XLOC_038129 (phgdh)


Basic Information

Item Value
gene id XLOC_038129
gene name phgdh
gene type coding
species zebrafish (Danio rerio)
category of species model fish

Chromosome Information

Item Value
chromosome id NC_007120.7
NCBI id CM002893.2
chromosome length 56459846
location 48185936 ~ 48214216 (-)
genome version GRCz11_2017_zebrafish_Genome

Sequence

>TCONS_00074763
CGGCGCGCGCGCACGCGATCATTCATTTGAAGCGAGAGTCGAGTCCGCAAGTCCACGATAATAATGGCTCCTATATCAGTCAAACGCGTTTTAATCAGTGAAAGCGTCGATCCCTGCTGTAAAAGTGTTCTCCAGGAAAATGGCATTGAGGTGACGGAGAAGCAGCAGATGACTAAAGAAGAGTTGATTGCAGAGATTCGGAATTATGATGGTTTAATAGTCCGATCAGCGACCAAAGTTACCGCTGATGTCATCAATGCTGGCAGTAGCTTGAAGATCATCGGCCGAGCCGGAACAGGAGTCGACAACGTGGATGTGGATGCGGCAACCAAGAGAGGCATCATTGTCATGAAcaCTCCAAGCGGAAACACACTCAGTGCTGCTGAACTCACCTGTGCTCTTGTGATGAGCTTGTCAAGACATATTCCTCAAGCTGTCATTTCAATGAAAGATGGAAAATGGGATCGTAAAAAGTTCATGGGTTCAGAGCTGTATGGAAAAGTTCTTGGCATTGTGGGACTTGGAAGGATCGGCAAAGAGGTGGCTACAAGAATGCAGTCTTTTGGTATGAAGACCATAGGTTATGACCCGATCACTCCTCCAGAGGTGTCTGCGAGCTGGGGTGTGGAGCAGATGACTCTGGATCAGTTGTGGCCGCAGTGTGATTATATCACAGTCCACACTCCCCTCATGGCCTCCACCACAGGTCTGCTCAATGATGCCTCATTTGCGAAGTGTAAGAAGGGTGTGAAGGTGGTGAACTGTGCCCGTGGAGGGATCATCGATGAAGCCGCTCTGCTTCGGGCTCTGGAGTCGGGTCAGTGTGGAGGAGCAGGACTGGACGTGTTTGTGGAGGAGCCTCCTAGAGAGCGGGCGCTGGTCAACCACCCCAATGTCATCAGCTGTCCTCATCTGGGTGCCAGCACAAAAGAAGCACAGGCTCGCTGCGGGAAAGACATCGCCCTGCAGATTGTGGACATGGCCACAGGAAAAGCTTTAGTGGGAGCTGTGAATGCTCAGGTGTTGGCCAGTACTTTCTCTCCTGACTCTCAGCAGTGGATTCGTCTGGGAGAGTCTATGGGCAAAGTGTTGAAGGCCTGCAGCGCTTCCACACAGCCCTGCAGTCAGCTCCATGTTACATCACTGGGTGAAGCTTTAAAGAAGTCCACTGGGTTTTTGAGCTCAGCAGCTGTTGTTGGTTTGCTCACTGAAGCTCCTCATAATGGACCCAACTTGGTGAATGCGCTGCCTCTGGCTAAAGAGACTGGAATCACCGTGCACACAGATCATAAGGCCTCGGATGAGCGGGAGGCATGTGTGATGGAGGTCTCTGTGAACGGCAGCCGTTATAAGGCTGTTGGTTCAGTGCAGGCTGGTGTTCCTGTGCTGTTGGAGCTCAATGGAAGTGTGTTTCGACAGCCTGTTCCTCTGACTGGACACCTGCTGTTCTTCAGGGCCAATTGTTCCACGGAGTTCCTGTCCTCCATAACCgGGGTTTTGGCCACTGCAGGTGTGGAGCTGCAGTCCTTCAGTGCCTCTAGCAGCAGCAGTGGTGGTGAGAAGTGGTACTGCATGGGCATCTCCTCTCTGCTGGGGGACATTGGGGCCTTGAAGTCTTTAGTGAAAGACGCTGCACAGCTCACCGTCTAAATACAACAGTGATCCAGCAGACCTGATCCGCTTAACATTCCAGCATCTAAAGCTCTAGCCGGACTGAGATCCATAGCGTACTGTTACTTACCTCGTTCATATCACTACAAACCTTAAAATAACAGCGTACTGTAGAAAGAGGAGTTTTACCGTTTCTGTTGTCATCTGTTTACTAAATCCACTATTTGTATTGCAGAAACAAAAATGTGTTTGATAAAAACAATAACCATCAGTGCTGGTGTCTCATTTTGAagtaaagtgttgtttttttctgtcacttaaaaatgtaaaaatcaataGCTGATGCCAGTTTATATTGCTAATATAGACATTTCTTGAATATGAAGTGGACTTTCATCATGAGAAAGGGCTCTTCGGGACTGCCCCAACCTTCTGTTTTTCCTTTTTGGATTAGCAATCATTAACCATGTTAACCATGGATCATAAAATCCACCAGTGAAACCATTCATCTGTGGGCGTTACAGGTAATGAACTTATCCATTTTCACAGGAGTTTACAGGGGTTTTCTGGAGGGGTGAAGTATTCAAAGCTTATTAAATGGTCATAGGGGTTCCTCAGGGTTCAGTTCTTGGACCTCTTCTGTTTTCTATTTACACAAGATACCTGGGACCTATCATTCAGGCTAATGGTTTCTactattaagctgctttgacacaatctacattgtaaaaccgCTATACtaataaagataaatttaattaaa

