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.t15 TSS g2506.t15 18328889 18328889
chr_3 g2506 g2506.t15 isoform g2506.t15 18329132 18331643
chr_3 g2506 g2506.t15 exon g2506.t15.exon1 18329132 18329255
chr_3 g2506 g2506.t15 cds g2506.t15.CDS1 18329132 18329255
chr_3 g2506 g2506.t15 exon g2506.t15.exon2 18330039 18330116
chr_3 g2506 g2506.t15 cds g2506.t15.CDS2 18330039 18330116
chr_3 g2506 g2506.t15 exon g2506.t15.exon3 18330192 18330314
chr_3 g2506 g2506.t15 cds g2506.t15.CDS3 18330192 18330314
chr_3 g2506 g2506.t15 exon g2506.t15.exon4 18331196 18331308
chr_3 g2506 g2506.t15 cds g2506.t15.CDS4 18331196 18331308
chr_3 g2506 g2506.t15 exon g2506.t15.exon5 18331502 18331643
chr_3 g2506 g2506.t15 cds g2506.t15.CDS5 18331502 18331642
chr_3 g2506 g2506.t15 TTS g2506.t15 NA NA

Sequences

>g2506.t15 Gene=g2506 Length=580
ATGCCAGAAACAACGACTAACATGAATGGTTATTCTAATGGACACAGTATTCACAATGGA
TATGAGCTTGAAGACAATTCTTCATTTCTCTTTACTTCAGAATCTGTCGGCGAAGGACAT
CCAGATAAAATGTGTGACCAAATTTCTGATGCTATCTTAGATGCTCATTTGAAACAAGAC
CCGAATGCAAAAGTTGCTTGTGAAACTGTCAGCAAGACTGGTATGATCCTCTTGTGCGGG
GAGATTACATCAAAAGCAAACGTCGACTATCAGAAAGTGGTTCGTGATACAGTCAAACAC
ATTGGATATGATGACTCCTCAAAGGGTTTTGATTACAAAACTTGTAGTCTTATGGTATGT
CTTGAGCAGCAAAGTCCAAATATTGCTGACGGGGTGCATGTTAATCGTAATGTCGAGGAT
ATTGGAGCTGGCGATCAGGGTTTGATGTTTGGATATGCTACAGACGAAACTGAAGAATGC
ATGCCTCTTACAGTCGTCTTAGCACATCGTTTGAACCAAAAGATTGCTGAACTTCGCAGA
TCTGGAGTTTTGAGCTGGGCACGTCCAGATTCTAAAACAC

>g2506.t15 Gene=g2506 Length=193
MPETTTNMNGYSNGHSIHNGYELEDNSSFLFTSESVGEGHPDKMCDQISDAILDAHLKQD
PNAKVACETVSKTGMILLCGEITSKANVDYQKVVRDTVKHIGYDDSSKGFDYKTCSLMVC
LEQQSPNIADGVHVNRNVEDIGAGDQGLMFGYATDETEECMPLTVVLAHRLNQKIAELRR
SGVLSWARPDSKT

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g2506.t15 Gene3D G3DSA:3.30.300.10 - 38 145 2.3E-44
9 g2506.t15 Gene3D G3DSA:3.30.300.10 - 146 193 7.2E-21
3 g2506.t15 PANTHER PTHR11964:SF11 S-ADENOSYLMETHIONINE SYNTHASE ISOFORM TYPE-1 18 193 1.9E-103
4 g2506.t15 PANTHER PTHR11964 S-ADENOSYLMETHIONINE SYNTHETASE 18 193 1.9E-103
2 g2506.t15 Pfam PF00438 S-adenosylmethionine synthetase, N-terminal domain 29 126 8.5E-44
1 g2506.t15 Pfam PF02772 S-adenosylmethionine synthetase, central domain 141 193 7.1E-22
7 g2506.t15 ProSitePatterns PS00376 S-adenosylmethionine synthase signature 1. 142 152 -
5 g2506.t15 SUPERFAMILY SSF55973 S-adenosylmethionine synthetase 28 135 6.67E-48
6 g2506.t15 SUPERFAMILY SSF55973 S-adenosylmethionine synthetase 136 193 1.33E-23

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