vdra (vdr,vdra,LOC103045919,LOC108435544,LOC107701250,LOC107702164,LOC107565314)


Basic Information

Item Value
gene id vdra
gene name vdr,vdra,LOC103045919,LOC108435544,LOC107701250,LOC107702164,LOC107565314
gene type coding
species striped catfish (Pangasianodon hypophthalmus)
category of species economic fish

Chromosome Information

Item Value
chromosome id NC_047610.1
NCBI id CM018556.1
chromosome length 25111544
location 21378129 ~ 21437863 (+)
genome version GENO_Phyp_1.0_2019_striped_catfish_Genome

Sequence

>XM_026920124.2
TGAGCCGAAGGGCGGGGCATAGCCGAGTCGATGATGTCCACCTCTTTGGTGGTTGACGAGTAGagaaaaaattacatatatatgtatatacacccATTTTGTGTGGAATTAACGTTGAGTTTGAAGTGAAGACCAGTATTTGGATGGTTCGAAAGTCAACTCGGATCTCCCCTGtaaTGGAGGCCATGGCCGTGAGCACATCTGCACAGGGTACGGATGAGTTTGACCGCAACGCCCCGCGGATCTGCGGCGTCTGCGGAGACAAGGCCACTGGATTCCACTTCAACGCCATGACCTGCGAAGGCTGCAAGGGCTTTTTCAGGCGCAGTATGAAGCGGAAGGCCAGTTTCACTTGTCCCTTTAACGGCAGCTGCACCATCACCAAAGACAACCGCAGACACTGCCAAGCCTGTCGCCTCAAGCGCTGCGTCGACATCGGCATGATGAAGGAGTTCATTCTGACTGATGAGGAGGTACAGAGGAAGAAGGAGCTGATCCTgaagagaaaggaggaggaggcgaTGCGGGAGGCGCAGAAGCCCCGGCTGACCGAGGAGCAGAGTCAGATCATCAACACGCTGGTGGAGGCGCATCACAAGACCTACGACGACTCCTACTCCGATTTTGTGAAATTCCGAccccCAGTGAGAGAGGGACCAGTGACGCGCAGTGCCAGCCGTGCTGCCTCGCTCCACTCACTCTCAGATGCCTCTTCAGATTCATTGAACAACTCAccagaGTCTATGGACAAAAAGCTCAGCAGTCTCTTCTCCATGTGTCAGGATGGCGTGATGAGCCCGGAGTCCAGGGATGAAAACTCCCGCCTCTCCATGCTGCCTCACCTGGCTGACCTCGTCAGCTACAGCATCCAGAAAGTGATCGGCTTTGCCAAGATGATCCCCGGCTTCAGggatCTGACTGCAGAAGATCAGATCGCTCTGCTGAAGTCCAGCGCTATTGAGATCATCATGTTGCGCTCCAACCAGTCCTTCAGTCTGGACGACATGAGCTGGAGCTGTGGAGGGCCCGACTTTAAGTACTGCATTAACGACGTCACCAAAGCTGGTCACACTCTGGAGCTGCTGGAGCCGCTGGTGAAGTTTCAGGTGGGGCTGAAAAAACTCAACATGCATGAAGAGGAACACGTGCTGCTAATGGCcatctgtctcctctctccagATCGTCCCGGCGTGCAGGACCACGTTCGGATCGAGGCGATGCAGGAGCGTTTGTGCGAGACGCTGCAGGCGTATATCCGCGTGCACCACCCGGGCGGCCGGCTGCTCTACGCCAAGATGATCCAGAAGCTGGCCGATCTGCGCAGCCTGAACGAGGAGCACTCCAAGCAGTACCGCTCGCTGTCCTTCCAGCCTGAGCACAGCATGCAACTCACACCGCTCGTGCTGGAGGTGTTCGGCAGCGAGGTGTCCTAGCGGCCAGGACCGTGTCTCCCACAGTGCCAGTCCAGCGCAGGGGCATGAGGG
>XM_034311568.1
