XLOC_025568 (pdxdc1)


Basic Information

Item Value
gene id XLOC_025568
gene name pdxdc1
gene type coding
species zebrafish (Danio rerio)
category of species model fish

Chromosome Information

Item Value
chromosome id NC_007114.7
NCBI id CM002887.2
chromosome length 62628489
location 36616713 ~ 36644776 (+)
genome version GRCz11_2017_zebrafish_Genome

Sequence

>TCONS_00050383
GGCTTAATACTTTTAAAGTAAACACCCCCAAAGAACAGACCGGGGTCTTGCTTCTCTTGACTCCTCTGCATCATTGCATATCTGTGCATTATCTAAAAAGGGACACTGTTAAGGGGGCGTATGTTTAGGCTACGTCAGCGTTGCCAGCGTGGAGCGGCATGATACCAGGAAGTAGCACATTTCAATTGACTATACAAATAACGAAGAGAAAGGGTAATCGAGGTGATTTTCCGGTGCTATTTGGATTCGCGTCCCTAAAATACACCGCACGGGGACACGGAGAGTCCCTGCGACTGGGTTATTAACGCCGCATGGAGAAGCCGCCCGTgaagATGATGGACCCTACGTTGGCTGAAATGGGGAACCATCTTTCTGATGCCATGAAGATCTTGGAAAGTGGGAAATTGGAAACCGAACAGGGCCAGGAAGGAAGAAAGATGAGCTGGAAAGAGATTCCAGGACCGTTACAAGGAGACGGTCAGGATGTTGTCAGCATTCTTCAGCTTGTGCAGAACCTGATGCATGGAGATGATGAAGAGCAGGGTCACCGGATGCAGTTTGTCGGAGAGCAGGGACACATGGCTCTGTTAGGACACAGTCTGGCCGCATATATTTCTGTCCTGGAGCGAGAGCGATTGAGAAAACTGACCACCCGCATCCTGTCAGACACCACTCTCTGGCTCTGCAGGCTTTTCAGATATGAAAATGGCTCTGCATATTTCCATGAAGATGACCGCGAGGGGCTGCTGAAGGTGTGTCGGCTGGTGATGAACACTCACTATGAGGACTTCACCACTGAGGGCTTCACAGCGCTCAGCTCCAAACATCCCGTCATCTACCAAAGTGCTGCATGCAGACCTGGCCTGGGACAACATCTCTGCAGTCAGCTAGGGCTTCCTCTgtcttgcctttgtgttgtgccCTGTAACACCATGTTTGGCTCCTTGCACCAAATGGATGTTGCGTTGCTTGACAAGCTTGTCAAAGATGATCGCGATTCTGGCAAGCTTCCTCTTCTGTTGATAGCGAACGCTGGAACACCAGGTGCCGGTCACACAGACAAACTCAGTCGACTGAAGGAGCTCTGCGTGCAGTACAACATGTGGCTCCATGTCGAAGGGGTTAATTTGGCAACACTTGTTCTTGGTCAGGTCTCCTCCACTGTCACGGCAGCGACCAAGTGTGACAGTATGACTTTAACCCCGGGCCCGTGGTTGGGTCTTCCAGCTGTGCCCGCTGTCACTCTATACAGACATGAGGATCCAGCTCTGTCTCTGGCCGCAGGTTTGACTTCCAGTCAGCCTGTGGAGAAGCTTCGGGCTCTTCCTCTCTGGCTGTCCCTTCAGTACCTTGGGCATGATGGGATTGTTGAGAGGATTAAACACGCTTCGCAGCTAAGTCAACAGCTGTTGGAACATTTGAAGACACTTGCTTCAATCAAAACCTCGGTGGAGGATGAACTCAATTCTCCAGTGGTGGTGTTCAGGTTTTCACATGAAAACAGTGCTCCTTCAAGTGGAGGATCGGTAGAAGGATCTTATGCAGGCGAGAGAGATATCCTTGATGCCTTTAACAGATGGCTGGGTGATCAGCTGGCAGAGCAGGTTCCCCTCAGTGGTGTGGATGTGGTAGAGCTGGAAGATGAAGGCACATGTGTTCGTTTCAGCCCTCTCATGACCGCTGCAGctcttGGCACTCAGGAGAATGATGTGGCTGCACTGGTAGAAAAGCTGGCAGAGATGATTCCACTGCTATGCTGCACGCTGCGCCTCAGGCAGGACTTCAGAGATGAGGTGCTCCAGCAGGCCTCTCTTTCATACATCGAGGACCTCAACTGGCCGGGTCTTGGTGTCGTGAGGTTTGAGCCCAGAACCACAGACCTGGATGAAGACAAAAGACAAGACAGGGTGGAGAAGATCAACAGTGACTTGCTGAAGAAACTGATGGAGCTGGACACAGATCTCAACTTCTCTGGTGGTCCTGAGTTTAGTGAAGAGAAAAATTGCATATTTATTGGAATTGCAACAGAAGACCTGGATGTTGCAGAGCTGGTGGAAACTATAATGTCATTAGGTAGAGACATTGAAGAAAGTGGAAAGTTGTTTGAGAACATGACAGAGGTAGTGAGAAAAGGCATTCAGGAAGCTGAACTACAGCTTCAGAAAGCAAATGAAGAAAAACTAATGGAGGAGGGCGTACTTCGACAAATTCCTCTGGTGAGCTCTGTGCTAAACTGGTTCTCCCCGGTCCAGGCCTCTGTCAAAGGAAGAACGTTTAACCTTGCTGAAGGTTGTCTGGACAGTACTGAGCCAGTTTATTCAATAAAAGCCCAGATGAGGAAAGAAGATTCTCCTGATTCCCCCAAGGCCAACACCAGACGCTTTCCAGGCCAGAAGCTCTTCCGGCGGCCGGGAGCGGGATCAGACTCCATCAGTGAGACCAGCTCTGTCAGCCAGCTTGAAGAATCCTTCAGGGAAACTCTACACTCACAGGCTGCCGATGAAGCAGAGGTCCCGCAGGAACGTCCCGCTCACATACTAGAGGAAACGGCTATAGCGGACCAGCGAGTACCAGAGGGACAAGAAGCAGAGAGCGTGGAGACCATCAGATAAGACCACTCCGAAAACAAAAAGAGATGCTCtatattaatgaaaaaataattaaatgcatccACGACCTCGATGCCTTGAGCAAACCACTCTCGAAATTAAGAAGCAGCTTTAAGTGCAAAACCACTGGAATtttgtgaaaatgaaaataacGTGTGAGCGTATCATCTCCTATTATTCGTTATAATCAGTTGCAcatttagttttcttttatttgGTTAATCATAGATACATTATAGGGTCTCCTTCCAGTTCTTTATGTGCACTGCCAGTGTGTGCTTCCATTGTGGATGACATActttaagttacttttttttttaggcttATCCATCCGTAGGCCTGTCTGACAGGTTTTTTTCTGATCCATTTCCGCTTGTTATTTACACAACGAAAGGGCTATTGTGGCCTTACCGTCATGGTTATTAATGTCAAAATGTCTTGTTTGCCAAAAGCTGCTTTATGTACTTTCCATAGGCAGATGCGCAGGAAGGAAAAGGTTGACGCTTGAAGACTCATGCAGCTGTTTCTAATCAAATGATAGCCTTATTGCACTTTTATGTACAGAATGTCACACTTTAATCAGAACAgcaggatatttatttattctagaaGTCGTCCAAGTCTGAGAGAAGTTCAAATCAGACAGAAATCCATCCGGCACTTTTGGCTTTACCAATAGTGAAACGATTATTACACTGTATTCACTGTGAAGAATGTTTCAGAGATGTCTCTTCAAGTAATTGTTACGTTTTTCTTTGGATGTTTATGAAGGCTAAAAGTAATATACTTAAatgaaaatctttatttttgatttacaccAATGGTAATTgttttagcacacacacacacattaataaaatgttactggggaaataatgtagttttgttTAGCTATGAATGTTGTAGGAGTTATCATCCATAAGAAGTCCACTACAGCTCCAATCCATCCtttcacccacccatccatccatccctccgtcCATTCATCCTTCCTTCCTTGGGCATAAAGTGCTCTAATTTTTCATAACTGTGCTTCCTTGCTGAATCATGTAATTGTAGATCTGCTCGTCTTTTTCAAAATGATTCTGTCTTAACTGGTGCAATAAATCATTgggattttttttcctttggggAAGATGAGTACTGACTTGAAATATTGTGTCAAAAGGAAGAATATAGAGGTTTTTTATAATTGCAGTTTTGTTTTACAATGAGGAGTGATGTAAATGATAATAAACTAAATGGTACTAAAGAA
>TCONS_00050384
ATGGAGAAGCCGCCCGTgaagATGATGGACCCTACGTTGGCTGAAATGGGGAACCATCTTTCTGATGCCATGAAGATCTTGGAAAGTGGGAAATTGGAAACCGAACAGGGCCAGGAAGGAAGAAAGATGAGCTGGAAAGAGATTCCAGGACCGTTACAAGGAGACGGTCAGGATGTTGTCAGCATTCTTCAGCTTGTGCAGAACCTGATGCATGGAGATGATGAAGAGCAGGGTCACCGcaGGATGCAGTTTGTCGGAGAGCAGGGACACATGGCTCTGTTAGGACACAGTCTGGCCGCATATATTTCTGTCCTGGAGCGAGAGCGATTGAGAAAACTGACCACCCGCATCCTGTCAGACACCACTCTCTGGCTCTGCAGGCTTTTCAGATATGAAAATGGCTCTGCATATTTCCATGAAGATGACCGCGAGGGGCTGCTGAAGGTGTGTCGGCTGGTGATGAACACTCACTATGAGGACTTCACCACTGAGGGCTTCACAGCGCTCAGCTCCAAACATCCCGTCATCTACCAAAGTGCTGCATGCAGACCTGGCCTGGGACAACATCTCTGCAGTCAGCTAGGGCTTCCTCTgtcttgcctttgtgttgtgccCTGTAACACCATGTTTGGCTCCTTGCACCAAATGGATGTTGCGTTGCTTGACAAGCTTGTCAAAGATGATCGCGATTCTGGCAAGCTTCCTCTTCTGTTGATAGCGAACGCTGGAACACCAGGTGCCGGTCACACAGACAAACTCAGTCGACTGAAGGAGCTCTGCGTGCAGTACAACATGTGGCTCCATGTCGAAGGGGTTAATTTGGCAACACTTGTTCTTGGTCAGGTCTCCTCCACTGTCACGGCAGCGACCAAGTGTGACAGTATGACTTTAACCCCGGGCCCGTGGTTGGGTCTTCCAGCTGTGCCCGCTGTCACTCTATACAGACATGAGGATCCAGCTCTGTCTCTGGCCGCAGGTTTGACTTCCAGTCAGCCTGTGGAGAAGCTTCGGGCTCTTCCTCTCTGGCTGTCCCTTCAGTACCTTGGGCATGATGGGATTGTTGAGAGGATTAAACACGCTTCGCAGCTAAGTCAACAGCTGTTGGAACATTTGAAGACACTTGCTTCAATCAAAACCTCGGATATCCTTGACAGTGAGGTGTCTCTCCTCGAGGCTTTGCGCATGGTGGAGGATGAACTCAATTCTCCAGTGGTGGTGTTCAGGTTTTCACATGAAAACAGTGCTCCTTCAAGTGGAGGATCGGTAGAAGGATCTTATGCAGGCGAGAGAGATATCCTTGATGCCTTTAACAGATGGCTGGGTGATCAGCTGGCAGAGCAGGTTCCCCTCAGTGGTGTGGATGTGGTAGAGCTGGAAGATGAAGGCACATGTGTTCGTTTCAGCCCTCTCATGACCGCTGCAGctcttGGCACTCAGGAGAATGATGTGGCTGCACTGGTAGAAAAGCTGGCAGAGATGATTCCACTGCTATGCTGCACGCTGCGCCTCAGGCAGGACTTCAGAGATGAGGTGCTCCAGCAGGCCTCTCTTTCATACATCGAGGACCTCAACTGGCCGGGTCTTGGTGTCGTGAGGTTTGAGCCCAGAACCACAGACCTGGATGAAGACAAAAGACAAGACAGGGTGGAGAAGATCAACAGTGACTTGCTGAAGAAACTGATGGAGCTGGACACAGATCTCAACTTCTCTGGTGGTCCTGAGTTTAGTGAAGAGAAAAATTGCATATTTATTGGAATTGCAACAGAAGACCTGGATGTTGCAGAGCTGGTGGAAACTATAATGTCATTAGGTAGAGACATTGAAGAAAGTGGAAAGTTGTTTGAGAACATGACAGAGGTAGTGAGAAAAGGCATTCAGGAAGCTGAACTACAGCTTCAGAAAGCAAATGAAGAAAAACTAATGGAGGAGGGCGTACTTCGACAAATTCCTCTGGTGAGCTCTGTGCTAAACTGGTTCTCCCCGGTCCAGGCCTCTGTCAAAGGAAGAACGTTTAACCTTGCTGAAGGTTGTCTGGACAGTACTGAGCCAGTTTATTCAATAAAAGCCCAGATGAGGAAAGAAGATTCTCCTGATTCCCCCAAGGCCAACACCAGACGCTTTCCAGGCCAGAAGCTCTTCCGGCGGCCGGGAGCGGGATCAGACTCCATCAGTGAGACCAGCTCTGTCAGCCAGCTTGAAGAATCCTTCAGGGAAACTCTACACTCACAGGCTGCCGATGAAGCAGAGGTCCCGCAGGAACGTCCCGCTCACATACTAGAGGAAACGGCTATAGCGGACCAGCGAGTACCAGAGGGACAAGAAGCAGAGAGCGTGGAGACCATCAGATAA
>TCONS_00050385
GATGCGGAGATACACCGGACAAACCACGGTCGACTGTTTCCTTTAGTGCACCGCTCAATGTAAAAGAGCTGGAgcaaaatgattttttaataGCTGGTGGTCTGTCATGTACTAATTTAGTCTTAAAAACCGTGTTGAAACGGCAACCGTCACAGTGTTGCAAAATTGAGGGATTGTGTTTGAGCAGGATGTGCTCCAGGACAAGGCTTGACATTCAGTGTTATCCTAGTCTGGACGAACAGATGAGAGCTGCTGAATTGAAATGAGCCTTGTCATCCGACAGGTTTTCGACTTCAACACACCCCTGCATCCTGAATATCAGGAATTCTGTGTGTGAAGAGAGAAAATGATGGACCCTACGTTGGCTGAAATGGGGAACCATCTTTCTGATGCCATGAAGATCTTGGAAAGTGGGAAATTGGAAACCGAACAGGGCCAGGAAGGAAGAAAGATGAGCTGGAAAGAGATTCCAGGACCGTTACAAGGAGACGGTCA

