General information for g10612.t5
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Serine hydroxymethyltransferase.
Parent gene
- The parent gene g10612 is located on chr_1: 10752819..10754743 (- strand)
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.t5 | TTS | g10612.t5 | 10752759 | 10752759 |
| chr_1 | g10612 | g10612.t5 | isoform | g10612.t5 | 10752819 | 10754743 |
| chr_1 | g10612 | g10612.t5 | exon | g10612.t5.exon1 | 10752819 | 10753894 |
| chr_1 | g10612 | g10612.t5 | cds | g10612.t5.CDS1 | 10752819 | 10753847 |
| chr_1 | g10612 | g10612.t5 | exon | g10612.t5.exon2 | 10754123 | 10754743 |
| chr_1 | g10612 | g10612.t5 | TSS | g10612.t5 | 10754843 | 10754843 |
Sequences
>g10612.t5 Gene=g10612 Length=1697
ATGTCAAGGAAGTTTTTGTTTGTAAATATTTTGAAAAATTATTCATTAAGAAGGCAAAAC
ATTCATTTATCGGCTAGACAGTATCAAATTGATGTAAGTTGATTATTGATTGATAATGAT
TTTTAAATAGTGTATTATGTTATCAAATGCATAAGGCTATCAACGTCATTATAAGAAAAA
ATAAATTTATTTAGTGCAAAAATTAAAAACATGTTTTGCTAGAAAAAGAGAGAAGTATAA
ATGAGAGAGAAAGAAAGATAAGGCAATAACGACAAAATAATAAAACTCTCATTCACAAGT
TGATCGTCGTGGTGTTAATACTCAAATATTTTGTTTAAGCATTCTTGAGTTTTTTCGTGT
TTTTGTAGAAAATGTCGGGATCGGCTAAAATTTTGCATCAAAATTTGTGGGATCAAGATG
AGGAGTTGTTTGCAATAATTAAAAAAGAAAAGCAGCGTCAATTGCGCGGGCTTGAGATGA
TTGCAAGCGAGAATTTTACTTCATTATCCGTTCTTCAATGTCTCAGTTCTTGTTTACACA
ACAAATATTCTGAAGGAATGCCAGGTCAACGGTGAGTCTATCTTATCAAATGATTTGATA
ATAATTCTTTTTAAACAGTATCTAATTTTGTTGTGTATACTGCATTAATTCAACCTCATG
ATAGAATTATGGGCTTAGACTTGCCTGATGGTGGTCATTTAACACATGGATTTATGACTC
CCAACAAACGCATTTCTGCTACATCAATTTTCTTCGAAAGTATGCCTTATAAAGTTGATC
CAGAGACTGGTATTATTGACTACAATAAAATGGAAGAGATGGCAAAACTTTTTAAACCAA
AAATTATTATTACTGGAATGTCATGTTATAGTCGTTGTCTTGATTATAAGAAGTTTAGAG
AAATTGCTGATCAAAATGGTGCATATCTTTTCTCTGATATGGCTCATGTTTCTGGTCTTG
TCGCAGCTAAATTAATTCCATCTCCTTTTGAATATTCGGATGTTGTTTCTACGACAACAC
ACAAGACGCTTCGTGGACCAAGAGCTGGTGTGATTTTCTATCGCAAAGGTGTACGATCAG
TAAAATCAAATGGTGAAAAAGTGATGTATGATCTGGAATCAAGAATCAATCAAGCAGTTT
TCCCAGCTCTTCAAGGTGGACCACATAATCATGCTATTGCTGCTATTGCGAATGCCATGA
AGCAAGCTCAATTGCCCGAGTTTCGTGAATATCAAGAGCAAGTTTTGAAAAATGCACGAA
GATTGTGTAAAGGATTAATGGATAAGGGCTACAAAATTGCTGCAGATGGTACTGATGTGC
ATTTAGTTCTTGTTGACTTACGACCATCTGGAATTACTGGCGCACGTGCAGAATACATTC
TTGAAGAAATCTCAATAGCATGCAATAAAAACACTGTTCCTGGTGATAAATCTGCTTTGA
ATCCTTCTGGAATTCGACTTGGTACACCAGCACTGACGACAAGAGGTTTACTTGAGGCAG
ATATTGATAAAGTCGTTGAATTTATTCATCGTGGTCTGGAATTGTCAAAAGAAATCGTTG
CCACATCTGGTCCGAAATTAGTAGATTTTAAAACAGCTGTTCATAGTGATCAATTTGCAT
CAAAAGTCAAGGCCATTAGAGATGAAGTTGAAGAATTCAGCATGAAATTCCCAATGCCTG
GCTATGATGAATATTAA
>g10612.t5 Gene=g10612 Length=342
MGLDLPDGGHLTHGFMTPNKRISATSIFFESMPYKVDPETGIIDYNKMEEMAKLFKPKII
ITGMSCYSRCLDYKKFREIADQNGAYLFSDMAHVSGLVAAKLIPSPFEYSDVVSTTTHKT
LRGPRAGVIFYRKGVRSVKSNGEKVMYDLESRINQAVFPALQGGPHNHAIAAIANAMKQA
QLPEFREYQEQVLKNARRLCKGLMDKGYKIAADGTDVHLVLVDLRPSGITGARAEYILEE
ISIACNKNTVPGDKSALNPSGIRLGTPALTTRGLLEADIDKVVEFIHRGLELSKEIVATS
GPKLVDFKTAVHSDQFASKVKAIRDEVEEFSMKFPMPGYDEY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g10612.t5 | CDD | cd00378 | SHMT | 1 | 330 | 2.17803E-148 |
| 7 | g10612.t5 | Gene3D | G3DSA:3.40.640.10 | - | 1 | 186 | 6.9E-88 |
| 6 | g10612.t5 | Gene3D | G3DSA:3.90.1150.10 | Aspartate Aminotransferase | 187 | 342 | 1.6E-61 |
| 2 | g10612.t5 | PANTHER | PTHR11680 | SERINE HYDROXYMETHYLTRANSFERASE | 1 | 341 | 3.6E-167 |
| 3 | g10612.t5 | PANTHER | PTHR11680:SF21 | SERINE HYDROXYMETHYLTRANSFERASE, CYTOSOLIC | 1 | 341 | 3.6E-167 |
| 8 | g10612.t5 | PIRSF | PIRSF000412 | SHMT | 1 | 342 | 4.6E-122 |
| 1 | g10612.t5 | Pfam | PF00464 | Serine hydroxymethyltransferase | 1 | 286 | 7.5E-140 |
| 5 | g10612.t5 | ProSitePatterns | PS00096 | Serine hydroxymethyltransferase pyridoxal-phosphate attachment site. | 111 | 127 | - |
| 4 | g10612.t5 | SUPERFAMILY | SSF53383 | PLP-dependent transferases | 1 | 339 | 1.28E-126 |
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.