TGAGCCGAAGGGCGGGGCATAGCCGAGTCGATGATGTCCACCTCTTTGGTGGTTGACGAGTAGagaaaaaattacatatatatgtatatacacccATTTTGTGTGGAATTAACGTTGAGTTTGAAGTGAAGACCAGTATTTGGATGGTTCGAAAGTCAACTCGGATCTCCCCTGAGTTGCCTGGATACATTTTGGGCAACTTGGAGCCCTAGGTTCAAGCAGCTGCAGGTAGGACAGgagcaggcaggcaggcaggagCAGGCAGGCGGGCAGAGGAGCCGTGCAGCGGGGCTTCATCCCAAACAGATCCATAACCCCTTCCCCATGCGCACTCTGCGCGCTCTGAAGTCATCTTCTGGAGACCCTTAAtaaTGGAGGCCATGGCCGTGAGCACATCTGCACAGGGTACGGATGAGTTTGACCGCAACGCCCCGCGGATCTGCGGCGTCTGCGGAGACAAGGCCACTGGATTCCACTTCAACGCCATGACCTGCGAAGGCTGCAAGGGCTTTTTCAGGCGCAGTATGAAGCGGAAGGCCAGTTTCACTTGTCCCTTTAACGGCAGCTGCACCATCACCAAAGACAACCGCAGACACTGCCAAGCCTGTCGCCTCAAGCGCTGCGTCGACATCGGCATGATGAAGGAGTTCATTCTGACTGATGAGGAGGTACAGAGGAAGAAGGAGCTGATCCTgaagagaaaggaggaggaggcgaTGCGGGAGGCGCAGAAGCCCCGGCTGACCGAGGAGCAGAGTCAGATCATCAACACGCTGGTGGAGGCGCATCACAAGACCTACGACGACTCCTACTCCGATTTTGTGAAATTCCGAccccCAGTGAGAGAGGGACCAGTGACGCGCAGTGCCAGCCGTGCTGCCTCGCTCCACTCACTCTCAGATGCCTCTTCAGATTCATTGAACAACTCAccagaGTCTATGGACAAAAAGCTCAGCAGTCTCTTCTCCATGTGTCAGGATGGCGTGATGAGCCCGGAGTCCAGGGATGAAAACTCCCGCCTCTCCATGCTGCCTCACCTGGCTGACCTCGTCAGCTACAGCATCCAGAAAGTGATCGGCTTTGCCAAGATGATCCCCGGCTTCAGggatCTGACTGCAGAAGATCAGATCGCTCTGCTGAAGTCCAGCGCTATTGAGATCATCATGTTGCGCTCCAACCAGTCCTTCAGTCTGGACGACATGAGCTGGAGCTGTGGAGGGCCCGACTTTAAGTACTGCATTAACGACGTCACCAAAGCTGGTCACACTCTGGAGCTGCTGGAGCCGCTGGTGAAGTTTCAGGTGGGGCTGAAAAAACTCAACATGCATGAAGAGGAACACGTGCTGCTAATGGCcatctgtctcctctctccagATCGTCCCGGCGTGCAGGACCACGTTCGGATCGAGGCGATGCAGGAGCGTTTGTGCGAGACGCTGCAGGCGTATATCCGCGTGCACCACCCGGGCGGCCGGCTGCTCTACGCCAAGATGATCCAGAAGCTGGCCGATCTGCGCAGCCTGAACGAGGAGCACTCCAAGCAGTACCGCTCGCTGTCCTTCCAGCCTGAGCACAGCATGCAACTCACACCGCTCGTGCTGGAGGTGTTCGGCAGCGAGGTGTCCTAGCGGCCAGGACCGTGTCTCCCACAGTGCCAGTCCAGCGCAGGGGCATGAGGG
>XM_034311569.1
CATAATGTCAGTGTTGGTCTGCTCTCAGGTAATAAATtaaTGGAGGCCATGGCCGTGAGCACATCTGCACAGGGTACGGATGAGTTTGACCGCAACGCCCCGCGGATCTGCGGCGTCTGCGGAGACAAGGCCACTGGATTCCACTTCAACGCCATGACCTGCGAAGGCTGCAAGGGCTTTTTCAGGCGCAGTATGAAGCGGAAGGCCAGTTTCACTTGTCCCTTTAACGGCAGCTGCACCATCACCAAAGACAACCGCAGACACTGCCAAGCCTGTCGCCTCAAGCGCTGCGTCGACATCGGCATGATGAAGGAGTTCATTCTGACTGATGAGGAGGTACAGAGGAAGAAGGAGCTGATCCTgaagagaaaggaggaggaggcgaTGCGGGAGGCGCAGAAGCCCCGGCTGACCGAGGAGCAGAGTCAGATCATCAACACGCTGGTGGAGGCGCATCACAAGACCTACGACGACTCCTACTCCGATTTTGTGAAATTCCGAccccCAGTGAGAGAGGGACCAGTGACGCGCAGTGCCAGCCGTGCTGCCTCGCTCCACTCACTCTCAGATGCCTCTTCAGATTCATTGAACAACTCAccagaGTCTATGGACAAAAAGCTCAGCAGTCTCTTCTCCATGTGTCAGGATGGCGTGATGAGCCCGGAGTCCAGGGATGAAAACTCCCGCCTCTCCATGCTGCCTCACCTGGCTGACCTCGTCAGCTACAGCATCCAGAAAGTGATCGGCTTTGCCAAGATGATCCCCGGCTTCAGggatCTGACTGCAGAAGATCAGATCGCTCTGCTGAAGTCCAGCGCTATTGAGATCATCATGTTGCGCTCCAACCAGTCCTTCAGTCTGGACGACATGAGCTGGAGCTGTGGAGGGCCCGACTTTAAGTACTGCATTAACGACGTCACCAAAGCTGGTCACACTCTGGAGCTGCTGGAGCCGCTGGTGAAGTTTCAGGTGGGGCTGAAAAAACTCAACATGCATGAAGAGGAACACGTGCTGCTAATGGCcatctgtctcctctctccagATCGTCCCGGCGTGCAGGACCACGTTCGGATCGAGGCGATGCAGGAGCGTTTGTGCGAGACGCTGCAGGCGTATATCCGCGTGCACCACCCGGGCGGCCGGCTGCTCTACGCCAAGATGATCCAGAAGCTGGCCGATCTGCGCAGCCTGAACGAGGAGCACTCCAAGCAGTACCGCTCGCTGTCCTTCCAGCCTGAGCACAGCATGCAACTCACACCGCTCGTGCTGGAGGTGTTCGGCAGCGAGGTGTCCTAGCGGCCAGGACCGTGTCTCCCACAGTGCCAGTCCAGCGCAGGGGCATGAGGG
>XM_034311570.1
TGACTACGCATACATGCACGACCTGGACACTGTGAGCACTGATGATGGATGCTTATTCATGCTCATAAGGTGCACACGGGGTGTCTGTGGTACTGCGTATTAAAGtaaTGGAGGCCATGGCCGTGAGCACATCTGCACAGGGTACGGATGAGTTTGACCGCAACGCCCCGCGGATCTGCGGCGTCTGCGGAGACAAGGCCACTGGATTCCACTTCAACGCCATGACCTGCGAAGGCTGCAAGGGCTTTTTCAGGCGCAGTATGAAGCGGAAGGCCAGTTTCACTTGTCCCTTTAACGGCAGCTGCACCATCACCAAAGACAACCGCAGACACTGCCAAGCCTGTCGCCTCAAGCGCTGCGTCGACATCGGCATGATGAAGGAGTTCATTCTGACTGATGAGGAGGTACAGAGGAAGAAGGAGCTGATCCTgaagagaaaggaggaggaggcgaTGCGGGAGGCGCAGAAGCCCCGGCTGACCGAGGAGCAGAGTCAGATCATCAACACGCTGGTGGAGGCGCATCACAAGACCTACGACGACTCCTACTCCGATTTTGTGAAATTCCGAccccCAGTGAGAGAGGGACCAGTGACGCGCAGTGCCAGCCGTGCTGCCTCGCTCCACTCACTCTCAGATGCCTCTTCAGATTCATTGAACAACTCAccagaGTCTATGGACAAAAAGCTCAGCAGTCTCTTCTCCATGTGTCAGGATGGCGTGATGAGCCCGGAGTCCAGGGATGAAAACTCCCGCCTCTCCATGCTGCCTCACCTGGCTGACCTCGTCAGCTACAGCATCCAGAAAGTGATCGGCTTTGCCAAGATGATCCCCGGCTTCAGggatCTGACTGCAGAAGATCAGATCGCTCTGCTGAAGTCCAGCGCTATTGAGATCATCATGTTGCGCTCCAACCAGTCCTTCAGTCTGGACGACATGAGCTGGAGCTGTGGAGGGCCCGACTTTAAGTACTGCATTAACGACGTCACCAAAGCTGGTCACACTCTGGAGCTGCTGGAGCCGCTGGTGAAGTTTCAGGTGGGGCTGAAAAAACTCAACATGCATGAAGAGGAACACGTGCTGCTAATGGCcatctgtctcctctctccagATCGTCCCGGCGTGCAGGACCACGTTCGGATCGAGGCGATGCAGGAGCGTTTGTGCGAGACGCTGCAGGCGTATATCCGCGTGCACCACCCGGGCGGCCGGCTGCTCTACGCCAAGATGATCCAGAAGCTGGCCGATCTGCGCAGCCTGAACGAGGAGCACTCCAAGCAGTACCGCTCGCTGTCCTTCCAGCCTGAGCACAGCATGCAACTCACACCGCTCGTGCTGGAGGTGTTCGGCAGCGAGGTGTCCTAGCGGCCAGGACCGTGTCTCCCACAGTGCCAGTCCAGCGCAGGGGCATGAGGG

