XLOC_010435 (prdm1a)


Basic Information

Item Value
gene id XLOC_010435
gene name prdm1a
gene type coding
species zebrafish (Danio rerio)
category of species model fish

Chromosome Information

Item Value
chromosome id NC_007127.7
NCBI id CM002900.2
chromosome length 55266484
location 7430998 ~ 7443388 (-)
genome version GRCz11_2017_zebrafish_Genome

Sequence

>TCONS_00020503
ATCTCAGGCACTTGCAGGAGAAGTCACTTACCATCTGGACTAGCAGTGGGACAAGACAGGCGAATTGTGAGCTGCACCTgtcccatacacacactcacacactcaggGGAGAGATCACACACAGCCTCTATGTGTGGCTGGGACCAGAGCGTCCTGGCTCCTTATCAAAACTCGGCTATGTTGACTACTGAGGCAGCACCCTACACCGCTGACAATGAGGAGCTCAAGATGGATGTAGAGGATGTAGACATGACAAAATGGACGGAGGACGAGTTCGAGGAGAAATGCACATACATTGTGAAAGACCACACCTGGGAAGGACCACTGGAGAACACGGACCTCACCCGGGCTGAGGCGTCTTTACCTAGAAACCTGGCTTTTAAGCACCCGGCAGACTCCAAAGAGGTTATTGGTGTAGTAAGCAGAGAATACATCCCTAAAGGCACGCGCTTTGGCCCCCTTGTGGGAGAAAGTTACACTGCAGAAAATGTCCCCAAAGATGCGAACAGGAAGTACTTCTGGCGGaTATACTCAGATGGAGAATTCCATCATTTTGTGGACGGATTGGACGAGGAAAAGAGTAACTGGATGCGCTATGTGAATCCAGCGCATTCCCAGCAGGAGCAGAACCTTGCCGCCTGTCAAAACGGCATGAACATCTATTTCTACACGGTGAAGGCCATTCCTGCAGACCAGGAGCTACTGGTGTGGTACTGCCCTGAGTTTGCCCGCCGTCTCAACTACCCTGCCTCTGGAGAGATTATGATGCAAAAACTCAAGCAGAGCCTGATTGAAGCCAAGCAGCAAGCAACCGAAGTCAAGCACCCAGTGAAAAGAGAACACAGTGTTTCGGAGATTTTGAAAGATGTGCTGCAAGAACCCAGCAGACCACTTCCCACCCGTCCCCGCTGTCCCAAAAGCCCAGACCGACCTCTATACCCCAGTGCTGTCTATCCACCCCGCCCTTCCCTAAACGAGGACTTTTTAAAGAGCACCACAGTATTCGGCCTCCCCACACGCTCTCACACACAGTGTTCGGTGACACCCAGCCCGTCAGCACACAGCAGCCCTGAGAGAAGTCCAGGAAGCAGTCCGACATCAGCATCAATTGAGCCAAGAGAAGCATTTCTCCCTTTCTCTCCAGCACTCTACAATCGTGGCCTGAACCACTACCCAGGATACTCACCAGCAGGCTCCATGCCATTTTACCCAAACCCGCACTACTCGCGCTACCTCATGCACCACTACCCTGTTAGTAGTTTGAGTGGGCCATCTACATTGGGGGGTATATTTCCACACATGTATCCATTTTACAGCAGCTTGGTACCTCCTCATGTACCATTCCCACCTTCCATGCTTTCATCCGAGGGCAGTCGTCAGTTTATGCTTCCACCTGACTCTCCGGCCCCCAGGGACATTCTGCTTCCAGCAGCCACCAGTGCCTTTTCTGCAGCCACTTCTCTGAAAGACAAACCCCTGCATGGGCATGGACACCCTTACGCTCCTGCTGGTGGATCTCCAACAGCCGGCTCTGCGGCCTCTACGGGATGCATTCCCACCAAGCCTACCTCTGCAATTCTGAGCACCAGCCGCTCAGAGGATGAGGCCATCAATCTGAGCAAGATGAAACGAGGTTCCACAGGCTACAAAAGTCTTGATTACCCACTTAAGAAGCAGAATGGGAAGATCAAGTATGAGTGCAATGTTTGCACCAAGACTTTTGGTCAACTTTCTAATCTTAAGGTGCACCTGCGTGTCCATAGTGGGGAACGACCCTTTAAGTGTCAGACCTGCAATAAAGGTTTCACTCAGCTCGCCCACCTGCAGAAACACTATTTGGtccacacaggagagaaaccCCACGAGTGCCAGGTGTGTCACAAGCGTTTCAGCAGCACTAGCAACCTGAAAACCCATTTGCGATTACATTCTGGGGAAAAGCCCTACCAGTGCAAGATCTGCCCAGCCAAGTTCACACAGTTTGTCCACCTCAAGCTGCACAAGCGGCTGCACACGCGAGAACGTCCACACCAATGCCCACATTGCCACCACAACTACATTCACCTCAGCAGCCTACGGTTCCACCTCAAGGGCTACTGCCTCGCAGTCTCTCCTTCTCCAAGCTGCAGCTTGGACGAACTCAACCGAGTCAACGAGGAAATTGAACGCTTTGACATCAGCGATAATGCCGACCGGCTAGAAGAAATGGAAGGGTTTGATGTGGAGGGCATGGTGGAGAAGCAGATATTTGGCCTGCTCTGGCAGGAGATGGATTTTAAGGCGTCTTATCACAAAGGTAGCACTGGAGGGGACCTGCACCCCCGAGCGCCTGCATTATCCGCGTATCATCTGAATGAGCATGACAGTGAAGCTTCTGTCATCAAAGTTCATCGCAGCAGCCCGATCCAACTCCTACCCATCAAGGTGAAAAAGGAGACAGAGGAGGCCATGGATACCTAGAGGCTTCCTGACCAGTTGACTGACTGAACATTCATAAGTTGTTCTTatcaaaacgaaacaaaaaaaaaataggctcAGGCCTATATATTCAGGGACTTCCGTACTCAGGGCTAACAGACATTGATCATCAGTGGTCCAGTATGTCCTACACAAATGATAAAGACAAtcatattcttttattattataactattattattattgttaatattatttgctCTAGTGTTCATTTCAGTTTGTaatctatttaatttattgttcaaCATGTCCTCCTTCACGACCGATACATGGAAATAATGTTTACAATGACTGGTTGATTCATTGTAATTTGCTGTCTTGTATATTTCTTCTTCTCTTTCCTTTTTGTAAATAGCGTCCCGATTGACTGTGATTTCATGTGCAACTGCAAAGAGCTTACCACATTCAGGTTGATTTTTAATGTAGGCCGATGTCCGAGGTAGAACTTTTTTGTTGAAGGCATTTCTTTTTGTACCCTAGGAGAGGTTGCATATCTATGTGTACGTGTTTTACATGACAGTTATTCTTTTAATGTTGAGCTCTACCACAATTTAATGAATACAAAAAGGGCATATTATATATTACCAACAACTGTTACCTCAAATGTGagcgagtgagtgtgtgtgtgtgcgtgtgttgagAGATGTGTGCTTGTATTGTGATATTTGTTTTGCTACTTGAAGAGGAAACCAAATGTCCCAATGTGCAGGTCTACATGCGGTCCAAAGAACAGCAGTCTGTCTAGCTGTCGCACACAGGCTGTGAGATTGACACTGACTCTGCATTTTCGTACTTATGTGCGGCACATTACTGAAAACCAAAATGATAAAGAAACGAGAATGTGGAACTGCTAACCAAAGTGAAATCTTTCAGAGTTTCAGAGATGTGTGTAAACTGTCTGTTCTGCAGGTCCGTGGTGATGTCTGTGGACTCTTCACGTCACCTCGGCCTTTTGTATGCACTGGTTTTATTTCTTTCGTCTTATGtttgtactttttgttttgtttttgtccagCGATGTTAGTAGGACAAAATGTCAGCGAGGCAGTACAATCTCAAACGCTCTCTGTCCTAAAGTATGACCAAAGTCTACACCTCATCTTCAGctttaaattaagaaaataagaGACTGTCTTTGTTTACATACTGGTTTACGTAGCTATTTAAGTACAGCTTtgacaaaatgtaaattataatataaatcttCACTGATCTAA

