General information for g10612.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Serine hydroxymethyltransferase, cytosolic.
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.t1 | TTS | g10612.t1 | 10752759 | 10752759 |
| chr_1 | g10612 | g10612.t1 | isoform | g10612.t1 | 10752819 | 10754743 |
| chr_1 | g10612 | g10612.t1 | exon | g10612.t1.exon1 | 10752819 | 10754019 |
| chr_1 | g10612 | g10612.t1 | cds | g10612.t1.CDS1 | 10752819 | 10754019 |
| chr_1 | g10612 | g10612.t1 | exon | g10612.t1.exon2 | 10754173 | 10754375 |
| chr_1 | g10612 | g10612.t1 | cds | g10612.t1.CDS2 | 10754173 | 10754375 |
| chr_1 | g10612 | g10612.t1 | exon | g10612.t1.exon3 | 10754651 | 10754743 |
| chr_1 | g10612 | g10612.t1 | cds | g10612.t1.CDS3 | 10754651 | 10754743 |
| chr_1 | g10612 | g10612.t1 | TSS | g10612.t1 | 10754843 | 10754843 |
Sequences
>g10612.t1 Gene=g10612 Length=1497
ATGTCAAGGAAGTTTTTGTTTGTAAATATTTTGAAAAATTATTCATTAAGAAGGCAAAAC
ATTCATTTATCGGCTAGACAGTATCAAATTGATAAAATGTCGGGATCGGCTAAAATTTTG
CATCAAAATTTGTGGGATCAAGATGAGGAGTTGTTTGCAATAATTAAAAAAGAAAAGCAG
CGTCAATTGCGCGGGCTTGAGATGATTGCAAGCGAGAATTTTACTTCATTATCCGTTCTT
CAATGTCTCAGTTCTTGTTTACACAACAAATATTCTGAAGGAATGCCAGGTCAACGCTAT
TATGGAGGCAATCAGTACATTGATGAAATTGAAATTTTAGCACAAAAGAGATCACTTGAA
GCATACGGCTTAAATCCAGATGAATGGGGTGTCAACGTTCAACCATATTCTGGTTCTCCC
GCTAATTTTGTTGTGTATACTGCATTAATTCAACCTCATGATAGAATTATGGGCTTAGAC
TTGCCTGATGGTGGTCATTTAACACATGGATTTATGACTCCCAACAAACGCATTTCTGCT
ACATCAATTTTCTTCGAAAGTATGCCTTATAAAGTTGATCCAGAGACTGGTATTATTGAC
TACAATAAAATGGAAGAGATGGCAAAACTTTTTAAACCAAAAATTATTATTACTGGAATG
TCATGTTATAGTCGTTGTCTTGATTATAAGAAGTTTAGAGAAATTGCTGATCAAAATGGT
GCATATCTTTTCTCTGATATGGCTCATGTTTCTGGTCTTGTCGCAGCTAAATTAATTCCA
TCTCCTTTTGAATATTCGGATGTTGTTTCTACGACAACACACAAGACGCTTCGTGGACCA
AGAGCTGGTGTGATTTTCTATCGCAAAGGTGTACGATCAGTAAAATCAAATGGTGAAAAA
GTGATGTATGATCTGGAATCAAGAATCAATCAAGCAGTTTTCCCAGCTCTTCAAGGTGGA
CCACATAATCATGCTATTGCTGCTATTGCGAATGCCATGAAGCAAGCTCAATTGCCCGAG
TTTCGTGAATATCAAGAGCAAGTTTTGAAAAATGCACGAAGATTGTGTAAAGGATTAATG
GATAAGGGCTACAAAATTGCTGCAGATGGTACTGATGTGCATTTAGTTCTTGTTGACTTA
CGACCATCTGGAATTACTGGCGCACGTGCAGAATACATTCTTGAAGAAATCTCAATAGCA
TGCAATAAAAACACTGTTCCTGGTGATAAATCTGCTTTGAATCCTTCTGGAATTCGACTT
GGTACACCAGCACTGACGACAAGAGGTTTACTTGAGGCAGATATTGATAAAGTCGTTGAA
TTTATTCATCGTGGTCTGGAATTGTCAAAAGAAATCGTTGCCACATCTGGTCCGAAATTA
GTAGATTTTAAAACAGCTGTTCATAGTGATCAATTTGCATCAAAAGTCAAGGCCATTAGA
GATGAAGTTGAAGAATTCAGCATGAAATTCCCAATGCCTGGCTATGATGAATATTAA
>g10612.t1 Gene=g10612 Length=498
MSRKFLFVNILKNYSLRRQNIHLSARQYQIDKMSGSAKILHQNLWDQDEELFAIIKKEKQ
RQLRGLEMIASENFTSLSVLQCLSSCLHNKYSEGMPGQRYYGGNQYIDEIEILAQKRSLE
AYGLNPDEWGVNVQPYSGSPANFVVYTALIQPHDRIMGLDLPDGGHLTHGFMTPNKRISA
TSIFFESMPYKVDPETGIIDYNKMEEMAKLFKPKIIITGMSCYSRCLDYKKFREIADQNG
AYLFSDMAHVSGLVAAKLIPSPFEYSDVVSTTTHKTLRGPRAGVIFYRKGVRSVKSNGEK
VMYDLESRINQAVFPALQGGPHNHAIAAIANAMKQAQLPEFREYQEQVLKNARRLCKGLM
DKGYKIAADGTDVHLVLVDLRPSGITGARAEYILEEISIACNKNTVPGDKSALNPSGIRL
GTPALTTRGLLEADIDKVVEFIHRGLELSKEIVATSGPKLVDFKTAVHSDQFASKVKAIR
DEVEEFSMKFPMPGYDEY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g10612.t1 | CDD | cd00378 | SHMT | 46 | 486 | 0.0 |
| 6 | g10612.t1 | Gene3D | G3DSA:3.90.1150.10 | Aspartate Aminotransferase | 48 | 493 | 9.1E-213 |
| 7 | g10612.t1 | Gene3D | G3DSA:3.40.640.10 | - | 73 | 346 | 9.1E-213 |
| 4 | g10612.t1 | Hamap | MF_00051 | Serine hydroxymethyltransferase [glyA]. | 43 | 494 | 42.633179 |
| 2 | g10612.t1 | PANTHER | PTHR11680 | SERINE HYDROXYMETHYLTRANSFERASE | 29 | 497 | 1.7E-235 |
| 3 | g10612.t1 | PANTHER | PTHR11680:SF21 | SERINE HYDROXYMETHYLTRANSFERASE, CYTOSOLIC | 29 | 497 | 1.7E-235 |
| 8 | g10612.t1 | PIRSF | PIRSF000412 | SHMT | 21 | 498 | 6.0E-174 |
| 1 | g10612.t1 | Pfam | PF00464 | Serine hydroxymethyltransferase | 46 | 442 | 1.1E-198 |
| 10 | g10612.t1 | ProSitePatterns | PS00096 | Serine hydroxymethyltransferase pyridoxal-phosphate attachment site. | 267 | 283 | - |
| 5 | g10612.t1 | SUPERFAMILY | SSF53383 | PLP-dependent transferases | 39 | 495 | 6.75E-180 |
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 transcript has been annotated with K00600 (glycine hydroxymethyltransferase)
Pathway
- This transcript belongs to the following pathways
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.