Function

symbol description
vdra Enables calcitriol binding activity; lithocholic acid binding activity; and nuclear receptor activity. Contributes to DNA-binding transcription factor activity and vitamin D response element binding activity. Acts upstream of or within several processes, including embryonic heart tube morphogenesis; hematopoietic stem cell proliferation; and transcription, DNA-templated. Predicted to be located in cytoplasm and nucleus. Is expressed in several structures, including brain; head; heart; integument; and pleuroperitoneal region. Used to study hematopoietic system disease and vitamin D-dependent rickets. Human ortholog(s) of this gene implicated in several diseases, including autoimmune disease (multiple); carcinoma (multiple); lipid storage disease (multiple); melanoma (multiple); and tuberculosis (multiple). Orthologous to human VDR (vitamin D receptor).
vdr Enables several functions, including lithocholic acid receptor activity; nuclear receptor activity; and steroid binding activity. Contributes to DNA-binding transcription factor activity and vitamin D response element binding activity. Involved in several processes, including decidualization; negative regulation of keratinocyte proliferation; and regulation of transcription by RNA polymerase II. Acts upstream of or within negative regulation of gene expression and negative regulation of transcription, DNA-templated. Located in cytosol and nucleoplasm. Part of RNA polymerase II transcription regulator complex and receptor complex. Implicated in several diseases, including autoimmune disease (multiple); carcinoma (multiple); lipid storage disease (multiple); melanoma (multiple); and tuberculosis (multiple). Biomarker of autosomal recessive limb-girdle muscular dystrophy type 2B; breast cancer; carcinoma (multiple); cholangitis (multiple); and non-alcoholic fatty liver disease.

GO:

id name namespace
GO:0006357 regulation of transcription by RNA polymerase II biological_process
GO:0070561 vitamin D receptor signaling pathway biological_process
GO:0001503 ossification biological_process
GO:0043401 steroid hormone mediated signaling pathway biological_process
GO:0055074 calcium ion homeostasis biological_process
GO:0005634 nucleus cellular_component
GO:0043565 sequence-specific DNA binding molecular_function
GO:0008134 transcription factor binding molecular_function
GO:0005499 vitamin D binding molecular_function
GO:0003707 steroid hormone receptor activity molecular_function
GO:0008270 zinc ion binding molecular_function

