Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Homocysteine S-methyltransferase 1.

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.t35 TTS g2569.t35 18786001 18786001
chr_3 g2569 g2569.t35 isoform g2569.t35 18786093 18787823
chr_3 g2569 g2569.t35 exon g2569.t35.exon1 18786093 18786533
chr_3 g2569 g2569.t35 cds g2569.t35.CDS1 18786285 18786533
chr_3 g2569 g2569.t35 exon g2569.t35.exon2 18786923 18787000
chr_3 g2569 g2569.t35 cds g2569.t35.CDS2 18786923 18787000
chr_3 g2569 g2569.t35 exon g2569.t35.exon3 18787056 18787204
chr_3 g2569 g2569.t35 cds g2569.t35.CDS3 18787056 18787204
chr_3 g2569 g2569.t35 exon g2569.t35.exon4 18787332 18787588
chr_3 g2569 g2569.t35 cds g2569.t35.CDS4 18787332 18787588
chr_3 g2569 g2569.t35 exon g2569.t35.exon5 18787711 18787823
chr_3 g2569 g2569.t35 cds g2569.t35.CDS5 18787711 18787823
chr_3 g2569 g2569.t35 TSS g2569.t35 18788728 18788728

Sequences

>g2569.t35 Gene=g2569 Length=1038
ATGTCAGACGAGTCACAACAACAACAACATATAACAGTCATTGATGGTGGATTTTCAACT
CAACTTAGTTTTCATGTCGGTGAAAATATCGATGGTAAGCAGGCTATATTTAAATTTAAT
GCAGTTAATCCCGAAGCTGTCATTCAAAGTCATTTAGATTTTCTTAATGCAGGAGCTGAA
ATAATTTTGACAAACACCTATCAAGCTAGTATTGAAGGATATCAAACTTATTTGGATCTA
GATTATCATGGAAGTTATGAGCTTATTAAGTCAACAGTGAAGCTAGCTCATATTGCGCGT
GACAAATTTTTATCTTCGCATATCAACCATGTGAAAAAACCTTTAATTTTTGCATCAATC
GGTCCTTATGGTGCGCATTTACATGATGGAAGTGAATATACTGGAAGTTATGAAAAAAGA
GTGTCACCTGCAGCAATCAAAAAATGGCACAAAGTGAGAATCGATGCATGTGTTGAATCG
GGGGTTGATGGATTAGCAATTGAAACTATTCCATGTTTGATGGAAGCAAATGCATTAGTT
GATCTCGTTCTCACGGAATATCCAAATTTAAAATTTTGGATATCTTTCCAATGCAAGAAC
GGTGAAGTAATTGCTAATGGACAAAGATTTTCTGACTGCATTTTATCTATTTGGAATCAA
GTAGAAGCAGCTAAACGTCCAGAAAATTTAGTTGCAGTTGGAATTAATTGTATAAATCCA
AGCTTTGTTTCACCACTTTTTTCTGAAATTGAGAAAAATTTGTGCAATTTCAATGTACCG
CTAGTCGTGTACCCAAACAGTGGTAAAATTTTATATACCTTATTATTTTTACTTAAAATA
TTTTAAAAATTAATATTCATTTTAGGTGAAGTTTATACTGTTGAAGAAGGTTGGCATGGG
AAAAATGACTGCATTCCATTAGAGAATTATATTGAAGAATGGGTCAAATTAGGAGCAAAA
TATATTGGAGGATGTTGTCGTACAAATGCTCATGATATTGAGAAAATCAAAAATAAAATT
GAGGCTCTAAAAAATTAA

>g2569.t35 Gene=g2569 Length=281
MSDESQQQQHITVIDGGFSTQLSFHVGENIDGKQAIFKFNAVNPEAVIQSHLDFLNAGAE
IILTNTYQASIEGYQTYLDLDYHGSYELIKSTVKLAHIARDKFLSSHINHVKKPLIFASI
GPYGAHLHDGSEYTGSYEKRVSPAAIKKWHKVRIDACVESGVDGLAIETIPCLMEANALV
DLVLTEYPNLKFWISFQCKNGEVIANGQRFSDCILSIWNQVEAAKRPENLVAVGINCINP
SFVSPLFSEIEKNLCNFNVPLVVYPNSGKILYTLLFLLKIF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
5 g2569.t35 Gene3D G3DSA:3.20.20.330 - 1 273 0.000
2 g2569.t35 PANTHER PTHR46015 ZGC:172121 6 269 0.000
3 g2569.t35 PANTHER PTHR46015:SF1 ZGC:172121 6 269 0.000
1 g2569.t35 Pfam PF02574 Homocysteine S-methyltransferase 13 269 0.000
6 g2569.t35 ProSiteProfiles PS50970 Homocysteine-binding domain profile. 1 281 32.063
4 g2569.t35 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. There were no conditions that were differentially expressed