XLOC_026663 (shmt1)


Basic Information

Item Value
gene id XLOC_026663
gene name shmt1
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 40260929 ~ 40276071 (-)
genome version GRCz11_2017_zebrafish_Genome

Sequence

>TCONS_00051929
ATTGGTCTCCAAATTTCGCGGACTTTGGCACGAGGAAAGCTGGAAGAGACCACAAAGTAGGTTTGGGCAAAACTTGTCTGACACATTTGCGAAGTTCATCAACCATGTCCCAGCTCAACGGTCATACTGAGAAAACATGGGAATCTCATAACAAGATGATGTTGGAGCCTCTGAGCACCAATGATCCTGAGGTGTTTGACATCATAAAGAAGGAGAAGAAGCGTCAGACGTATGGGTTAGAGCTCATTGCTTCTGAAAACTTCACAAGTCGAGCTGTTTTGGAGGCTCTGGGCTCCTGCATGAACAACAAGTACTCTGAAGGTTATCCTGGCCAGAGGTATTATGGAGGCACAGAGCATGTTGATGAGCTGGAGCGTTTGTGTCAGGACCGAGCTTTGAAGGTGTACGGCCTCGACCCGGAGAAATGGGGAGTGAATGTTCAGCCGTACTCTGGGTCGCCCGCAAACTTTGCCGTATACACAGCTATAGTGGAGCCCCATGGGCGAATCATGGGCCTTGATCTGCCAGATGGTGGTCATCTCACTCACGGCTTTATGACTGACAAGAAGAAAATCTCTGCCACGTCCATTTTTTTTGAGTCCATGCCTTATAAGGTCAATCCAGAAACTGGGTACATCGATTATAACAGACTTGAGGAAAATGCTCGTCTCTTCCACCCAAGACTAATCATTGCAGGCACCAGTTGCTATTCCCGAAACTTGGACTACAGTCGGCTGAGAAAGATTGCAGATGAGAACGGAGCGTATCTTCTGGCAGACATGGCTCATATCAGTGGTCTGGTGGCAGCAGGGGTCGTTCCTTCTCCATTTGAATACTGTGATGTTGTTTCCACGACCACCCATAAGACTCTGAGGGGCTGCAGGGCAGGAGTCATATTTTTCAGGAAGGGAGTTCGTAGTGTTGATGCAAAGACCGGCAAGGAGACGATGTACAATTTGGAAAGTCTGATTAATCAGGCTGTGTTTCCTGGACTGCAGGGCGGCCCGCATAACCATGCCATCGCAGGTGTCGCTGTTGCTTTGAAGCAGGCGCTGACTCCTGAGTTTAAAACCTATCAGTTGCAAGTTCTGGCAAACTGCAAGGCTTTGGCCTCTGCTCTGATGGACAAGGGCTACAAAGTTGTTACTGgcgGCTCTGATAATCACCTCATCTTGGTTGATCTCCGTTCAAATGGAACTGATGGAGGAAGAGCAGAGAAAGTTCTGGAAGCCTGTGCCATCGCCTGCAACAAAAACACCTGCCCAGGTGATAAAAGTGCCTTGCGGCCCAGCGGCTTGCGTTTAGGGTCTCCGGCTCTCACATCTCGAGGACTGTTGGAGGAACATTTCCATAAGGTTGCAGAGTTCATTCACCAGGGCATTGTGTTGACTTTGGAGATCCAGAAAAACATGAACCCTAAAGCAACATTGAAGGAGTTTAAGGAGGAACTGGCTCAAAATGAGAAGTACCAACTGAAAATAAAGGAAATCCGAAAGGAAGTGGAAGACTTTGCTGGAAAGTTCCCAATGCCCGGGTTGCCAGAGTTATAACACATTTCTGCTTGACTTTTCTGTCCAAAAGATTTCCTTTACATTTGATGAGCACAGAGGCTTCAGTACAGATCACTGCAGTCAGAATACACATCAATCAGATGATTTCCCAATTATACAAGTCATGTTTGTCCTCAATATCACACATCAGGGTGGTTTCTGTAGACTTTTCTTGTATGTGGGCAAACTATAGTGTAACCTGAAACTGCACAACCAAGAATGTGTACATGCTGTGCAAATAAAGCTGGAAATATTGTCAATGTGAACACGTGACGTCTTTCTTGATGACTGTGTAGAATTTACTTTAA
