XLOC_012026 (vrk1)


Basic Information

Item Value
gene id XLOC_012026
gene name vrk1
gene type coding
species zebrafish (Danio rerio)
category of species model fish

Chromosome Information

Item Value
chromosome id NC_007128.7
NCBI id CM002901.2
chromosome length 53461100
location 18773961 ~ 18797245 (-)
genome version GRCz11_2017_zebrafish_Genome

Sequence

>TCONS_00023732
TGCTCTAGGCAAGTGCATTGACCACTGCTCTTCCATCTTTTCCATCCCtgtgtttgtgtctttatttttgacTGGAAGACTCCCAAGCGAAAGAAAGCAGAGGAAAAAGGCCAGTCTGCTGACGAAACCGATAGCACCCCAGCAAAGAAGAGGCGAGCTCCTCAGAAGAAGGAAGTGAATGGGGCTAAAAAGACAGCAAGTCCTGCAAAGCGTCCAGTGAAGAAAGAAGCTCAGGCCTCCTCTGAGCCAGCGGTGAAGAAAAGCCGAGGAAGGCCTAAGAAGAACTCTTAATCCTTTTTGCACTCCAGTTCAAGTCGTTTTCTTTTTGTATCTTTTAAATTGTCTGGTCTGTATTTGTTCTCTGTGGTTGAATTTTCTTAAACTTTAGCAGGGTGTTGGGCACACTCTCGCAgtgaaatgataataaatatgggGTAAAGAAAAAAAA
>TCONS_00023733
CATTCACGGTGCTTCACTCTGAACAGTCGTTTTGCGGGAAGTTTGGAGAGCAGAGCGGTTGCAACTACTTACCGCTCACGTGAGGAAAGTTTTTATAAATAAGGAAGATGCCACCAAAGAAGGCAGACGGGGTGAAGAAAGCAAGAGCTCCAGCTAAGAGGAAACTGGCTGAAGAATTCCCGTCTGGAGAAGTCCTGACAGATAACGCAAAGAAAAAATGGAAGCTTGGATCAGCTGTTGGACAAGGAGGTTTTGGCCTGCTGTATCTTGCAAATGAAGACTCTTCAGGACCTGTCACCGCTGATGCACCTTATGTCATTAAAGTGGAACCAAGTGACAACGGCCCTCTCTTCTCTGAACTGAAGTTCTACATGCGAGCTGCCAAACCTGATCTAATCGGGGCTTGGATGAAGTCAAAGAAAATGGAGTATTTGGGAGTTCCAAAATATTGGGGTTCTGGTTTTCATGAGAAAAATGGAAAGAGGTACAGATTTATGGTGATGGATCGATTTGGAACAGATCTACAGAAATTGTTTGAAGGAAATGGGAAGAAGTTTTCAAGGAAGCTGGTTCTTCAGCTGGGCCTTCGACTTCTTGACATTCTGGAGTACATCCATGACCATGAATATGTGCATGCAGACATCAAAGCCTCCAACCTCCTCCTGTCCTACACCAACCCCAATCAGGTATTTTTAGTAGATTATGGACTGGCCTATAGATATGCTCCTGAGGGAGTGCCAAAGGAGTATAAGGAAGACCCAAAGAGGTGTCATGACGGTACCATTGAGTTCACAAGTATTGACGCACACAAAGGAGTCTCTCCTTCAAGGCGAGCAGACCTGGAAATCATGGGCTACTGCATGATCCAGTGGTTATGTAGCCGTCTGCCCTGGGAAGACAAACTTCAGGACCCACTCTACGTCAGAGACTCCAAGCTCAGGTGTAGAGACAATATTGATGAGTTCTTGAAAAGCTGTTTCGCTTCAGGAAATATAccagCTGAAATGGGAAAGTTCATGCAAGAGGTCAAGGTTCTGGGATACACAGACAGGCCAGATTACGACAAATTGCGAGGTATTTTGCAGCAAGGCCTAAAGTCCATAGGGTCAACAGATGACAAAAAGCTGGACTTCGGAGTGGCGACCAACAGCACAAGTTTGCCCTCTGTCAAGACTCCCAAGCGAAAGAAAGCAGAGGAAAAAGGCCAGTCTGCTGACGAAACCGATAGCACCCCAGCAAAGAAGAGGCGAGCTCCTCAGAAGAAGGAAGTGAATGGGGCTAAAAAGACAGCAAGTCCTGCAAAGCGTCCAGTGAAGAAAGAAGCTCAGGCCTCCTCTGAGCCAGCGGTGAAGAAAAGCCGAGGAAGGCCTAAGAAGAACTCTTAATCCTTTTTGCACTCCAGTTCAAGTCGTTTTCTTTTTGTATCTTTTAAATTGTCTGGTCTGTATTTGTTCTCTGTGGTTGAATTTTCTTAAACTTTAGCAGGGTGTTGGGCACACTCTCGCAgtgaaatgataataaatatgggGTAAAGAAAAAAAA

