Gene loci information

Transcript annotation

  • This transcript has been annotated as 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.t1 TTS g2569.t1 18786001 18786001
chr_3 g2569 g2569.t1 isoform g2569.t1 18786093 18787823
chr_3 g2569 g2569.t1 exon g2569.t1.exon1 18786093 18786265
chr_3 g2569 g2569.t1 cds g2569.t1.CDS1 18786093 18786265
chr_3 g2569 g2569.t1 exon g2569.t1.exon2 18786329 18786533
chr_3 g2569 g2569.t1 cds g2569.t1.CDS2 18786329 18786533
chr_3 g2569 g2569.t1 exon g2569.t1.exon3 18786923 18787000
chr_3 g2569 g2569.t1 cds g2569.t1.CDS3 18786923 18787000
chr_3 g2569 g2569.t1 exon g2569.t1.exon4 18787056 18787204
chr_3 g2569 g2569.t1 cds g2569.t1.CDS4 18787056 18787204
chr_3 g2569 g2569.t1 exon g2569.t1.exon5 18787332 18787588
chr_3 g2569 g2569.t1 cds g2569.t1.CDS5 18787332 18787588
chr_3 g2569 g2569.t1 exon g2569.t1.exon6 18787649 18787670
chr_3 g2569 g2569.t1 cds g2569.t1.CDS6 18787649 18787670
chr_3 g2569 g2569.t1 exon g2569.t1.exon7 18787730 18787823
chr_3 g2569 g2569.t1 cds g2569.t1.CDS7 18787730 18787823
chr_3 g2569 g2569.t1 TSS g2569.t1 18788728 18788728

Sequences

>g2569.t1 Gene=g2569 Length=978
ATGTCAGACGAGTCACAACAACAACAACATATAACAGTCATTGATGGTGGATTTTCAACT
CAACTTAGTTTTCATGTCGGTGAAAATATCGATGGTGATCCTTTGTGGTCTGCAAGATTT
AATGCAGTTAATCCCGAAGCTGTCATTCAAAGTCATTTAGATTTTCTTAATGCAGGAGCT
GAAATAATTTTGACAAACACCTATCAAGCTAGTATTGAAGGATATCAAACTTATTTGGAT
CTAGATTATCATGGAAGTTATGAGCTTATTAAGTCAACAGTGAAGCTAGCTCATATTGCG
CGTGACAAATTTTTATCTTCGCATATCAACCATGTGAAAAAACCTTTAATTTTTGCATCA
ATCGGTCCTTATGGTGCGCATTTACATGATGGAAGTGAATATACTGGAAGTTATGAAAAA
AGAGTGTCACCTGCAGCAATCAAAAAATGGCACAAAGTGAGAATCGATGCATGTGTTGAA
TCGGGGGTTGATGGATTAGCAATTGAAACTATTCCATGTTTGATGGAAGCAAATGCATTA
GTTGATCTCGTTCTCACGGAATATCCAAATTTAAAATTTTGGATATCTTTCCAATGCAAG
AACGGTGAAGTAATTGCTAATGGACAAAGATTTTCTGACTGCATTTTATCTATTTGGAAT
CAAGTAGAAGCAGCTAAACGTCCAGAAAATTTAGTTGCAGTTGGAATTAATTGTATAAAT
CCAAGCTTTGTTTCACCACTTTTTTCTGAAATTGAGAAAAATTTGTGCAATTTCAATGTA
CCGCTAGTCGTGTACCCAAACAGTGGTGAAGTTTATACTGTTGAAGAAGGTTGGCATGGG
AAAAATGACTGCATTCCATTAGAGAATTATATTGAAGAATGGGTCAAATTAGGAGCAAAA
TATATTGGAGGATGTTGTCGTACAAATGCTCATGATATTGAGAAAATCAAAAATAAAATT
GAGGCTCTAAAAAATTAA

>g2569.t1 Gene=g2569 Length=325
MSDESQQQQHITVIDGGFSTQLSFHVGENIDGDPLWSARFNAVNPEAVIQSHLDFLNAGA
EIILTNTYQASIEGYQTYLDLDYHGSYELIKSTVKLAHIARDKFLSSHINHVKKPLIFAS
IGPYGAHLHDGSEYTGSYEKRVSPAAIKKWHKVRIDACVESGVDGLAIETIPCLMEANAL
VDLVLTEYPNLKFWISFQCKNGEVIANGQRFSDCILSIWNQVEAAKRPENLVAVGINCIN
PSFVSPLFSEIEKNLCNFNVPLVVYPNSGEVYTVEEGWHGKNDCIPLENYIEEWVKLGAK
YIGGCCRTNAHDIEKIKNKIEALKN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g2569.t1 Coils Coil Coil 313 325 -
5 g2569.t1 Gene3D G3DSA:3.20.20.330 - 1 320 4.2E-92
2 g2569.t1 PANTHER PTHR11103:SF10 HOMOCYSTEINE S-METHYLTRANSFERASE 1-RELATED 6 323 4.1E-95
3 g2569.t1 PANTHER PTHR11103 SLR1189 PROTEIN 6 323 4.1E-95
8 g2569.t1 PIRSF PIRSF037505 BHMT 4 191 5.7E-5
9 g2569.t1 PIRSF PIRSF037505 BHMT 272 324 0.0083
1 g2569.t1 Pfam PF02574 Homocysteine S-methyltransferase 13 319 4.5E-67
7 g2569.t1 ProSiteProfiles PS50970 Homocysteine-binding domain profile. 1 320 40.501
4 g2569.t1 SUPERFAMILY SSF82282 Homocysteine S-methyltransferase 6 323 5.49E-72

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.

Raw TPM values