KEGG:

id description
K08539 VDR, NR1I1; vitamin D3 receptor

RNA

RNA id representative length rna type GC content exon number start site end site
XM_026920124.2 False 1484 mRNA 0.56 9 21378129 21437863
XM_034311568.1 True 1679 mRNA 0.57 10 21378129 21437863
XM_034311569.1 False 1347 mRNA 0.57 9 21402243 21437863
XM_034311570.1 False 1415 mRNA 0.57 9 21413898 21437863

Neighbor

gene id symbol gene type direction distance location
calcrl2 LOC108276023 coding upstream 26113 21323924 ~ 21352016 (+)
ttc29 ttc29 coding upstream 54906 21315381 ~ 21323223 (+)
LOC117599257 NA coding upstream 65334 21310075 ~ 21312795 (+)
LOC113530283 LOC108276019 coding upstream 90521 21275430 ~ 21287608 (+)
LOC113530257 LOC108275533,LOC108435580,LOC107565311,LOC107570205 coding upstream 120841 21242246 ~ 21257288 (+)
LOC113530406 LOC108276167,LOC105022368 coding downstream 14405 21452268 ~ 21455848 (+)
LOC117599284 NA coding downstream 83483 21521346 ~ 21535366 (+)
zmp:0000001174 rai2,LOC107653213,LOC107550168,LOC107752425 coding downstream 173940 21611803 ~ 21626745 (+)
LOC113530651 cdkl5,LOC108276197 coding downstream 236474 21674337 ~ 21748403 (+)
LOC113530955 ap1s2,zgc:162858,LOC108275964,LOC107564403,LOC107653210,LOC103463884,LOC106942561,LOC108435569,LOC106921341,LOC102795551,LOC107095773,LOC101477195,LOC104928285,LOC107752427,LOC107396045,LOC101174095 coding downstream 316984 21754847 ~ 21795371 (+)
G258680 NA non-coding upstream 23399 21354440 ~ 21354730 (+)
G258459 ppp1r14c,LOC107697847,LOC107738512,LOC107664259 non-coding upstream 246076 21115050 ~ 21132053 (+)
G258462 NA non-coding upstream 270114 21107347 ~ 21108015 (+)
G258483 iyd non-coding upstream 273028 21103714 ~ 21105101 (+)
G258476 selenoi,si:ch211-197l9.4,LOC107549067 non-coding upstream 284285 21093329 ~ 21093844 (+)
G258753 NA non-coding downstream 41369 21479232 ~ 21556438 (+)
G258758 NA non-coding downstream 62115 21499978 ~ 21510994 (+)
LOC113530300 NA non-coding downstream 162759 21600622 ~ 21602468 (+)
G258883 NA non-coding downstream 312148 21750011 ~ 21752454 (+)
LOC117599289 NA non-coding downstream 532515 21970378 ~ 21982618 (+)
si:ch73-290k24.5 LOC108275473 other upstream 139130 21228320 ~ 21238999 (+)
ubxn10 ubxn10,LOC108275535,LOC108433381,LOC107385551,LOC107699345 other upstream 470670 20903105 ~ 20907459 (+)
LOC113530729 hnrnpa1,LOC108275985,LOC108275986,LOC107707002,LOC107714994 other upstream 863934 20510244 ~ 20514195 (+)
G258096 hoxc6,hoxc6a,LOC107593966,LOC108433405,LOC107664205,LOC107714999,LOC103034651 other upstream 979415 20390809 ~ 20398714 (+)
si:ch73-206d17.1 LOC108275771 other upstream 1673066 19625529 ~ 19705063 (+)
LOC117599233 NA other downstream 100182 21538045 ~ 21542427 (+)
LOC113530514 LOC108275916 other downstream 1233535 22671398 ~ 22680542 (+)
LOC117599309 NA other downstream 1933881 23371744 ~ 23383653 (+)
G259993 NA other downstream 1949675 23387538 ~ 23389314 (+)
G260415 NA other downstream 2594364 24032227 ~ 24032724 (+)

Expression


Co-expression Network