General information for g2569.t40
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Homocysteine S-methyltransferase 1.
Parent gene
- The parent gene g2569 is located on chr_3: 18787120..18790735 (- 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_3 | g2569 | g2569.t40 | TTS | g2569.t40 | 18786001 | 18786001 |
| chr_3 | g2569 | g2569.t40 | isoform | g2569.t40 | 18786093 | 18788730 |
| chr_3 | g2569 | g2569.t40 | exon | g2569.t40.exon1 | 18786093 | 18786265 |
| chr_3 | g2569 | g2569.t40 | cds | g2569.t40.CDS1 | 18786093 | 18786265 |
| chr_3 | g2569 | g2569.t40 | exon | g2569.t40.exon2 | 18786329 | 18786533 |
| chr_3 | g2569 | g2569.t40 | cds | g2569.t40.CDS2 | 18786329 | 18786533 |
| chr_3 | g2569 | g2569.t40 | exon | g2569.t40.exon3 | 18786923 | 18787000 |
| chr_3 | g2569 | g2569.t40 | cds | g2569.t40.CDS3 | 18786923 | 18787000 |
| chr_3 | g2569 | g2569.t40 | exon | g2569.t40.exon4 | 18787056 | 18787204 |
| chr_3 | g2569 | g2569.t40 | cds | g2569.t40.CDS4 | 18787056 | 18787204 |
| chr_3 | g2569 | g2569.t40 | exon | g2569.t40.exon5 | 18787332 | 18787588 |
| chr_3 | g2569 | g2569.t40 | cds | g2569.t40.CDS5 | 18787332 | 18787588 |
| chr_3 | g2569 | g2569.t40 | exon | g2569.t40.exon6 | 18787711 | 18787859 |
| chr_3 | g2569 | g2569.t40 | cds | g2569.t40.CDS6 | 18787711 | 18787823 |
| chr_3 | g2569 | g2569.t40 | exon | g2569.t40.exon7 | 18788651 | 18788730 |
| chr_3 | g2569 | g2569.t40 | TSS | g2569.t40 | 18788728 | 18788728 |
Sequences
>g2569.t40 Gene=g2569 Length=1091
TAGTACTGTGTAGAATCTCTAATAATCAACTTCAAACATCATTAAAAGGAGACATTTTCG
GAAGAAAAAAAGTCTTAAAGATTAAAACCTGACCTGCAAAACGAGGAGAAAAAATAATGT
CAGACGAGTCACAACAACAACAACATATAACAGTCATTGATGGTGGATTTTCAACTCAAC
TTAGTTTTCATGTCGGTGAAAATATCGATGGTAAGCAGGCTATATTTAAATTTAATGCAG
TTAATCCCGAAGCTGTCATTCAAAGTCATTTAGATTTTCTTAATGCAGGAGCTGAAATAA
TTTTGACAAACACCTATCAAGCTAGTATTGAAGGATATCAAACTTATTTGGATCTAGATT
ATCATGGAAGTTATGAGCTTATTAAGTCAACAGTGAAGCTAGCTCATATTGCGCGTGACA
AATTTTTATCTTCGCATATCAACCATGTGAAAAAACCTTTAATTTTTGCATCAATCGGTC
CTTATGGTGCGCATTTACATGATGGAAGTGAATATACTGGAAGTTATGAAAAAAGAGTGT
CACCTGCAGCAATCAAAAAATGGCACAAAGTGAGAATCGATGCATGTGTTGAATCGGGGG
TTGATGGATTAGCAATTGAAACTATTCCATGTTTGATGGAAGCAAATGCATTAGTTGATC
TCGTTCTCACGGAATATCCAAATTTAAAATTTTGGATATCTTTCCAATGCAAGAACGGTG
AAGTAATTGCTAATGGACAAAGATTTTCTGACTGCATTTTATCTATTTGGAATCAAGTAG
AAGCAGCTAAACGTCCAGAAAATTTAGTTGCAGTTGGAATTAATTGTATAAATCCAAGCT
TTGTTTCACCACTTTTTTCTGAAATTGAGAAAAATTTGTGCAATTTCAATGTACCGCTAG
TCGTGTACCCAAACAGTGGTGAAGTTTATACTGTTGAAGAAGGTTGGCATGGGAAAAATG
ACTGCATTCCATTAGAGAATTATATTGAAGAATGGGTCAAATTAGGAGCAAAATATATTG
GAGGATGTTGTCGTACAAATGCTCATGATATTGAGAAAATCAAAAATAAAATTGAGGCTC
TAAAAAATTAA
>g2569.t40 Gene=g2569 Length=324
MSDESQQQQHITVIDGGFSTQLSFHVGENIDGKQAIFKFNAVNPEAVIQSHLDFLNAGAE
IILTNTYQASIEGYQTYLDLDYHGSYELIKSTVKLAHIARDKFLSSHINHVKKPLIFASI
GPYGAHLHDGSEYTGSYEKRVSPAAIKKWHKVRIDACVESGVDGLAIETIPCLMEANALV
DLVLTEYPNLKFWISFQCKNGEVIANGQRFSDCILSIWNQVEAAKRPENLVAVGINCINP
SFVSPLFSEIEKNLCNFNVPLVVYPNSGEVYTVEEGWHGKNDCIPLENYIEEWVKLGAKY
IGGCCRTNAHDIEKIKNKIEALKN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g2569.t40 | Gene3D | G3DSA:3.20.20.330 | - | 1 | 319 | 0.00000 |
| 2 | g2569.t40 | PANTHER | PTHR46015 | ZGC:172121 | 6 | 321 | 0.00000 |
| 3 | g2569.t40 | PANTHER | PTHR46015:SF1 | ZGC:172121 | 6 | 321 | 0.00000 |
| 7 | g2569.t40 | PIRSF | PIRSF037505 | BHMT | 6 | 217 | 0.00028 |
| 8 | g2569.t40 | PIRSF | PIRSF037505 | BHMT | 271 | 323 | 0.00830 |
| 1 | g2569.t40 | Pfam | PF02574 | Homocysteine S-methyltransferase | 13 | 318 | 0.00000 |
| 6 | g2569.t40 | ProSiteProfiles | PS50970 | Homocysteine-binding domain profile. | 1 | 319 | 40.15200 |
| 4 | g2569.t40 | SUPERFAMILY | SSF82282 | Homocysteine S-methyltransferase | 6 | 322 | 0.00000 |
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:0008270 | zinc ion binding | MF |
| GO:0047150 | betaine-homocysteine S-methyltransferase activity | MF |
| GO:0009086 | methionine biosynthetic process | BP |
KEGG
Orthology
- This transcript has been annotated with K00547 (homocysteine S-methyltransferase)
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.