>TCONS_00051930
CATTTGGCAGTCTTGTATTGATTAATAATGTTTATTCCAGTTCATCAACCATGTCCCAGCTCAACGGTCATACTGAGAAAACATGGGAATCTCATAACAAGATGATGTTGGAGCCTCTGAGCACCAATGATCCTGAGGTGTTTGACATCATAAAGAAGGAGAAGAAGCGTCAGACGTATGGGTTAGAGCTCATTGCTTCTGAAAACTTCACAAGTCGAGCTGTTTTGGAGGCTCTGGGCTCCTGCATGAACAACAAGTACTCTGAAGGTTATCCTGGCCAGAGGTATTATGGAGGCACAGAGCATGTTGATGAGCTGGAGCGTTTGTGTCAGGACCGAGCTTTGAAGGTGTACGGCCTCGACCCGGAGAAATGGGGAGTGAATGTTCAGCCGTACTCTGGGTCGCCCGCAAACTTTGCCGTATACACAGCTATAGTGGAGCCCCATGGGCGAATCATGGGCCTTGATCTGCCAGATGGTGGTCATCTCACTCACGGCTTTATGACTGACAAGAAGAAAATCTCTGCCACGTCCATTTTTTTTGAGTCCATGCCTTATAAGGTCAATCCAGAAACTGGGTACATCGATTATAACAGACTTGAGGAAAATGCTCGTCTCTTCCACCCAAGACTAATCATTGCAGGCACCAGTTGCTATTCCCGAAACTTGGACTACAGTCGGCTGAGAAAGATTGCAGATGAGAACGGAGCGTATCTTCTGGCAGACATGGCTCATATCAGTGGTCTGGTGGCAGCAGGGGTCGTTCCTTCTCCATTTGAATACTGTGATGTTGTT
>TCONS_00051931
TTCGCGGACTTTGGCACGAGGAAAGCTGGAAGAGACCACAAATTCATCAACCATGTCCCAGCTCAACGGTCATACTGAGAAAACATGGGAATCTCATAACAAGATGATGTTGGAGCCTCTGAGCACCAATGATCCTGAGGTGTTTGACATCATAAAGAAGGAGAAGAAGCGTCAGACGTATGGGTTAGAGCTCATTGCTTCTGAAAACTTCACAAGTCGAGCTGTTTTGGAGGCTCTGGGCTCCTGCATGAACAACAAGTACTCTGAAGGTTATCCTGGCCAGAGGTATTATGGAGGCACAGAGCATGTTGATGAGCTGGAGCGTTTGTGTCAGGACCGAGCTTTGAAGGTGTACGGCCTCGACCCGGAGAAATGGGGAGTGAATGTTCAGCCGTACTCTGGGTCGCCCGCAAACTTTGCCGTATACACAGCTATAGTGGAGCCCCATGGGCGAATCATGGGCCTTGATCTGCCAGATGGTGGTCATCTCACTCACGGCTTTATGACTGACAAGAAGAAAATCTCTGCCACGTCCATTTTTTTTGAGTCCATGCCTTATAAGGTCAATCCAGAAACTGGGTACATCGATTATAACAGACTTGAGGAAAATGCTCGTCTCTTCCACCCAAGACTAATCATTGCAGGCACCAGTTGCTATTCCCGAAACTTGGACTACAGTCGGCTGAGAAAGATTGCAGATGAGAACGGAGCGTATCTTCTGGCAGACATGGCTCATATCAGTGGTCTGGTGGCAGCAGG