Function

symbol description
vrk1 Predicted to enable protein serine/threonine kinase activity. Predicted to be involved in Golgi disassembly and peptidyl-serine phosphorylation. Predicted to act upstream of or within cell division and protein phosphorylation. Predicted to be located in Golgi stack. Predicted to be active in cytoplasm and nucleus. Human ortholog(s) of this gene implicated in pontocerebellar hypoplasia type 1A. Orthologous to human VRK1 (VRK serine/threonine kinase 1).

GO:

id name namespace
GO:0000291 nuclear-transcribed mRNA catabolic process, exonucleolytic biological_process
GO:0022402 cell cycle process biological_process
GO:0034427 nuclear-transcribed mRNA catabolic process, exonucleolytic, 3'-5' biological_process
GO:0016072 rRNA metabolic process biological_process
GO:0018105 peptidyl-serine phosphorylation biological_process
GO:0016073 snRNA metabolic process biological_process
GO:0016075 rRNA catabolic process biological_process
GO:0071025 RNA surveillance biological_process
GO:0071027 nuclear RNA surveillance biological_process
GO:0016078 tRNA catabolic process biological_process
GO:0071028 nuclear mRNA surveillance biological_process
GO:0034968 histone lysine methylation biological_process
GO:0071029 nuclear ncRNA surveillance biological_process
GO:0071035 nuclear polyadenylation-dependent rRNA catabolic process biological_process
GO:0071038 nuclear polyadenylation-dependent tRNA catabolic process biological_process
GO:0022613 ribonucleoprotein complex biogenesis biological_process
GO:0071042 nuclear polyadenylation-dependent mRNA catabolic process biological_process
GO:0071046 nuclear polyadenylation-dependent ncRNA catabolic process biological_process
GO:0071047 polyadenylation-dependent mRNA catabolic process biological_process
GO:0034470 ncRNA processing biological_process
GO:0006364 rRNA processing biological_process
GO:0034472 snRNA 3'-end processing biological_process
GO:0034473 U1 snRNA 3'-end processing biological_process
GO:0034475 U4 snRNA 3'-end processing biological_process
GO:0034476 U5 snRNA 3'-end processing biological_process
GO:0090304 nucleic acid metabolic process biological_process
GO:0006396 RNA processing biological_process
GO:0006974 cellular response to DNA damage stimulus biological_process
GO:0043628 ncRNA 3'-end processing biological_process
GO:0043633 polyadenylation-dependent RNA catabolic process biological_process
GO:0043634 polyadenylation-dependent ncRNA catabolic process biological_process
GO:0006139 nucleobase-containing compound metabolic process biological_process
GO:0043928 exonucleolytic catabolism of deadenylated mRNA biological_process
GO:0016180 snRNA processing biological_process
GO:0018205 peptidyl-lysine modification biological_process
GO:0006725 cellular aromatic compound metabolic process biological_process
GO:1901360 organic cyclic compound metabolic process biological_process
GO:0044237 cellular metabolic process biological_process
GO:0006468 protein phosphorylation biological_process
GO:0007049 cell cycle biological_process
GO:0000459 exonucleolytic trimming involved in rRNA processing biological_process
GO:0000460 maturation of 5.8S rRNA biological_process
GO:0051276 chromosome organization biological_process
GO:0016571 histone methylation biological_process
GO:0000467 exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) biological_process
GO:0051568 histone H3-K4 methylation biological_process
GO:0051301 cell division biological_process
GO:0031123 RNA 3'-end processing biological_process
GO:0031125 rRNA 3'-end processing biological_process
GO:0090166 Golgi disassembly biological_process
GO:0006807 nitrogen compound metabolic process biological_process
GO:0018022 peptidyl-lysine methylation biological_process
GO:0034641 cellular nitrogen compound metabolic process biological_process
GO:0016310 phosphorylation biological_process
GO:0006259 DNA metabolic process biological_process
GO:0046483 heterocycle metabolic process biological_process
GO:0006281 DNA repair biological_process
GO:0090501 RNA phosphodiester bond hydrolysis biological_process
GO:0090503 RNA phosphodiester bond hydrolysis, exonucleolytic biological_process
GO:0000288 nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay biological_process
GO:0034708 methyltransferase complex cellular_component
GO:0044422 obsolete organelle part cellular_component
GO:0044424 obsolete intracellular part cellular_component
GO:0044428 obsolete nuclear part cellular_component
GO:0005795 Golgi stack cellular_component
GO:0070013 intracellular organelle lumen cellular_component
GO:0044446 obsolete intracellular organelle part cellular_component
GO:0044451 obsolete nucleoplasm part cellular_component
GO:0044464 obsolete cell part cellular_component
GO:1905354 exoribonuclease complex cellular_component
GO:0035097 histone methyltransferase complex cellular_component
GO:0032991 protein-containing complex cellular_component
GO:0000176 nuclear exosome (RNase complex) cellular_component
GO:0000177 cytoplasmic exosome (RNase complex) cellular_component
GO:0000178 exosome (RNase complex) cellular_component
GO:0005622 intracellular anatomical structure cellular_component
GO:0005623 obsolete cell cellular_component
GO:0005634 nucleus cellular_component
GO:0031974 membrane-enclosed lumen cellular_component
GO:0005694 chromosome cellular_component
GO:0031981 nuclear lumen cellular_component
GO:0043226 organelle cellular_component
GO:0043227 membrane-bounded organelle cellular_component
GO:0043229 intracellular organelle cellular_component
GO:0043231 intracellular membrane-bounded organelle cellular_component
GO:0043233 organelle lumen cellular_component
GO:0005737 cytoplasm cellular_component
GO:0016740 transferase activity molecular_function
GO:0005524 ATP binding molecular_function
GO:0003676 nucleic acid binding molecular_function
GO:1901363 heterocyclic compound binding molecular_function
GO:0000166 nucleotide binding molecular_function
GO:0004672 protein kinase activity molecular_function
GO:0004674 protein serine/threonine kinase activity molecular_function
GO:0016301 kinase activity molecular_function