Function

symbol description
prdm1a Enables DNA-binding transcription factor activity. Acts upstream of or within several processes, including negative regulation of macromolecule metabolic process; positive regulation of cell differentiation; and skeletal system morphogenesis. Predicted to be active in cytoplasm and nucleus. Is expressed in several structures, including digestive system; ectoderm; fin bud; mesoderm; and nervous system. Orthologous to human PRDM1 (PR/SET domain 1).

GO:

id name namespace
GO:0060351 cartilage development involved in endochondral bone morphogenesis biological_process
GO:0010629 negative regulation of gene expression biological_process
GO:0051155 positive regulation of striated muscle cell differentiation biological_process
GO:0006357 regulation of transcription by RNA polymerase II biological_process
GO:0007521 muscle cell fate determination biological_process
GO:0045165 cell fate commitment biological_process
GO:0000122 negative regulation of transcription by RNA polymerase II biological_process
GO:0010468 regulation of gene expression biological_process
GO:0035118 embryonic pectoral fin morphogenesis biological_process
GO:0014032 neural crest cell development biological_process
GO:0014033 neural crest cell differentiation biological_process
GO:0035138 pectoral fin morphogenesis biological_process
GO:0000578 embryonic axis specification biological_process
GO:0048066 developmental pigmentation biological_process
GO:0045666 positive regulation of neuron differentiation biological_process
GO:0033333 fin development biological_process
GO:0060037 pharyngeal system development biological_process
GO:0048701 embryonic cranial skeleton morphogenesis biological_process
GO:0048702 embryonic neurocranium morphogenesis biological_process
GO:0048703 embryonic viscerocranium morphogenesis biological_process
GO:0005634 nucleus cellular_component
GO:0005737 cytoplasm cellular_component
GO:0046872 metal ion binding molecular_function
GO:0003676 nucleic acid binding molecular_function
GO:0003700 DNA-binding transcription factor activity molecular_function
GO:0000978 RNA polymerase II cis-regulatory region sequence-specific DNA binding molecular_function
GO:0042826 histone deacetylase binding molecular_function

KEGG: NA

ZFIN:

id description
ZDB-GENE-030131-2193 Enables DNA-binding transcription factor activity. Acts upstream of or within several processes, including negative regulation of macromolecule metabolic process; positive regulation of cell differentiation; and skeletal system morphogenesis. Predicted to be active in cytoplasm and nucleus. Is expressed in several structures, including digestive system; ectoderm; fin bud; mesoderm; and nervous system. Orthologous to human PRDM1 (PR/SET domain 1).

Ensembl:

ensembl_id ENSDARG00000002445

RNA

RNA id representative length rna type GC content exon number start site end site
TCONS_00020503 True 3694 mRNA 0.47 7 7430998 7443388

Neighbor

gene id symbol gene type direction distance location
XLOC_010434 med18 coding downstream 51670 7376471 ~ 7379328 (-)
XLOC_010433 foxo6a coding downstream 68192 7315144 ~ 7362806 (-)
XLOC_010432 si:ch73-341k19.1 coding downstream 191490 7202082 ~ 7239508 (-)
XLOC_010431 pmvk coding downstream 486071 6937186 ~ 6944927 (-)
XLOC_010429 mbpb coding downstream 581217 6803470 ~ 6849781 (-)
XLOC_010436 NA coding upstream 64713 7508101 ~ 7621115 (-)
XLOC_010437 pimr209 coding upstream 244980 7688368 ~ 7692568 (-)
XLOC_010438 BX511173.1 coding upstream 250493 7693881 ~ 7696216 (-)
XLOC_010439 trim71 coding upstream 299270 7742658 ~ 7793457 (-)
XLOC_010440 tcaim coding upstream 359342 7802730 ~ 7828848 (-)
XLOC_010626 CR392024.2 misc upstream 13451724 20895112 ~ 20895175 (-)
XLOC_010430 AL845419.1 non-coding downstream 601363 6828552 ~ 6829635 (-)
XLOC_010428 NA non-coding downstream 779279 6648030 ~ 6651719 (-)
XLOC_010427 NA non-coding downstream 795702 6605385 ~ 6635296 (-)
XLOC_010426 NA non-coding downstream 839828 6588022 ~ 6591170 (-)
XLOC_010425 NA non-coding downstream 874497 6512346 ~ 6556501 (-)
XLOC_010441 NA non-coding upstream 390831 7834219 ~ 7881277 (-)
XLOC_010442 CU856516.1 non-coding upstream 524632 7968020 ~ 7984901 (-)
XLOC_010444 NA non-coding upstream 697324 8140712 ~ 8142312 (-)

Expression


Co-expression Network

Homologous

species gene id symbol gene type chromosome NCBI id location
grasscarp (Ctenopharyngodon idella) CI01000065_00906591_00915144 PRDM1, PRDM1A coding CI01000065 null 905392 ~ 915144 (-)