Gene loci information

Transcript annotation

  • This transcript has been annotated as Serine hydroxymethyltransferase.

Parent gene

Gene structure

  • The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.

Chromosome Gene Transcript Category ID Start End
chr_1 g10612 g10612.t3 TTS g10612.t3 10752759 10752759
chr_1 g10612 g10612.t3 isoform g10612.t3 10752819 10753894
chr_1 g10612 g10612.t3 exon g10612.t3.exon1 10752819 10753279
chr_1 g10612 g10612.t3 cds g10612.t3.CDS1 10752819 10753279
chr_1 g10612 g10612.t3 exon g10612.t3.exon2 10753361 10753894
chr_1 g10612 g10612.t3 cds g10612.t3.CDS2 10753361 10753847
chr_1 g10612 g10612.t3 TSS g10612.t3 10754453 10754453

Sequences

>g10612.t3 Gene=g10612 Length=995
CTAATTTTGTTGTGTATACTGCATTAATTCAACCTCATGATAGAATTATGGGCTTAGACT
TGCCTGATGGTGGTCATTTAACACATGGATTTATGACTCCCAACAAACGCATTTCTGCTA
CATCAATTTTCTTCGAAAGTATGCCTTATAAAGTTGATCCAGAGACTGGTATTATTGACT
ACAATAAAATGGAAGAGATGGCAAAACTTTTTAAACCAAAAATTATTATTACTGGAATGT
CATGTTATAGTCGTTGTCTTGATTATAAGAAGTTTAGAGAAATTGCTGATCAAAATGGTG
CATATCTTTTCTCTGATATGGCTCATGTTTCTGGTCTTGTCGCAGCTAAATTAATTCCAT
CTCCTTTTGAATATTCGGATGTTGTTTCTACGACAACACACAAGACGCTTCGTGGACCAA
GAGCTGGTGTGATTTTCTATCGCAAAGGTGTACGATCAGTAAAATCAAATGGTGAAAAAG
TGATGTATGATCTGGAATCAAGAATCAATCAAGCAGTTTTCCCAGCTCTTCAAGAGCAAG
TTTTGAAAAATGCACGAAGATTGTGTAAAGGATTAATGGATAAGGGCTACAAAATTGCTG
CAGATGGTACTGATGTGCATTTAGTTCTTGTTGACTTACGACCATCTGGAATTACTGGCG
CACGTGCAGAATACATTCTTGAAGAAATCTCAATAGCATGCAATAAAAACACTGTTCCTG
GTGATAAATCTGCTTTGAATCCTTCTGGAATTCGACTTGGTACACCAGCACTGACGACAA
GAGGTTTACTTGAGGCAGATATTGATAAAGTCGTTGAATTTATTCATCGTGGTCTGGAAT
TGTCAAAAGAAATCGTTGCCACATCTGGTCCGAAATTAGTAGATTTTAAAACAGCTGTTC
ATAGTGATCAATTTGCATCAAAAGTCAAGGCCATTAGAGATGAAGTTGAAGAATTCAGCA
TGAAATTCCCAATGCCTGGCTATGATGAATATTAA

>g10612.t3 Gene=g10612 Length=315
MGLDLPDGGHLTHGFMTPNKRISATSIFFESMPYKVDPETGIIDYNKMEEMAKLFKPKII
ITGMSCYSRCLDYKKFREIADQNGAYLFSDMAHVSGLVAAKLIPSPFEYSDVVSTTTHKT
LRGPRAGVIFYRKGVRSVKSNGEKVMYDLESRINQAVFPALQEQVLKNARRLCKGLMDKG
YKIAADGTDVHLVLVDLRPSGITGARAEYILEEISIACNKNTVPGDKSALNPSGIRLGTP
ALTTRGLLEADIDKVVEFIHRGLELSKEIVATSGPKLVDFKTAVHSDQFASKVKAIRDEV
EEFSMKFPMPGYDEY

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g10612.t3 Gene3D G3DSA:3.40.640.10 - 1 173 2.8E-74
3 g10612.t3 PANTHER PTHR11680 SERINE HYDROXYMETHYLTRANSFERASE 1 162 1.8E-146
5 g10612.t3 PANTHER PTHR11680:SF21 SERINE HYDROXYMETHYLTRANSFERASE, CYTOSOLIC 1 162 1.8E-146
2 g10612.t3 PANTHER PTHR11680 SERINE HYDROXYMETHYLTRANSFERASE 162 314 1.8E-146
4 g10612.t3 PANTHER PTHR11680:SF21 SERINE HYDROXYMETHYLTRANSFERASE, CYTOSOLIC 162 314 1.8E-146
1 g10612.t3 Pfam PF00464 Serine hydroxymethyltransferase 1 162 2.3E-79
7 g10612.t3 ProSitePatterns PS00096 Serine hydroxymethyltransferase pyridoxal-phosphate attachment site. 111 127 -
6 g10612.t3 SUPERFAMILY SSF53383 PLP-dependent transferases 1 312 1.32E-110

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0004372 glycine hydroxymethyltransferase activity MF
GO:0035999 tetrahydrofolate interconversion BP
GO:0003824 catalytic activity MF
GO:0030170 pyridoxal phosphate binding MF
GO:0019264 glycine biosynthetic process from serine BP

KEGG

Orthology

This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).

Expression

Transcript expression in Pv11 cells

TPM values are indicated as average +/- STDEV.

Differential expression

Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below. There were no conditions that were differentially expressed