General information for g2569.t53
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Homocysteine S-methyltransferase YbgG.
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.t53 | TTS | g2569.t53 | 18786001 | 18786001 |
| chr_3 | g2569 | g2569.t53 | isoform | g2569.t53 | 18786093 | 18788730 |
| chr_3 | g2569 | g2569.t53 | exon | g2569.t53.exon1 | 18786093 | 18786265 |
| chr_3 | g2569 | g2569.t53 | exon | g2569.t53.exon2 | 18786329 | 18787000 |
| chr_3 | g2569 | g2569.t53 | cds | g2569.t53.CDS1 | 18786890 | 18787000 |
| chr_3 | g2569 | g2569.t53 | exon | g2569.t53.exon3 | 18787056 | 18787204 |
| chr_3 | g2569 | g2569.t53 | cds | g2569.t53.CDS2 | 18787056 | 18787204 |
| chr_3 | g2569 | g2569.t53 | exon | g2569.t53.exon4 | 18787332 | 18787608 |
| chr_3 | g2569 | g2569.t53 | cds | g2569.t53.CDS3 | 18787332 | 18787608 |
| chr_3 | g2569 | g2569.t53 | exon | g2569.t53.exon5 | 18787730 | 18787859 |
| chr_3 | g2569 | g2569.t53 | cds | g2569.t53.CDS4 | 18787730 | 18787780 |
| chr_3 | g2569 | g2569.t53 | exon | g2569.t53.exon6 | 18788651 | 18788730 |
| chr_3 | g2569 | g2569.t53 | TSS | g2569.t53 | 18788728 | 18788728 |
Sequences
>g2569.t53 Gene=g2569 Length=1481
TAGTACTGTGTAGAATCTCTAATAATCAACTTCAAACATCATTAAAAGGAGACATTTTCG
GAAGAAAAAAAGTCTTAAAGATTAAAACCTGACCTGCAAAACGAGGAGAAAAAATAATGT
CAGACGAGTCACAACAACAACAACATATAACAGTCATTGATGGTGGATTTTCAACTCAAC
TTAGTTTTCATGTCGGTGAAAATATCGATGATTACCTTTTTTATTTTTAGATTTAATGCA
GTTAATCCCGAAGCTGTCATTCAAAGTCATTTAGATTTTCTTAATGCAGGAGCTGAAATA
ATTTTGACAAACACCTATCAAGCTAGTATTGAAGGATATCAAACTTATTTGGATCTAGAT
TATCATGGAAGTTATGAGCTTATTAAGTCAACAGTGAAGCTAGCTCATATTGCGCGTGAC
AAATTTTTATCTTCGCATATCAACCATGTGAAAAAACCTTTAATTTTTGCATCAATCGGT
CCTTATGGTGCGCATTTACATGATGGAAGTGAATATACTGGAAGTTATGAAAAAAGAGTG
TCACCTGCAGCAATCAAAAAATGGCACAAAGTGAGAATCGATGCATGTGTTGAATCGGGG
GTTGATGGATTAGCAATTGAAACTATTCCATGTTTGATGGAAGCAAATGCATTAGTTGAT
CTCGTTCTCACGGAATATCCAAATTTAAAATTTTGGATATCTTTCCAATGCAAGGTAAGA
TTTTCAAATTCAAAATTATGTCTGTGACTAATATAATTAATCATATATACTGTCTTTATC
TATTTTATTTATACCTAACAAGCAAGTATGTATACATGTCTCTATTCAAGTGTTCGTTTT
TATTCATTTTATCGGTTTAGTATGATGATTTCATTTGTAAAAATATTTTGTTCTCATAAA
ATTTTTATCCATCAAATTTTAAATAGAAACTTTCATATCTAAAATTTTAATGACTAAAAT
TTAAATAGAAGTAGAGCTTAATATGCAATTTTTCAATTTATTGCAACATGATTTTTTCAT
TTAGCGCATGTGTAAAATTATAAATGATGTATAAATCAGCAAAAAGGCACGTTTTTCACA
CATTCTTATAAATACATTTACAGAACGGTGAAGTAATTGCTAATGGACAAAGATTTTCTG
ACTGCATTTTATCTATTTGGAATCAAGTAGAAGCAGCTAAACGTCCAGAAAATTTAGTTG
CAGTTGGAATTAATTGTATAAATCCAAGCTTTGTTTCACCACTTTTTTCTGAAATTGAGA
AAAATTTGTGCAATTTCAATGTACCGCTAGTCGTGTACCCAAACAGTGGTGAAGTTTATA
CTGTTGAAGAAGGTTGGCATGGGAAAAATGACTGCATTCCATTAGAGAATTATATTGAAG
AATGGGTCAAATTAGGAGCAAAATATATTGGAGGATGTTGTCGTACAAATGCTCATGATA
TTGAGAAAATCAAAAATAAAATTGAGGCTCTAAAAAATTAA
>g2569.t53 Gene=g2569 Length=195
MVDFQLNLVFMSVKISMITFFIFRFNAVNPEAVIQSHLDFLNAGAEIILTNTYQASIEGY
QTYLDLDYHGSYELIKSTVKLAHIARDKFLSSHINHVKKPLIFASIGPYGAHLHDGSEYT
GSYEKRVSPAAIKKWHKVRIDACVESGVDGLAIETIPCLMEANALVDLVLTEYPNLKFWI
SFQCKVRFSNSKLCL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g2569.t53 | Gene3D | G3DSA:3.20.20.330 | - | 19 | 194 | 8.3E-49 |
| 2 | g2569.t53 | PANTHER | PTHR11103:SF10 | HOMOCYSTEINE S-METHYLTRANSFERASE 1-RELATED | 27 | 185 | 4.1E-47 |
| 3 | g2569.t53 | PANTHER | PTHR11103 | SLR1189 PROTEIN | 27 | 185 | 4.1E-47 |
| 1 | g2569.t53 | Pfam | PF02574 | Homocysteine S-methyltransferase | 28 | 185 | 3.7E-35 |
| 8 | g2569.t53 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 5 | - |
| 9 | g2569.t53 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 6 | 25 | - |
| 7 | g2569.t53 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 26 | 195 | - |
| 6 | g2569.t53 | ProSiteProfiles | PS50970 | Homocysteine-binding domain profile. | 1 | 195 | 21.962 |
| 4 | g2569.t53 | SUPERFAMILY | SSF82282 | Homocysteine S-methyltransferase | 24 | 184 | 5.36E-35 |
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. There were no conditions that were differentially expressed