Gene loci information

Transcript annotation

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

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.t42 TTS g2569.t42 18786001 18786001
chr_3 g2569 g2569.t42 isoform g2569.t42 18786093 18788730
chr_3 g2569 g2569.t42 exon g2569.t42.exon1 18786093 18786265
chr_3 g2569 g2569.t42 cds g2569.t42.CDS1 18786093 18786265
chr_3 g2569 g2569.t42 exon g2569.t42.exon2 18786329 18786533
chr_3 g2569 g2569.t42 cds g2569.t42.CDS2 18786329 18786533
chr_3 g2569 g2569.t42 exon g2569.t42.exon3 18786923 18787000
chr_3 g2569 g2569.t42 cds g2569.t42.CDS3 18786923 18787000
chr_3 g2569 g2569.t42 exon g2569.t42.exon4 18787056 18787204
chr_3 g2569 g2569.t42 exon g2569.t42.exon5 18787332 18787612
chr_3 g2569 g2569.t42 exon g2569.t42.exon6 18787730 18787859
chr_3 g2569 g2569.t42 exon g2569.t42.exon7 18788651 18788730
chr_3 g2569 g2569.t42 TSS g2569.t42 18788728 18788728

Sequences

>g2569.t42 Gene=g2569 Length=1096
TAGTACTGTGTAGAATCTCTAATAATCAACTTCAAACATCATTAAAAGGAGACATTTTCG
GAAGAAAAAAAGTCTTAAAGATTAAAACCTGACCTGCAAAACGAGGAGAAAAAATAATGT
CAGACGAGTCACAACAACAACAACATATAACAGTCATTGATGGTGGATTTTCAACTCAAC
TTAGTTTTCATGTCGGTGAAAATATCGATGATTCATTACCTTTTTTATTTTTAGATTTAA
TGCAGTTAATCCCGAAGCTGTCATTCAAAGTCATTTAGATTTTCTTAATGCAGGAGCTGA
AATAATTTTGACAAACACCTATCAAGCTAGTATTGAAGGATATCAAACTTATTTGGATCT
AGATTATCATGGAAGTTATGAGCTTATTAAGTCAACAGTGAAGCTAGCTCATATTGCGCG
TGACAAATTTTTATCTTCGCATATCAACCATGTGAAAAAACCTTTAATTTTTGCATCAAT
CGGTCCTTATGGTGCGCATTTACATGATGGAAGTGAATATACTGGAAGTTATGAAAAAAG
AGTGTCACCTGCAGCAATCAAAAAATGGCACAAAGTGAGAATCGATGCATGTGTTGAATC
GGGGGTTGATGGATTAGCAATTGAAACTATTCCATGTTTGATGGAAGCAAATGCATTAGT
TGATCTCGTTCTCACGGAATATCCAAATTTAAAATTTTGGATATCTTTCCAATGCAAGAA
CGGTGAAGTAATTGCTAATGGACAAAGATTTTCTGACTGCATTTTATCTATTTGGAATCA
AGTAGAAGCAGCTAAACGTCCAGAAAATTTAGTTGCAGTTGGAATTAATTGTATAAATCC
AAGCTTTGTTTCACCACTTTTTTCTGAAATTGAGAAAAATTTGTGCAATTTCAATGTACC
GCTAGTCGTGTACCCAAACAGTGGTGAAGTTTATACTGTTGAAGAAGGTTGGCATGGGAA
AAATGACTGCATTCCATTAGAGAATTATATTGAAGAATGGGTCAAATTAGGAGCAAAATA
TATTGGAGGATGTTGTCGTACAAATGCTCATGATATTGAGAAAATCAAAAATAAAATTGA
GGCTCTAAAAAATTAA

>g2569.t42 Gene=g2569 Length=151
MEANALVDLVLTEYPNLKFWISFQCKNGEVIANGQRFSDCILSIWNQVEAAKRPENLVAV
GINCINPSFVSPLFSEIEKNLCNFNVPLVVYPNSGEVYTVEEGWHGKNDCIPLENYIEEW
VKLGAKYIGGCCRTNAHDIEKIKNKIEALKN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
5 g2569.t42 Gene3D G3DSA:3.20.20.330 - 1 146 0.000
2 g2569.t42 PANTHER PTHR46015 ZGC:172121 2 148 0.000
3 g2569.t42 PANTHER PTHR46015:SF1 ZGC:172121 2 148 0.000
1 g2569.t42 Pfam PF02574 Homocysteine S-methyltransferase 2 145 0.000
6 g2569.t42 ProSiteProfiles PS50970 Homocysteine-binding domain profile. 1 146 17.629
4 g2569.t42 SUPERFAMILY SSF82282 Homocysteine S-methyltransferase 2 148 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. There were no conditions that were differentially expressed