTAGTGGCCTTTTGGATCACTAAGAGAATATTTTGCAATCAAAACAGACCGTTTCATTGTCCACAAACACGCAAGTGGGATTTGCTGCTTATTTTTTGAAAGGAAACTCACTCAGTTCATGTTGCCAGAGTTCTgtagcaaaataaaatacatatagcTGTGTTTGACTAATAATGGTTCGGACCTTTAGATACGATTTGAGGGTGTATTAAACTTTTGAGATGGTTGAATTGTTGAACAAACTATGCTTACTAATGATTGTCTTAGTTTTGTACGGATGTTGAGAACGAGAGTTTATAGATGTTATGATTTTATACAGTTGATCAAACTGTacatttcagttatttttcatttaatgtcGTTTTACACAGTTCTGATATTGAGACCTTTGGGCCATACATTAATTTACAAACTGCATCTATGATGTTTAGGTAATTTGCACAGTTTGAACAACTGAAAAGCCAAAGTAAGACAGCAATATGACAATCACGGGCAAAAAATATGCGTATATGATCTTATTtttgtcgaaaaaaaaaaaaaagaatgtggtTTTTATGTTTGTAATGTGTCCTAGACGTTTTCACAGTTgactttaaaacaaaatgttcttaaaaataaacaaatctagtTTCTCAGA
>TCONS_00040965
ATGTTTAAAGTGAGAGCGGTGGAGGTCAGTCGGGAGCGTACAGTAGCAGACGGAGGCGTGCTCAACACCCGCATGTGACCCATTGCTTAGGGAGAAACAGGTGGATGCAGGTCAGATTGGAGACGGAGAGCAAACGGAGCATCTCCTGCCAGAGGTAAAACAGGCCCGTTTTGGATTCCTCCAACAGACATCAAGTTGGTTTTATCAATCGGAAGGCCTTATCCCAGCAATCGAATGCATTTGTCACTGGACACCATGAACATGGTGGATGACAGCTGTCTTTCGCCCAGTAATTTCCATGATATGGTCAAAGCTGGGGGCGCAGTGGTTGGCACTCGTGTCCACAGCATAGATGTGATCCTGGGCTTCAACAAGGACCAGGATTCGTTGCTCAACCCTGGAGCCAATGCTGTAGCACACAAAGTTGGAGGGGAGAGTCTTGGAGAACCAGGAAAGCTGGACCAACGGGTTCAACCTTACGGACATCTGCCACCCCTTAGGGATGGATCGGAGCAACCTACATTTCACGGTAAGTCCTTCATGGAAGTCTTGTTGAGATGTAAGTTGTGTTCACTGCATAAAGTTATTGCTTAGCTAACGTTTTGGGATGGAAACACACAGTTGCTAAAATCCAGGGACTGCACAAACATTTAAGGTAGGTTGCCAAGATGTCCCTGTTTTCCATGGGTCATGGTAATCTTGTCTCCAATTAGAGCCATTTTGATAAGAAAAATGTTAATCTAAAAATGTGTATTGTCCCCATTTTTGAAACTATTATACAGTAATAACAGCAAAAACACAGGAATTACTTCACCTGGAAAGTTAAAATGTGAAGTTATTGGTAATGTTACAAAAAATTACCAAGTTTTACAGAATatttaaaaagggcctgttcacatgTGATCTCTTCACAGCAATGTACTAGTATTTTTCTAAAA

Function

symbol description
rx1 Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Acts upstream of or within camera-type eye photoreceptor cell differentiation and retina layer formation. Predicted to be located in nucleus. Is expressed in eye; optic cup; optic primordium; and optic vesicle. Human ortholog(s) of this gene implicated in isolated microphthalmia 3. Orthologous to human RAX (retina and anterior neural fold homeobox).

GO:

id name namespace
GO:0006355 regulation of transcription, DNA-templated biological_process
GO:0003407 neural retina development biological_process
GO:0007275 multicellular organism development biological_process
GO:0060219 camera-type eye photoreceptor cell differentiation biological_process
GO:0010842 retina layer formation biological_process
GO:0005634 nucleus cellular_component
GO:0043565 sequence-specific DNA binding molecular_function
GO:0003677 DNA binding molecular_function

KEGG: NA

ZFIN:

id description
ZDB-GENE-990415-236 Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Acts upstream of or within camera-type eye photoreceptor cell differentiation and retina layer formation. Predicted to be located in nucleus. Is expressed in eye; optic cup; optic primordium; and optic vesicle. Human ortholog(s) of this gene implicated in isolated microphthalmia 3. Orthologous to human RAX (retina and anterior neural fold homeobox).

Ensembl:

ensembl_id ENSDARG00000071684

RNA

RNA id representative length rna type GC content exon number start site end site
TCONS_00040963 False 4131 mRNA 0.44 3 4997784 5006119
TCONS_00040964 False 2884 mRNA 0.45 4 4999256 5006801
TCONS_00040965 True 938 lncRNA 0.44 2 5005336 5006730

Neighbor

gene id symbol gene type direction distance location
XLOC_020772 cherp coding downstream 7739 4962370 ~ 4990045 (-)
XLOC_020771 pku300 coding downstream 52989 4939559 ~ 4944795 (-)
XLOC_020770 si:ch73-256j6.2 coding downstream 66721 4926777 ~ 4931063 (-)
XLOC_020769 si:ch73-256j6.3 coding downstream 84753 4908913 ~ 4913031 (-)
XLOC_020768 si:ch73-256j6.4 coding downstream 104847 4884980 ~ 4892937 (-)
XLOC_020774 matk coding upstream 29378 5036179 ~ 5054773 (-)
XLOC_020775 zfr2 coding upstream 49487 5056288 ~ 5099824 (-)
XLOC_020776 CR936300.2 coding upstream 117113 5123914 ~ 5163133 (-)
XLOC_020777 CR936300.1 coding upstream 133729 5140530 ~ 5145022 (-)
XLOC_020778 tnfaip8l1 coding upstream 146660 5153461 ~ 5171829 (-)
XLOC_020765 NA non-coding downstream 143969 4853062 ~ 4853815 (-)
XLOC_020756 NA non-coding downstream 262447 4733007 ~ 4735337 (-)
XLOC_020752 CU074310.1 non-coding downstream 684666 4311803 ~ 4313118 (-)
XLOC_020750 NA non-coding downstream 1111100 3883607 ~ 3886684 (-)
XLOC_020749 NA non-coding downstream 1256500 3740586 ~ 3741284 (-)
XLOC_020780 NA non-coding upstream 260722 5267523 ~ 5274962 (-)
XLOC_020781 NA non-coding upstream 306170 5312971 ~ 5315589 (-)
XLOC_020784 NA non-coding upstream 446442 5453243 ~ 5463115 (-)
XLOC_020788 NA non-coding upstream 617572 5624373 ~ 5631081 (-)

Expression


Co-expression Network