General information for g2569.t38
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.t38 | TTS | g2569.t38 | 18786001 | 18786001 |
| chr_3 | g2569 | g2569.t38 | isoform | g2569.t38 | 18786093 | 18788658 |
| chr_3 | g2569 | g2569.t38 | exon | g2569.t38.exon1 | 18786093 | 18786265 |
| chr_3 | g2569 | g2569.t38 | cds | g2569.t38.CDS1 | 18786093 | 18786265 |
| chr_3 | g2569 | g2569.t38 | exon | g2569.t38.exon2 | 18786329 | 18786533 |
| chr_3 | g2569 | g2569.t38 | cds | g2569.t38.CDS2 | 18786329 | 18786533 |
| chr_3 | g2569 | g2569.t38 | exon | g2569.t38.exon3 | 18786923 | 18787000 |
| chr_3 | g2569 | g2569.t38 | cds | g2569.t38.CDS3 | 18786923 | 18787000 |
| chr_3 | g2569 | g2569.t38 | exon | g2569.t38.exon4 | 18787056 | 18787204 |
| chr_3 | g2569 | g2569.t38 | cds | g2569.t38.CDS4 | 18787056 | 18787204 |
| chr_3 | g2569 | g2569.t38 | exon | g2569.t38.exon5 | 18787332 | 18787614 |
| chr_3 | g2569 | g2569.t38 | cds | g2569.t38.CDS5 | 18787332 | 18787614 |
| chr_3 | g2569 | g2569.t38 | exon | g2569.t38.exon6 | 18787730 | 18787859 |
| chr_3 | g2569 | g2569.t38 | cds | g2569.t38.CDS6 | 18787730 | 18787780 |
| chr_3 | g2569 | g2569.t38 | exon | g2569.t38.exon7 | 18788651 | 18788658 |
| chr_3 | g2569 | g2569.t38 | TSS | g2569.t38 | 18788728 | 18788728 |
Sequences
>g2569.t38 Gene=g2569 Length=1026
TCTTAAAGATTAAAACCTGACCTGCAAAACGAGGAGAAAAAATAATGTCAGACGAGTCAC
AACAACAACAACATATAACAGTCATTGATGGTGGATTTTCAACTCAACTTAGTTTTCATG
TCGGTGAAAATATCGATGTCATTCATTACCTTTTTTATTTTTAGATTTAATGCAGTTAAT
CCCGAAGCTGTCATTCAAAGTCATTTAGATTTTCTTAATGCAGGAGCTGAAATAATTTTG
ACAAACACCTATCAAGCTAGTATTGAAGGATATCAAACTTATTTGGATCTAGATTATCAT
GGAAGTTATGAGCTTATTAAGTCAACAGTGAAGCTAGCTCATATTGCGCGTGACAAATTT
TTATCTTCGCATATCAACCATGTGAAAAAACCTTTAATTTTTGCATCAATCGGTCCTTAT
GGTGCGCATTTACATGATGGAAGTGAATATACTGGAAGTTATGAAAAAAGAGTGTCACCT
GCAGCAATCAAAAAATGGCACAAAGTGAGAATCGATGCATGTGTTGAATCGGGGGTTGAT
GGATTAGCAATTGAAACTATTCCATGTTTGATGGAAGCAAATGCATTAGTTGATCTCGTT
CTCACGGAATATCCAAATTTAAAATTTTGGATATCTTTCCAATGCAAGAACGGTGAAGTA
ATTGCTAATGGACAAAGATTTTCTGACTGCATTTTATCTATTTGGAATCAAGTAGAAGCA
GCTAAACGTCCAGAAAATTTAGTTGCAGTTGGAATTAATTGTATAAATCCAAGCTTTGTT
TCACCACTTTTTTCTGAAATTGAGAAAAATTTGTGCAATTTCAATGTACCGCTAGTCGTG
TACCCAAACAGTGGTGAAGTTTATACTGTTGAAGAAGGTTGGCATGGGAAAAATGACTGC
ATTCCATTAGAGAATTATATTGAAGAATGGGTCAAATTAGGAGCAAAATATATTGGAGGA
TGTTGTCGTACAAATGCTCATGATATTGAGAAAATCAAAAATAAAATTGAGGCTCTAAAA
AATTAA
>g2569.t38 Gene=g2569 Length=312
MVDFQLNLVFMSVKISMSFITFFIFRFNAVNPEAVIQSHLDFLNAGAEIILTNTYQASIE
GYQTYLDLDYHGSYELIKSTVKLAHIARDKFLSSHINHVKKPLIFASIGPYGAHLHDGSE
YTGSYEKRVSPAAIKKWHKVRIDACVESGVDGLAIETIPCLMEANALVDLVLTEYPNLKF
WISFQCKNGEVIANGQRFSDCILSIWNQVEAAKRPENLVAVGINCINPSFVSPLFSEIEK
NLCNFNVPLVVYPNSGEVYTVEEGWHGKNDCIPLENYIEEWVKLGAKYIGGCCRTNAHDI
EKIKNKIEALKN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g2569.t38 | Gene3D | G3DSA:3.20.20.330 | - | 21 | 307 | 4.3E-81 |
| 2 | g2569.t38 | PANTHER | PTHR46015 | ZGC:172121 | 24 | 309 | 2.9E-83 |
| 3 | g2569.t38 | PANTHER | PTHR46015:SF1 | ZGC:172121 | 24 | 309 | 2.9E-83 |
| 11 | g2569.t38 | PIRSF | PIRSF037505 | BHMT | 26 | 180 | 5.5E-4 |
| 10 | g2569.t38 | PIRSF | PIRSF037505 | BHMT | 259 | 311 | 0.0078 |
| 1 | g2569.t38 | Pfam | PF02574 | Homocysteine S-methyltransferase | 30 | 306 | 9.4E-61 |
| 8 | g2569.t38 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 5 | - |
| 9 | g2569.t38 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 6 | 25 | - |
| 7 | g2569.t38 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 26 | 312 | - |
| 6 | g2569.t38 | ProSiteProfiles | PS50970 | Homocysteine-binding domain profile. | 1 | 307 | 36.275 |
| 4 | g2569.t38 | SUPERFAMILY | SSF82282 | Homocysteine S-methyltransferase | 23 | 309 | 5.76E-64 |
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 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