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.t31 TTS g2569.t31 18786001 18786001
chr_3 g2569 g2569.t31 isoform g2569.t31 18786093 18787823
chr_3 g2569 g2569.t31 exon g2569.t31.exon1 18786093 18786265
chr_3 g2569 g2569.t31 cds g2569.t31.CDS1 18786093 18786265
chr_3 g2569 g2569.t31 exon g2569.t31.exon2 18786329 18786533
chr_3 g2569 g2569.t31 cds g2569.t31.CDS2 18786329 18786533
chr_3 g2569 g2569.t31 exon g2569.t31.exon3 18786923 18787000
chr_3 g2569 g2569.t31 cds g2569.t31.CDS3 18786923 18787000
chr_3 g2569 g2569.t31 exon g2569.t31.exon4 18787056 18787204
chr_3 g2569 g2569.t31 cds g2569.t31.CDS4 18787056 18787204
chr_3 g2569 g2569.t31 exon g2569.t31.exon5 18787332 18787588
chr_3 g2569 g2569.t31 cds g2569.t31.CDS5 18787332 18787588
chr_3 g2569 g2569.t31 exon g2569.t31.exon6 18787711 18787823
chr_3 g2569 g2569.t31 cds g2569.t31.CDS6 18787711 18787823
chr_3 g2569 g2569.t31 TSS g2569.t31 18788728 18788728

Sequences

>g2569.t31 Gene=g2569 Length=975
ATGTCAGACGAGTCACAACAACAACAACATATAACAGTCATTGATGGTGGATTTTCAACT
CAACTTAGTTTTCATGTCGGTGAAAATATCGATGGTAAGCAGGCTATATTTAAATTTAAT
GCAGTTAATCCCGAAGCTGTCATTCAAAGTCATTTAGATTTTCTTAATGCAGGAGCTGAA
ATAATTTTGACAAACACCTATCAAGCTAGTATTGAAGGATATCAAACTTATTTGGATCTA
GATTATCATGGAAGTTATGAGCTTATTAAGTCAACAGTGAAGCTAGCTCATATTGCGCGT
GACAAATTTTTATCTTCGCATATCAACCATGTGAAAAAACCTTTAATTTTTGCATCAATC
GGTCCTTATGGTGCGCATTTACATGATGGAAGTGAATATACTGGAAGTTATGAAAAAAGA
GTGTCACCTGCAGCAATCAAAAAATGGCACAAAGTGAGAATCGATGCATGTGTTGAATCG
GGGGTTGATGGATTAGCAATTGAAACTATTCCATGTTTGATGGAAGCAAATGCATTAGTT
GATCTCGTTCTCACGGAATATCCAAATTTAAAATTTTGGATATCTTTCCAATGCAAGAAC
GGTGAAGTAATTGCTAATGGACAAAGATTTTCTGACTGCATTTTATCTATTTGGAATCAA
GTAGAAGCAGCTAAACGTCCAGAAAATTTAGTTGCAGTTGGAATTAATTGTATAAATCCA
AGCTTTGTTTCACCACTTTTTTCTGAAATTGAGAAAAATTTGTGCAATTTCAATGTACCG
CTAGTCGTGTACCCAAACAGTGGTGAAGTTTATACTGTTGAAGAAGGTTGGCATGGGAAA
AATGACTGCATTCCATTAGAGAATTATATTGAAGAATGGGTCAAATTAGGAGCAAAATAT
ATTGGAGGATGTTGTCGTACAAATGCTCATGATATTGAGAAAATCAAAAATAAAATTGAG
GCTCTAAAAAATTAA

>g2569.t31 Gene=g2569 Length=324
MSDESQQQQHITVIDGGFSTQLSFHVGENIDGKQAIFKFNAVNPEAVIQSHLDFLNAGAE
IILTNTYQASIEGYQTYLDLDYHGSYELIKSTVKLAHIARDKFLSSHINHVKKPLIFASI
GPYGAHLHDGSEYTGSYEKRVSPAAIKKWHKVRIDACVESGVDGLAIETIPCLMEANALV
DLVLTEYPNLKFWISFQCKNGEVIANGQRFSDCILSIWNQVEAAKRPENLVAVGINCINP
SFVSPLFSEIEKNLCNFNVPLVVYPNSGEVYTVEEGWHGKNDCIPLENYIEEWVKLGAKY
IGGCCRTNAHDIEKIKNKIEALKN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g2569.t31 Coils Coil Coil 305 324 -
5 g2569.t31 Gene3D G3DSA:3.20.20.330 - 1 319 1.9E-87
2 g2569.t31 PANTHER PTHR46015 ZGC:172121 6 321 2.2E-88
3 g2569.t31 PANTHER PTHR46015:SF1 ZGC:172121 6 321 2.2E-88
8 g2569.t31 PIRSF PIRSF037505 BHMT 6 217 2.8E-4
9 g2569.t31 PIRSF PIRSF037505 BHMT 271 323 0.0083
1 g2569.t31 Pfam PF02574 Homocysteine S-methyltransferase 13 318 1.2E-64
7 g2569.t31 ProSiteProfiles PS50970 Homocysteine-binding domain profile. 1 319 40.152
4 g2569.t31 SUPERFAMILY SSF82282 Homocysteine S-methyltransferase 6 322 1.57E-68

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

Pathway

  • This transcript belongs to the following pathways

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