Function

symbol description
phgdh Predicted to enable phosphoglycerate dehydrogenase activity. Predicted to act upstream of or within L-serine biosynthetic process. Human ortholog(s) of this gene implicated in Neu-Laxova syndrome 1; PHGDH deficiency; and amino acid metabolic disorder. Orthologous to human PHGDH (phosphoglycerate dehydrogenase).

GO:

id name namespace
GO:0055114 oxidation-reduction process biological_process
GO:0006520 cellular amino acid metabolic process biological_process
GO:0008652 cellular amino acid biosynthetic process biological_process
GO:0006564 L-serine biosynthetic process biological_process
GO:0005575 cellular_component cellular_component
GO:0016491 oxidoreductase activity molecular_function
GO:0004617 phosphoglycerate dehydrogenase activity molecular_function
GO:0051287 NAD binding molecular_function
GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor molecular_function

KEGG:

id description
ko00680 Methane metabolism
ko00260 Glycine, serine and threonine metabolism
ko00270 Cysteine and methionine metabolism
ko04147 Exosome

ZFIN:

id description
ZDB-GENE-030131-647 Predicted to enable phosphoglycerate dehydrogenase activity. Predicted to act upstream of or within L-serine biosynthetic process. Human ortholog(s) of this gene implicated in Neu-Laxova syndrome 1; PHGDH deficiency; and amino acid metabolic disorder. Orthologous to human PHGDH (phosphoglycerate dehydrogenase).

Ensembl:

ensembl_id ENSDARG00000001873

RNA

RNA id representative length rna type GC content exon number start site end site
TCONS_00074763 True 2374 mRNA 0.47 12 48185936 48214216

Neighbor

gene id symbol gene type direction distance location
XLOC_038128 klhl23 coding downstream 1113 48134394 ~ 48184823 (-)
XLOC_038127 BX321905.1 coding downstream 51651 48134214 ~ 48134285 (-)
XLOC_038126 arpc2 coding downstream 108902 48043162 ~ 48077034 (-)
XLOC_038125 NA coding downstream 231379 47899770 ~ 47954557 (-)
XLOC_038124 tns1b coding downstream 531732 47436010 ~ 47654204 (-)
XLOC_038130 klhl41a coding upstream 56163 48270379 ~ 48281941 (-)
XLOC_038131 bbs5 coding upstream 70390 48284606 ~ 48296469 (-)
XLOC_038132 col28a2a coding upstream 83196 48297412 ~ 48371379 (-)
XLOC_038133 zgc:172182 coding upstream 172712 48386928 ~ 48407408 (-)
XLOC_038134 BX927361.1 coding upstream 418644 48632860 ~ 48632996 (-)
XLOC_038123 AL929460.1 non-coding downstream 765429 47420391 ~ 47420507 (-)
XLOC_038121 BX005007.1 non-coding downstream 1390369 46795447 ~ 46795567 (-)
XLOC_038120 NA non-coding downstream 1484611 46692085 ~ 46701325 (-)
XLOC_038137 CR626882.1 non-coding upstream 536210 48750426 ~ 48750727 (-)
XLOC_038139 NA non-coding upstream 655491 48869707 ~ 48937240 (-)
XLOC_038140 NA non-coding upstream 917798 49132014 ~ 49244598 (-)
XLOC_038142 NA non-coding upstream 1530136 49744352 ~ 49754435 (-)

Expression


Co-expression Network

Homologous

species gene id symbol gene type chromosome NCBI id location
grasscarp (Ctenopharyngodon idella) CI01000009_15726357_15736168 PHGDH coding CI01000009 null 15726145 ~ 15736168 (-)