General information for g2569.t56
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.t56 | TTS | g2569.t56 | 18786001 | 18786001 |
| chr_3 | g2569 | g2569.t56 | isoform | g2569.t56 | 18786093 | 18788730 |
| chr_3 | g2569 | g2569.t56 | exon | g2569.t56.exon1 | 18786093 | 18786533 |
| chr_3 | g2569 | g2569.t56 | cds | g2569.t56.CDS1 | 18786285 | 18786533 |
| chr_3 | g2569 | g2569.t56 | exon | g2569.t56.exon2 | 18786923 | 18787000 |
| chr_3 | g2569 | g2569.t56 | cds | g2569.t56.CDS2 | 18786923 | 18787000 |
| chr_3 | g2569 | g2569.t56 | exon | g2569.t56.exon3 | 18787056 | 18787204 |
| chr_3 | g2569 | g2569.t56 | cds | g2569.t56.CDS3 | 18787056 | 18787204 |
| chr_3 | g2569 | g2569.t56 | exon | g2569.t56.exon4 | 18787332 | 18787588 |
| chr_3 | g2569 | g2569.t56 | cds | g2569.t56.CDS4 | 18787332 | 18787588 |
| chr_3 | g2569 | g2569.t56 | exon | g2569.t56.exon5 | 18787711 | 18787859 |
| chr_3 | g2569 | g2569.t56 | cds | g2569.t56.CDS5 | 18787711 | 18787823 |
| chr_3 | g2569 | g2569.t56 | exon | g2569.t56.exon6 | 18788651 | 18788730 |
| chr_3 | g2569 | g2569.t56 | TSS | g2569.t56 | 18788728 | 18788728 |
Sequences
>g2569.t56 Gene=g2569 Length=1154
TAGTACTGTGTAGAATCTCTAATAATCAACTTCAAACATCATTAAAAGGAGACATTTTCG
GAAGAAAAAAAGTCTTAAAGATTAAAACCTGACCTGCAAAACGAGGAGAAAAAATAATGT
CAGACGAGTCACAACAACAACAACATATAACAGTCATTGATGGTGGATTTTCAACTCAAC
TTAGTTTTCATGTCGGTGAAAATATCGATGGTAAGCAGGCTATATTTAAATTTAATGCAG
TTAATCCCGAAGCTGTCATTCAAAGTCATTTAGATTTTCTTAATGCAGGAGCTGAAATAA
TTTTGACAAACACCTATCAAGCTAGTATTGAAGGATATCAAACTTATTTGGATCTAGATT
ATCATGGAAGTTATGAGCTTATTAAGTCAACAGTGAAGCTAGCTCATATTGCGCGTGACA
AATTTTTATCTTCGCATATCAACCATGTGAAAAAACCTTTAATTTTTGCATCAATCGGTC
CTTATGGTGCGCATTTACATGATGGAAGTGAATATACTGGAAGTTATGAAAAAAGAGTGT
CACCTGCAGCAATCAAAAAATGGCACAAAGTGAGAATCGATGCATGTGTTGAATCGGGGG
TTGATGGATTAGCAATTGAAACTATTCCATGTTTGATGGAAGCAAATGCATTAGTTGATC
TCGTTCTCACGGAATATCCAAATTTAAAATTTTGGATATCTTTCCAATGCAAGAACGGTG
AAGTAATTGCTAATGGACAAAGATTTTCTGACTGCATTTTATCTATTTGGAATCAAGTAG
AAGCAGCTAAACGTCCAGAAAATTTAGTTGCAGTTGGAATTAATTGTATAAATCCAAGCT
TTGTTTCACCACTTTTTTCTGAAATTGAGAAAAATTTGTGCAATTTCAATGTACCGCTAG
TCGTGTACCCAAACAGTGGTAAAATTTTATATACCTTATTATTTTTACTTAAAATATTTT
AAAAATTAATATTCATTTTAGGTGAAGTTTATACTGTTGAAGAAGGTTGGCATGGGAAAA
ATGACTGCATTCCATTAGAGAATTATATTGAAGAATGGGTCAAATTAGGAGCAAAATATA
TTGGAGGATGTTGTCGTACAAATGCTCATGATATTGAGAAAATCAAAAATAAAATTGAGG
CTCTAAAAAATTAA
>g2569.t56 Gene=g2569 Length=281
MSDESQQQQHITVIDGGFSTQLSFHVGENIDGKQAIFKFNAVNPEAVIQSHLDFLNAGAE
IILTNTYQASIEGYQTYLDLDYHGSYELIKSTVKLAHIARDKFLSSHINHVKKPLIFASI
GPYGAHLHDGSEYTGSYEKRVSPAAIKKWHKVRIDACVESGVDGLAIETIPCLMEANALV
DLVLTEYPNLKFWISFQCKNGEVIANGQRFSDCILSIWNQVEAAKRPENLVAVGINCINP
SFVSPLFSEIEKNLCNFNVPLVVYPNSGKILYTLLFLLKIF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g2569.t56 | Gene3D | G3DSA:3.20.20.330 | - | 1 | 273 | 0.000 |
| 2 | g2569.t56 | PANTHER | PTHR46015 | ZGC:172121 | 6 | 269 | 0.000 |
| 3 | g2569.t56 | PANTHER | PTHR46015:SF1 | ZGC:172121 | 6 | 269 | 0.000 |
| 1 | g2569.t56 | Pfam | PF02574 | Homocysteine S-methyltransferase | 13 | 269 | 0.000 |
| 6 | g2569.t56 | ProSiteProfiles | PS50970 | Homocysteine-binding domain profile. | 1 | 281 | 32.063 |
| 4 | g2569.t56 | SUPERFAMILY | SSF82282 | Homocysteine S-methyltransferase | 6 | 268 | 0.000 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
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.