KEGG: NA

ZFIN:

id description
ZDB-GENE-040426-2709 Predicted to enable protein serine/threonine kinase activity. Predicted to be involved in Golgi disassembly and peptidyl-serine phosphorylation. Predicted to act upstream of or within cell division and protein phosphorylation. Predicted to be located in Golgi stack. Predicted to be active in cytoplasm and nucleus. Human ortholog(s) of this gene implicated in pontocerebellar hypoplasia type 1A. Orthologous to human VRK1 (VRK serine/threonine kinase 1).

Ensembl:

ensembl_id ENSDARG00000018006

RNA

RNA id representative length rna type GC content exon number start site end site
TCONS_00023732 False 448 lncRNA 0.44 2 18773961 18774494
TCONS_00023733 True 1542 mRNA 0.46 13 18773961 18797245

Neighbor

gene id symbol gene type direction distance location
XLOC_012025 BX510991.1 coding downstream 423116 18350726 ~ 18350845 (-)
XLOC_012024 BX465857.2 coding downstream 489898 18283949 ~ 18284063 (-)
XLOC_012023 NA coding downstream 591403 18148782 ~ 18182558 (-)
XLOC_012022 NA coding downstream 743704 18025736 ~ 18030257 (-)
XLOC_012021 hhipl1 coding downstream 825374 17939095 ~ 17948587 (-)
XLOC_012027 ak7b coding upstream 80673 18877918 ~ 18888959 (-)
XLOC_012028 galcb coding upstream 92392 18889637 ~ 18898115 (-)
XLOC_012029 flrt2 coding upstream 220149 19017394 ~ 19022990 (-)
XLOC_012030 NA coding upstream 433489 19230734 ~ 19398185 (-)
XLOC_012031 gsc coding upstream 545770 19343015 ~ 19345521 (-)
XLOC_012020 CU855697.1 non-coding downstream 894252 17879594 ~ 17879709 (-)
XLOC_012037 dre-mir-2187 non-coding upstream 1103509 19900754 ~ 19900857 (-)
XLOC_012038 NA non-coding upstream 1169921 19967166 ~ 19972044 (-)
XLOC_012049 NA non-coding upstream 1813231 20610476 ~ 20611884 (-)
XLOC_012051 NA non-coding upstream 1873153 20670398 ~ 20673891 (-)

Expression


Co-expression Network

Homologous

species gene id symbol gene type chromosome NCBI id location
grasscarp (Ctenopharyngodon idella) CI01000106_01259364_01269803 VRK1 coding CI01000106 null 1259225 ~ 1269803 (-)