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.t2 isoform g2506.t2 18328331 18331877
chr_3 g2506 g2506.t2 exon g2506.t2.exon1 18328331 18328458
chr_3 g2506 g2506.t2 TSS g2506.t2 18328343 18328343
chr_3 g2506 g2506.t2 exon g2506.t2.exon2 18329059 18329255
chr_3 g2506 g2506.t2 cds g2506.t2.CDS1 18329132 18329255
chr_3 g2506 g2506.t2 exon g2506.t2.exon3 18330039 18330116
chr_3 g2506 g2506.t2 cds g2506.t2.CDS2 18330039 18330116
chr_3 g2506 g2506.t2 exon g2506.t2.exon4 18330192 18330314
chr_3 g2506 g2506.t2 cds g2506.t2.CDS3 18330192 18330314
chr_3 g2506 g2506.t2 exon g2506.t2.exon5 18330555 18330667
chr_3 g2506 g2506.t2 cds g2506.t2.CDS4 18330555 18330667
chr_3 g2506 g2506.t2 exon g2506.t2.exon6 18331502 18331645
chr_3 g2506 g2506.t2 cds g2506.t2.CDS5 18331502 18331645
chr_3 g2506 g2506.t2 exon g2506.t2.exon7 18331872 18331877
chr_3 g2506 g2506.t2 cds g2506.t2.CDS6 18331872 18331877
chr_3 g2506 g2506.t2 TTS g2506.t2 NA NA

Sequences

>g2506.t2 Gene=g2506 Length=789
CATTTCGCATTCATCATTCGTTCGGGAACCTTCAATTAGAGAAGCATCTCTCTCACCCTT
AGTCTTTCGACTTTAAGATTTAGAAGTAAAGTTTTTAACATTTTTATAAAACTAGTTTAA
CATTTCGTAAAATCTAAAGTGAAAAAAATTCAATCGGCCCAAAAGTGAAAAATAAGAAGA
GAGTTCTTAGCCTGAATTAAAATGCCAGAAACAACGACTAACATGAATGGTTATTCTAAT
GGACACAGTATTCACAATGGATATGAGCTTGAAGACAATTCTTCATTTCTCTTTACTTCA
GAATCTGTCGGCGAAGGACATCCAGATAAAATGTGTGACCAAATTTCTGATGCTATCTTA
GATGCTCATTTGAAACAAGACCCGAATGCAAAAGTTGCTTGTGAAACTGTCAGCAAGACT
GGTATGATCCTCTTGTGCGGGGAGATTACATCAAAAGCAAACGTCGACTATCAGAAAGTG
GTTCGTGATACAGTCAAACACATTGGATATGATGACTCCTCAAAGGGCTTCGACTGGAAG
ACTCTTAACTTGTTAGTGGCAATTGAACAGCAATCGCCTGATATCGCTCAAGGAGTACAC
TTAAATCGCGAAGAATATGATGTAGGAGCCGGTGATCAGGGTTTGATGTTTGGATATGCT
ACAGACGAAACTGAAGAATGCATGCCTCTTACAGTCGTCTTAGCACATCGTTTGAACCAA
AAGATTGCTGAACTTCGCAGATCTGGAGTTTTGAGCTGGGCACGTCCAGATTCTAAAACA
CAAGTTACA

>g2506.t2 Gene=g2506 Length=196
MPETTTNMNGYSNGHSIHNGYELEDNSSFLFTSESVGEGHPDKMCDQISDAILDAHLKQD
PNAKVACETVSKTGMILLCGEITSKANVDYQKVVRDTVKHIGYDDSSKGFDWKTLNLLVA
IEQQSPDIAQGVHLNREEYDVGAGDQGLMFGYATDETEECMPLTVVLAHRLNQKIAELRR
SGVLSWARPDSKTQVT

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g2506.t2 Gene3D G3DSA:3.30.300.10 - 38 131 2.7E-45
8 g2506.t2 Gene3D G3DSA:3.30.300.10 - 132 196 1.1E-26
3 g2506.t2 PANTHER PTHR11964:SF11 S-ADENOSYLMETHIONINE SYNTHASE ISOFORM TYPE-1 18 196 1.0E-106
4 g2506.t2 PANTHER PTHR11964 S-ADENOSYLMETHIONINE SYNTHETASE 18 196 1.0E-106
2 g2506.t2 Pfam PF00438 S-adenosylmethionine synthetase, N-terminal domain 29 126 1.0E-43
1 g2506.t2 Pfam PF02772 S-adenosylmethionine synthetase, central domain 141 196 2.3E-24
7 g2506.t2 ProSitePatterns PS00376 S-adenosylmethionine synthase signature 1. 142 152 -
5 g2506.t2 SUPERFAMILY SSF55973 S-adenosylmethionine synthetase 28 135 5.49E-49
6 g2506.t2 SUPERFAMILY SSF55973 S-adenosylmethionine synthetase 137 196 3.26E-25

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