Function

symbol description
pdxdc1 Predicted to enable 2-keto-4-methylthiobutyrate aminotransferase activity; carboxy-lyase activity; and pyridoxal phosphate binding activity. Predicted to act upstream of or within carboxylic acid metabolic process. Predicted to be active in intracellular membrane-bounded organelle. Is expressed in EVL; notochord; periderm; pharynx; and polster. Orthologous to human PDXDC1 (pyridoxal dependent decarboxylase domain containing 1).

GO:

id name namespace
GO:0030149 sphingolipid catabolic process biological_process
GO:0006665 sphingolipid metabolic process biological_process
GO:0001667 ameboidal-type cell migration biological_process
GO:0019752 carboxylic acid metabolic process biological_process
GO:0005783 endoplasmic reticulum cellular_component
GO:0008117 sphinganine-1-phosphate aldolase activity molecular_function
GO:0030170 pyridoxal phosphate binding molecular_function
GO:0016829 lyase activity molecular_function
GO:0016831 carboxy-lyase activity molecular_function
GO:0003824 catalytic activity molecular_function

KEGG: NA

ZFIN:

id description
ZDB-GENE-040912-16 Predicted to enable 2-keto-4-methylthiobutyrate aminotransferase activity; carboxy-lyase activity; and pyridoxal phosphate binding activity. Predicted to act upstream of or within carboxylic acid metabolic process. Predicted to be active in intracellular membrane-bounded organelle. Is expressed in EVL; notochord; periderm; pharynx; and polster. Orthologous to human PDXDC1 (pyridoxal dependent decarboxylase domain containing 1).

Ensembl:

ensembl_id ENSDARG00000101886

RNA

RNA id representative length rna type GC content exon number start site end site
TCONS_00050383 False 3864 mRNA 0.46 23 36616713 36644776
TCONS_00050384 False 2349 mRNA 0.51 24 36617024 36643524
TCONS_00050385 True 495 processed_transcript 0.46 4 36617142 36619802

Neighbor

gene id symbol gene type direction distance location
XLOC_025567 si:dkeyp-72e1.9 coding upstream 29734 36515376 ~ 36586979 (+)
XLOC_025566 NA coding upstream 190880 36424002 ~ 36425833 (+)
XLOC_025565 rgs9a coding upstream 213479 36366053 ~ 36403234 (+)
XLOC_025564 slc16a6b coding upstream 288041 36313532 ~ 36328672 (+)
XLOC_025563 zgc:86896 coding upstream 310310 36275633 ~ 36306403 (+)
XLOC_025569 gspt1l coding downstream 1278 36646054 ~ 36664310 (+)
XLOC_025570 nde1 coding downstream 26809 36671585 ~ 36684388 (+)
XLOC_025571 abcc1 coding downstream 68701 36713477 ~ 36743962 (+)
XLOC_025572 NA coding downstream 190411 36835187 ~ 36849836 (+)
XLOC_025573 ezh1 coding downstream 214925 36859701 ~ 36892651 (+)
XLOC_025429 BX649540.1 misc upstream 6367677 30248739 ~ 30249036 (+)
XLOC_025559 NA non-coding upstream 498966 36115306 ~ 36117747 (+)
XLOC_025558 NA non-coding upstream 593181 36017823 ~ 36023532 (+)
XLOC_025557 dre-mir-365-2 non-coding upstream 655627 35960989 ~ 35961086 (+)
XLOC_025556 dre-mir-193a-1 non-coding upstream 656703 35959912 ~ 35960010 (+)
XLOC_025574 NA non-coding downstream 250656 36895432 ~ 36936135 (+)
XLOC_025579 NA non-coding downstream 831013 37475789 ~ 37477433 (+)
XLOC_025581 NA non-coding downstream 950565 37595341 ~ 37596530 (+)
XLOC_025582 NA non-coding downstream 951953 37596729 ~ 37627885 (+)

Expression


Co-expression Network