Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Homocysteine S-methyltransferase YbgG.

Parent gene

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.t59 TTS g2569.t59 18786001 18786001
chr_3 g2569 g2569.t59 isoform g2569.t59 18786919 18788730
chr_3 g2569 g2569.t59 exon g2569.t59.exon1 18786919 18787000
chr_3 g2569 g2569.t59 cds g2569.t59.CDS1 18786920 18787000
chr_3 g2569 g2569.t59 exon g2569.t59.exon2 18787056 18787204
chr_3 g2569 g2569.t59 cds g2569.t59.CDS2 18787056 18787204
chr_3 g2569 g2569.t59 exon g2569.t59.exon3 18787332 18787608
chr_3 g2569 g2569.t59 cds g2569.t59.CDS3 18787332 18787608
chr_3 g2569 g2569.t59 exon g2569.t59.exon4 18787730 18787859
chr_3 g2569 g2569.t59 cds g2569.t59.CDS4 18787730 18787780
chr_3 g2569 g2569.t59 exon g2569.t59.exon5 18788651 18788730
chr_3 g2569 g2569.t59 TSS g2569.t59 18788728 18788728

Sequences

>g2569.t59 Gene=g2569 Length=718
TAGTACTGTGTAGAATCTCTAATAATCAACTTCAAACATCATTAAAAGGAGACATTTTCG
GAAGAAAAAAAGTCTTAAAGATTAAAACCTGACCTGCAAAACGAGGAGAAAAAATAATGT
CAGACGAGTCACAACAACAACAACATATAACAGTCATTGATGGTGGATTTTCAACTCAAC
TTAGTTTTCATGTCGGTGAAAATATCGATGATTACCTTTTTTATTTTTAGATTTAATGCA
GTTAATCCCGAAGCTGTCATTCAAAGTCATTTAGATTTTCTTAATGCAGGAGCTGAAATA
ATTTTGACAAACACCTATCAAGCTAGTATTGAAGGATATCAAACTTATTTGGATCTAGAT
TATCATGGAAGTTATGAGCTTATTAAGTCAACAGTGAAGCTAGCTCATATTGCGCGTGAC
AAATTTTTATCTTCGCATATCAACCATGTGAAAAAACCTTTAATTTTTGCATCAATCGGT
CCTTATGGTGCGCATTTACATGATGGAAGTGAATATACTGGAAGTTATGAAAAAAGAGTG
TCACCTGCAGCAATCAAAAAATGGCACAAAGTGAGAATCGATGCATGTGTTGAATCGGGG
GTTGATGGATTAGCAATTGAAACTATTCCATGTTTGATGGAAGCAAATGCATTAGTTGAT
CTCGTTCTCACGGAATATCCAAATTTAAAATTTTGGATATCTTTCCAATGCAAGGTAA

>g2569.t59 Gene=g2569 Length=186
MVDFQLNLVFMSVKISMITFFIFRFNAVNPEAVIQSHLDFLNAGAEIILTNTYQASIEGY
QTYLDLDYHGSYELIKSTVKLAHIARDKFLSSHINHVKKPLIFASIGPYGAHLHDGSEYT
GSYEKRVSPAAIKKWHKVRIDACVESGVDGLAIETIPCLMEANALVDLVLTEYPNLKFWI
SFQCKV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
5 g2569.t59 Gene3D G3DSA:3.20.20.330 - 19 186 1.3E-48
2 g2569.t59 PANTHER PTHR11103:SF10 HOMOCYSTEINE S-METHYLTRANSFERASE 1-RELATED 27 185 6.1E-47
3 g2569.t59 PANTHER PTHR11103 SLR1189 PROTEIN 27 185 6.1E-47
1 g2569.t59 Pfam PF02574 Homocysteine S-methyltransferase 28 185 6.2E-35
8 g2569.t59 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 5 -
9 g2569.t59 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 6 25 -
7 g2569.t59 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 26 186 -
6 g2569.t59 ProSiteProfiles PS50970 Homocysteine-binding domain profile. 1 186 22.163
4 g2569.t59 SUPERFAMILY SSF82282 Homocysteine S-methyltransferase 24 184 5.62E-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.

Raw TPM values