XLOC_004499 (pde6c)


Basic Information

Item Value
gene id XLOC_004499
gene name pde6c
gene type coding
species zebrafish (Danio rerio)
category of species model fish

Chromosome Information

Item Value
chromosome id NC_007123.7
NCBI id CM002896.2
chromosome length 49182954
location 5129245 ~ 5154099 (+)
genome version GRCz11_2017_zebrafish_Genome

Sequence

>TCONS_00008979
GGACGATGAGCCTGTCTGAAGGAGGAGGCCACTGAGAGCTTCACTTTTCATCCCGACAGCCTACAAGTAATGAATCTGTGAGAGGACCAGGCAGAGAAACACACTTCAAACATGGCAGACAAGGATAGCGTGGAGAAGTACTTGGAGAATAACCCCCAGTTCGCCAAAGAGTATTTTGACAAGAAGGTGCGATGCGAGGTGATCGCCGCCGCGTTCGAGGAGAAGCTGGACATCAAGGATCCAGCTTCGTTCAAGGATGTCACGCAAGTGCAGGAAGCCGCCATCCTCTTTGACATGATCCAAGACATGCATTCACAGCCTGTCATGGAGAAGGCCATGCACAAGGTCCTGCAGAGGATATGTTTGCTGGTCAACGCCGACCGCTGCAGCTATTTTATATCTCGCGCCAGAAACGGCATCCCTGAGCTCGCCACATGTCTTTTCGATGTCACTCCTACGTCCAAATACGAGGCCAACCTGGTAAACCCGCAGTCTGAGATTGTGTTCCCCACTGACACTGGCATAGTTGGCCAAATAGTGACCACCAAAAAACCAGCCAATGTTCCAGATGTCAAACAGAATCCCAGGTTCAGTGATTTTGTGGACAAGCAGACGGGATACACCACTAAAAACATGATGGCCGCTCCACTCATGCAGGGAAAAGACCCACTCGGTGTGGTCATGGCAATAAACAAGGTCGGAGCAAACGAATTCTCCAAAGAAGATGAAGATGTATTCAGCAAGTACATCATATTTGCCACAGTCATCGCCCTGCAGCATTACACCAATTACATGTATAATGTGGAATCCAGAAGAAGCCAGGTTCTTCTGTGGTCTGCGAGCAAAGTGTTTGAAGAGCTGACGGACATCGAGCGTCAGTTTCACAAGGCTCTGTACACCGTCAGAACTTACCTTCAGTGCGAAAGGTACTCGTGCGGCCTGCTGGACATGACCAAAGAGAAGGAGTTCTACGACGAGTGGCCGATTAAACTGGGAGACGTGGAGCCGTATAAAGGCCCGAAGACTCCTGATGGCAGGGAGATCATCTTCTACAAGATCATTGATTATCTGCTGGAAGGCAAAGAAGAGATCAAAGTTATACCGAACCCTCCTGCAGACCACTGGGCACTGGTTAGTGGACTGCCCAGCTATGTTGCTGAAAACGGCTTTATCTGTAACATGATGAATGTTGCTGCTGATGAATACTTCACATTCCAGAAAGAAGCTGTGGACGAGACTGGCTTCGTGATCAAAAACGTTCTCTCCCTTCCCATTGTCAACAAGAAAGAAGAAATTGTCGGTGTGGCCACTTTCTTCAATCGAAAAGACGGCAAGCCATTCGAAGAGCAGGATGAACAGATTACTGAAGCTCTAACACAGTTCCTGGGATGGTCCGTACTGAACTGCGACACATATGACAAACTGAACCGGATGGAGTGGAGGAAAGAAATTGCAGAAGAAATGGTCATGTATCAGACCAAAGCCACTCCGGCTGAAGTCCAGCAGATTCTGAACACAAAGGAGAAGTTTGACCAGAACCCGGAAGACTGCGATCAGAAAGAAATGTACAAACTCTTGAGAGCCAACATTCCAGAGGCCAAAGATGTCGATCTGCTAGAATTTAGTTTCAGTGACTTCCCTCTGACTGAAACCGATCTCATCAAGTGCGGCATTCGCTGCTTCTTTGAACTGGGAGTGGTGGAGAAGTTCAAGGTGCCAGCAGAGGTCCTGACCAGATGGATGTACACGGTGCGTAAGGGCTACAGAGACATCACCTACCATAACTGGAGGCATGGCTTCAACGTGGGCCAGACCATGTTCTGTCTTCTGCAGACCGGAAAGCTGAGAAGATACTACACAGATCTTGATGCCTTCGCGATGGTAGCGGCTGCATTCTGTCATGATATTGACCACAGGGGTACCAACAATCTCTACCAGACAAAGAGCGCATCACCTCTGGCCAAGCTTCACGGCTCCTCCATCCTGGAAAGGCACCATCTTCAATACAGCAAGAATCTGATGGCTGAAGAGAACGTTAACATCTTTCAAAGTCTGCAGAAACGCCAGTTCGAGACGGTCCAGCATTTGCATGATGTCTGCATCATTGCGACTGACCTGGCTTTGTATTTCAAAAAAAGGACAATGTTCCAGAAGATCGTTGACGCCACCGAACCTATGACTAAGGAGGAGGAGATGGTCGCCCATGTGGCCAACAATCCCATCAGGAAGGAAATCATCATGGCAATGATGATGACCGGATGTGACTTGTCTGCCATTACCAAGCCATGGGAAGTCCAGAGCAAAGTGGCTCTCATGGTGGCAGCTGAATTCTGGGAACAGGGAGACTTGGAGAGGACTGTGCTAGACCAACAACCCATTCCCATGATGGACAGAAACAAATCAGATGAACTTCCGAAGATGCAGTGCGGTTTCATTGACTTTGTGTGCTCGTTCGTGTACAAGGAATTTTCTAGGTTCCACAAAGAAATCACTCCCATGTTTGATGGCTTGAACAACAACAGAGTCCACTGGAAGGAACTGGCCGATATTTACCAAGCAAAAATAGACGCTATAGCCAATGAGAAAAAGAGACTAGAAGAGGAGCAGGCTAAAAAGGGAGGTGAGGAAGGAGGAGAGGGAGGAAAGTCCAAAACCTGCACCATCTTTTAAACCACCAGAAATTGAAAGCCACAGAGGAGTCTGGGCCAGCTGGAAAACGCATAGAGGAAGCTGAAACATGCTCCTAGGATCACTACGTTTTCGCCAGCTTTCTCATTCTCTCCGTCTCATTTCCTCGGAATTACCTTCATCAAGTGAACATGTAGGCTTTGACCAGAAATGGAAGAACTGTACCTGTCAGATTCACTTTCTGATGGGGGCGCCAGAGCTAATCGTCACCACATGGACAATTTCATGCTTGCTCCTAATCGCTGTAACATCAACCTTCGCTGGAGGAAGCACCACATTTGCCACACAACGGTGGCCGAAACACTACACAAATGATTAATGCGCTGTAGTTCAGAGCTTACTTTGTGTTTGGCAGTTCAATGACAGCAAAAAACATTAAGAATTAGAGCAATATGCTGAATAACTTCCGGAACGGTTACTAATTTATTGGAAAAACGAATAAATAGCTTAAATCTTCAATGACTTCAGAATCACATTGTATTTAGCTTCTCTGTAAACGAATCATCGAAGCTTCCAGATCGATTTGTTGTTTGGCAAACgcacttaaaggtgcagtgtgcCATTTATGTGCCGCCAAAACAATTGCTATTCAATTATTCTACACTTCGATTAACTACGGTTAGGCCTGCTTGAATGGAGGCATTTCAACATCAAATGAAATGGCACACTTCACCTTGAAGTTACCTATATTTGAAGGCATTTCCATTGCTTTGTTTTGGGATGAAGGTTCAGCTCATTTGAACAAGAGTTTTGAGAAGCTGTGGCTCACGCTAACTCTTCAAAAGAGAAAACGGCACTCAATTTCTCCTAACTTGCGGTGTTAACGACTTGTTGCATTTGCAATTGTTTTTAGACTGCTGCGATACAGGATGTCTTTTCTACtgttttgttctttaaaaaaaagctgcGATACGGCTAATTCTGTGTCAAGAGCGTTCCAGAACATTTATGACcagatgttttttgttgtttaaccATTTAATGATAAGCATCACGCATAGTTTTCAACCATAATGTATTATCAAACGTATAAAATTGAGCGCACATAGAATATCAATTGATAATATAGAGGTATTTGCTTAAACCAAACGTTGATACTATTTTGAAGCGGTATTCTACGGAGGTCAGGGAATATTTAAATCCAGTGCATGTTATGCCGTGACAAGGCGAGAGGGAACGGTCAGTACTTGGAGATGTGTAAACCTATAAGGAGATTTGAAGTGAGTTTGATGGGGGGAGCAGCTCCTGAGATTCACTCTGTTTTAATCTTTAAATACCATGCTTATTTAAAGCAGACTACTGAAGCCTCTAGATATCACCCTTTTTAAGGTTAAAGTCTCTCTCTTTTTGTTGGGATGTTTAGAGAATCTGATGACAGCGGTGTTTGAACTAGTGAAAGAACTGTTTATTTCAGATAGCTGCATGCTGATATCCAAAATAGGTCATTCCTTGCTTAATCGCTGATTTGACCAAACACAAACGTGTATATATAAACAACCAATGTGAAGATTTAGCAAATATACATCAAATATTATGCAACATACGCTTGTTGGTAAATCAGTTAAGGCCTTTAATCCAATAACCAGGCCCACGGCTGTTTAAATAACTCCTCTGGAACTAAACGTAAATGTCAAACCCTCTAAATCCAGGTCAGCCAGAGGCCAAAAGTGAGTCAATCTCATCTCAGGTTTATGGTTTGCGCACATTGTTAGGCTCGTGAATAACTCCATGTACTGCATCATATGAAGTGAGCGTGCAATCCGATCCTCTTATTTACTGATTATGCATATAAGATACTGTAAAGGATGTCATGTGAACGAATAAACACATTGAAACGGA