Function

symbol description
shmt1 Enables glycine hydroxymethyltransferase activity. Predicted to be involved in several processes, including L-serine metabolic process; folic acid-containing compound metabolic process; and protein homotetramerization. Predicted to act upstream of or within methylation. Located in cytosol and nucleus. Is expressed in several structures, including digestive system; immature eye; midbrain; neural tube; and oocyte. Human ortholog(s) of this gene implicated in breast cancer. Orthologous to human SHMT1 (serine hydroxymethyltransferase 1).

GO:

id name namespace
GO:1904482 cellular response to tetrahydrofolate biological_process
GO:0019264 glycine biosynthetic process from serine biological_process
GO:0009113 purine nucleobase biosynthetic process biological_process
GO:0006730 one-carbon metabolic process biological_process
GO:0046653 tetrahydrofolate metabolic process biological_process
GO:0046655 folic acid metabolic process biological_process
GO:0051289 protein homotetramerization biological_process
GO:0006544 glycine metabolic process biological_process
GO:0006565 L-serine catabolic process biological_process
GO:0032259 methylation biological_process
GO:0035999 tetrahydrofolate interconversion biological_process
GO:0005829 cytosol cellular_component
GO:0005634 nucleus cellular_component
GO:0005737 cytoplasm cellular_component
GO:0050897 cobalt ion binding molecular_function
GO:0016740 transferase activity molecular_function
GO:0008168 methyltransferase activity molecular_function
GO:0000900 translation repressor activity, mRNA regulatory element binding molecular_function
GO:0030170 pyridoxal phosphate binding molecular_function
GO:0042803 protein homodimerization activity molecular_function
GO:0008270 zinc ion binding molecular_function
GO:0070905 serine binding molecular_function
GO:0016597 amino acid binding molecular_function
GO:0048027 mRNA 5'-UTR binding molecular_function
GO:0004372 glycine hydroxymethyltransferase activity molecular_function
GO:0003824 catalytic activity molecular_function

KEGG: NA

ZFIN:

id description
ZDB-GENE-040426-1558 Enables glycine hydroxymethyltransferase activity. Predicted to be involved in several processes, including L-serine metabolic process; folic acid-containing compound metabolic process; and protein homotetramerization. Predicted to act upstream of or within methylation. Located in cytosol and nucleus. Is expressed in several structures, including digestive system; immature eye; midbrain; neural tube; and oocyte. Human ortholog(s) of this gene implicated in breast cancer. Orthologous to human SHMT1 (serine hydroxymethyltransferase 1).

Ensembl:

ensembl_id ENSDARG00000052816

RNA

RNA id representative length rna type GC content exon number start site end site
TCONS_00051929 False 1858 mRNA 0.47 12 40260929 40276071
TCONS_00051930 False 794 mRNA 0.47 6 40268324 40275096
TCONS_00051931 True 759 mRNA 0.49 7 40268361 40276057

Neighbor

gene id symbol gene type direction distance location
XLOC_026662 top3a coding downstream 6295 40235288 ~ 40254634 (-)
XLOC_026661 flii coding downstream 28314 40206031 ~ 40232615 (-)
XLOC_026660 znf598 coding downstream 58322 40185253 ~ 40202607 (-)
XLOC_026659 NA coding downstream 79275 40180136 ~ 40181654 (-)
XLOC_026658 drg2 coding downstream 98062 40153819 ~ 40162867 (-)
XLOC_026664 pdap1b coding upstream 1633 40277704 ~ 40284744 (-)
XLOC_026665 atp5mf coding upstream 20714 40296785 ~ 40301467 (-)
XLOC_026666 NA coding upstream 119992 40396063 ~ 40405386 (-)
XLOC_026667 actb2 coding upstream 250036 40526107 ~ 40529804 (-)
XLOC_026668 rnf216 coding upstream 324699 40600770 ~ 40664913 (-)
XLOC_026657 BX649547.1 non-coding downstream 172128 40088685 ~ 40088801 (-)
XLOC_026654 BX649356.3 non-coding downstream 303455 39957358 ~ 39957474 (-)
XLOC_026653 BX649356.2 non-coding downstream 309402 39945865 ~ 39951527 (-)
XLOC_026651 BX322795.1 non-coding downstream 611367 39649445 ~ 39649562 (-)
XLOC_026671 NA non-coding upstream 498347 40774418 ~ 40777723 (-)
XLOC_026680 CR769786.1 non-coding upstream 1035951 41312022 ~ 41312143 (-)
XLOC_026681 BX537310.2 non-coding upstream 1120052 41396123 ~ 41512210 (-)
XLOC_026687 NA non-coding upstream 1907282 42183353 ~ 42205112 (-)

Expression


Co-expression Network