Gene loci information

Transcript annotation

  • This transcript has been annotated as S-adenosylmethionine synthase.

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 g2506 g2506.t18 TSS g2506.t18 18328889 18328889
chr_3 g2506 g2506.t18 isoform g2506.t18 18329132 18331945
chr_3 g2506 g2506.t18 exon g2506.t18.exon1 18329132 18329255
chr_3 g2506 g2506.t18 cds g2506.t18.CDS1 18329132 18329255
chr_3 g2506 g2506.t18 exon g2506.t18.exon2 18330039 18330116
chr_3 g2506 g2506.t18 cds g2506.t18.CDS2 18330039 18330116
chr_3 g2506 g2506.t18 exon g2506.t18.exon3 18330192 18330314
chr_3 g2506 g2506.t18 cds g2506.t18.CDS3 18330192 18330314
chr_3 g2506 g2506.t18 exon g2506.t18.exon4 18331196 18331308
chr_3 g2506 g2506.t18 cds g2506.t18.CDS4 18331196 18331308
chr_3 g2506 g2506.t18 exon g2506.t18.exon5 18331502 18331645
chr_3 g2506 g2506.t18 cds g2506.t18.CDS5 18331502 18331645
chr_3 g2506 g2506.t18 exon g2506.t18.exon6 18331872 18331945
chr_3 g2506 g2506.t18 cds g2506.t18.CDS6 18331872 18331943
chr_3 g2506 g2506.t18 TTS g2506.t18 NA NA

Sequences

>g2506.t18 Gene=g2506 Length=656
ATGCCAGAAACAACGACTAACATGAATGGTTATTCTAATGGACACAGTATTCACAATGGA
TATGAGCTTGAAGACAATTCTTCATTTCTCTTTACTTCAGAATCTGTCGGCGAAGGACAT
CCAGATAAAATGTGTGACCAAATTTCTGATGCTATCTTAGATGCTCATTTGAAACAAGAC
CCGAATGCAAAAGTTGCTTGTGAAACTGTCAGCAAGACTGGTATGATCCTCTTGTGCGGG
GAGATTACATCAAAAGCAAACGTCGACTATCAGAAAGTGGTTCGTGATACAGTCAAACAC
ATTGGATATGATGACTCCTCAAAGGGTTTTGATTACAAAACTTGTAGTCTTATGGTATGT
CTTGAGCAGCAAAGTCCAAATATTGCTGACGGGGTGCATGTTAATCGTAATGTCGAGGAT
ATTGGAGCTGGCGATCAGGGTTTGATGTTTGGATATGCTACAGACGAAACTGAAGAATGC
ATGCCTCTTACAGTCGTCTTAGCACATCGTTTGAACCAAAAGATTGCTGAACTTCGCAGA
TCTGGAGTTTTGAGCTGGGCACGTCCAGATTCTAAAACACAAGTTACAGCAGAATACATT
TTCCAAAAAGGAGCTTGCATTCCAAAGCGAGTTCACACGGTTGTCGTCTCTTTACA

>g2506.t18 Gene=g2506 Length=218
MPETTTNMNGYSNGHSIHNGYELEDNSSFLFTSESVGEGHPDKMCDQISDAILDAHLKQD
PNAKVACETVSKTGMILLCGEITSKANVDYQKVVRDTVKHIGYDDSSKGFDYKTCSLMVC
LEQQSPNIADGVHVNRNVEDIGAGDQGLMFGYATDETEECMPLTVVLAHRLNQKIAELRR
SGVLSWARPDSKTQVTAEYIFQKGACIPKRVHTVVVSL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g2506.t18 Gene3D G3DSA:3.30.300.10 - 38 144 3.7E-44
8 g2506.t18 Gene3D G3DSA:3.30.300.10 - 145 218 1.1E-29
3 g2506.t18 PANTHER PTHR11964:SF11 S-ADENOSYLMETHIONINE SYNTHASE ISOFORM TYPE-1 18 217 1.2E-113
4 g2506.t18 PANTHER PTHR11964 S-ADENOSYLMETHIONINE SYNTHETASE 18 217 1.2E-113
2 g2506.t18 Pfam PF00438 S-adenosylmethionine synthetase, N-terminal domain 29 126 1.2E-43
1 g2506.t18 Pfam PF02772 S-adenosylmethionine synthetase, central domain 141 217 1.2E-30
7 g2506.t18 ProSitePatterns PS00376 S-adenosylmethionine synthase signature 1. 142 152 -
6 g2506.t18 SUPERFAMILY SSF55973 S-adenosylmethionine synthetase 28 135 9.42E-48
5 g2506.t18 SUPERFAMILY SSF55973 S-adenosylmethionine synthetase 138 217 2.12E-33

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:0005524 ATP binding MF
GO:0004478 methionine adenosyltransferase activity MF
GO:0006556 S-adenosylmethionine biosynthetic process BP

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