Function

symbol description
pde6c Predicted to enable 3',5'-cyclic-nucleotide phosphodiesterase activity. Acts upstream of or within embryonic retina morphogenesis in camera-type eye; photoreceptor cell maintenance; and visual perception. Is expressed in head and visual system. Used to study retinal degeneration. Human ortholog(s) of this gene implicated in cone-rod dystrophy. Orthologous to human PDE6C (phosphodiesterase 6C).

GO:

id name namespace
GO:0045494 photoreceptor cell maintenance biological_process
GO:0007601 visual perception biological_process
GO:0007165 signal transduction biological_process
GO:0060059 embryonic retina morphogenesis in camera-type eye biological_process
GO:0046872 metal ion binding molecular_function
GO:0016787 hydrolase activity molecular_function
GO:0004114 3',5'-cyclic-nucleotide phosphodiesterase activity molecular_function
GO:0008081 phosphoric diester hydrolase activity molecular_function

KEGG:

id description
ko00230 Purine metabolism

ZFIN:

id description
ZDB-GENE-040426-1664 Predicted to enable 3',5'-cyclic-nucleotide phosphodiesterase activity. Acts upstream of or within embryonic retina morphogenesis in camera-type eye; photoreceptor cell maintenance; and visual perception. Is expressed in head and visual system. Used to study retinal degeneration. Human ortholog(s) of this gene implicated in cone-rod dystrophy. Orthologous to human PDE6C (phosphodiesterase 6C).

Ensembl:

ensembl_id ENSDARG00000100397

RNA

RNA id representative length rna type GC content exon number start site end site
TCONS_00008979 True 4527 mRNA 0.45 22 5129245 5154099

Neighbor

gene id symbol gene type direction distance location
XLOC_004498 cep55l coding upstream 15856 5102670 ~ 5113389 (+)
XLOC_004496 prrt2 coding upstream 33471 5081759 ~ 5095774 (+)
XLOC_004497 AL929469.3 coding upstream 39315 5089815 ~ 5089930 (+)
XLOC_004495 AL929469.1 coding upstream 67548 5061567 ~ 5061697 (+)
XLOC_004494 AL929469.2 coding upstream 71889 5057221 ~ 5057356 (+)
XLOC_004500 lgi1b coding downstream 35677 5189776 ~ 5204629 (+)
XLOC_004501 SLC35G1 coding downstream 55723 5209822 ~ 5224777 (+)
XLOC_004502 plce1 coding downstream 97548 5251647 ~ 5398578 (+)
XLOC_004503 drd6b coding downstream 304363 5458462 ~ 5460203 (+)
XLOC_004504 ace coding downstream 376148 5530247 ~ 5582060 (+)
XLOC_004493 AL929469.4 non-coding upstream 76667 5052443 ~ 5052578 (+)
XLOC_004492 AL929469.5 non-coding upstream 77548 5051562 ~ 5051697 (+)
XLOC_004512 NA non-coding downstream 990606 6144705 ~ 6152579 (+)
XLOC_004513 NA non-coding downstream 994908 6149007 ~ 6153121 (+)
XLOC_004514 NA non-coding downstream 1002864 6156963 ~ 6171928 (+)
XLOC_004515 NA non-coding downstream 1041071 6195170 ~ 6451609 (+)
XLOC_004517 CU184911.1 non-coding downstream 1554030 6708129 ~ 6708243 (+)

Expression


Co-expression Network

Homologous

species gene id symbol gene type chromosome NCBI id location
grasscarp (Ctenopharyngodon idella) CI01000047_03115498_03127047 PDE6C coding CI01000047 null 3115187 ~ 3128105 (-)