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.t22 TSS g2506.t22 18328889 18328889
chr_3 g2506 g2506.t22 isoform g2506.t22 18329132 18332582
chr_3 g2506 g2506.t22 exon g2506.t22.exon1 18329132 18329255
chr_3 g2506 g2506.t22 cds g2506.t22.CDS1 18329132 18329255
chr_3 g2506 g2506.t22 exon g2506.t22.exon2 18330039 18330120
chr_3 g2506 g2506.t22 cds g2506.t22.CDS2 18330039 18330120
chr_3 g2506 g2506.t22 exon g2506.t22.exon3 18330202 18330314
chr_3 g2506 g2506.t22 cds g2506.t22.CDS3 18330202 18330314
chr_3 g2506 g2506.t22 exon g2506.t22.exon4 18331196 18331308
chr_3 g2506 g2506.t22 cds g2506.t22.CDS4 18331196 18331308
chr_3 g2506 g2506.t22 exon g2506.t22.exon5 18331502 18331645
chr_3 g2506 g2506.t22 cds g2506.t22.CDS5 18331502 18331645
chr_3 g2506 g2506.t22 exon g2506.t22.exon6 18331872 18332407
chr_3 g2506 g2506.t22 cds g2506.t22.CDS6 18331872 18332407
chr_3 g2506 g2506.t22 exon g2506.t22.exon7 18332477 18332582
chr_3 g2506 g2506.t22 cds g2506.t22.CDS7 18332477 18332582
chr_3 g2506 g2506.t22 TTS g2506.t22 18333570 18333570

Sequences

>g2506.t22 Gene=g2506 Length=1218
ATGCCAGAAACAACGACTAACATGAATGGTTATTCTAATGGACACAGTATTCACAATGGA
TATGAGCTTGAAGACAATTCTTCATTTCTCTTTACTTCAGAATCTGTCGGCGAAGGACAT
CCAGATAAAATGTGTGACCAAATTTCTGATGCTATCTTAGATGCTCATTTGAAACAAGAC
CCGAATGCAAAAGTTGCTTGTGGTAACAAGACTGGTATGATCCTCTTGTGCGGGGAGATT
ACATCAAAAGCAAACGTCGACTATCAGAAAGTGGTTCGTGATACAGTCAAACACATTGGA
TATGATGACTCCTCAAAGGGTTTTGATTACAAAACTTGTAGTCTTATGGTATGTCTTGAG
CAGCAAAGTCCAAATATTGCTGACGGGGTGCATGTTAATCGTAATGTCGAGGATATTGGA
GCTGGCGATCAGGGTTTGATGTTTGGATATGCTACAGACGAAACTGAAGAATGCATGCCT
CTTACAGTCGTCTTAGCACATCGTTTGAACCAAAAGATTGCTGAACTTCGCAGATCTGGA
GTTTTGAGCTGGGCACGTCCAGATTCTAAAACACAAGTTACAGCAGAATACATTTTCCAA
AAAGGAGCTTGCATTCCAAAGCGAGTTCACACGGTTGTCGTCTCTTTACAGCATTCTGAA
AAGGTTACATTGGAAGAATTACGAAAAGAGATTACTGAAAAAGTTGTTCGTGTCGTCATT
CCCGAAAAGTATTTGGATAATGAAACTATTGTTCACATCAATCCATGTGGAAATTTTGTA
ATTGGTGGACCACAAGGTGATGCAGGTTTAACTGGACGCAAAATTATTGTCGATACCTAT
GGCGGATGGGGAGCTCATGGTGGTGGAGCATTTTCAGGAAAGGACTTTACAAAGGTCGAT
CGCTCTGCTGCTTATGCTGCTCGTTGGGTTGCAAAATCATTGGTCAAAGCTGGTGTTTGC
AGAAGATGCTTGGTTCAAGTAAGCTACGCCATTGGTGTCGCTGAACCATTGTCAATAACA
GTCTTTGACTATGGAACATCAAGTTATACACAAAAACAACTTTTGGAAATCATTAAAAAG
AACTTTGATCTTCGCCCAGGCAAAATTGTTAATGACTTAAATTTGCGCACACCATTTTAC
CAACAAACAAGCACATATGGTCATTTTGGTCGTGAAGGTTTTCCATGGGAAAAACCAAAG
ACATTGATTCTTGAATGA

>g2506.t22 Gene=g2506 Length=405
MPETTTNMNGYSNGHSIHNGYELEDNSSFLFTSESVGEGHPDKMCDQISDAILDAHLKQD
PNAKVACGNKTGMILLCGEITSKANVDYQKVVRDTVKHIGYDDSSKGFDYKTCSLMVCLE
QQSPNIADGVHVNRNVEDIGAGDQGLMFGYATDETEECMPLTVVLAHRLNQKIAELRRSG
VLSWARPDSKTQVTAEYIFQKGACIPKRVHTVVVSLQHSEKVTLEELRKEITEKVVRVVI
PEKYLDNETIVHINPCGNFVIGGPQGDAGLTGRKIIVDTYGGWGAHGGGAFSGKDFTKVD
RSAAYAARWVAKSLVKAGVCRRCLVQVSYAIGVAEPLSITVFDYGTSSYTQKQLLEIIKK
NFDLRPGKIVNDLNLRTPFYQQTSTYGHFGREGFPWEKPKTLILE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g2506.t22 CDD cd18079 S-AdoMet_synt 30 400 0.0
12 g2506.t22 Gene3D G3DSA:3.30.300.10 - 30 263 1.7E-169
10 g2506.t22 Gene3D G3DSA:3.30.300.10 - 36 300 1.7E-169
11 g2506.t22 Gene3D G3DSA:3.30.300.10 - 138 397 1.7E-169
6 g2506.t22 Hamap MF_00086 S-adenosylmethionine synthase [metK]. 27 403 48.487335
4 g2506.t22 PANTHER PTHR11964:SF11 S-ADENOSYLMETHIONINE SYNTHASE ISOFORM TYPE-1 18 403 4.5E-216
5 g2506.t22 PANTHER PTHR11964 S-ADENOSYLMETHIONINE SYNTHETASE 18 403 4.5E-216
13 g2506.t22 PIRSF PIRSF000497 MAT 23 404 7.8E-162
3 g2506.t22 Pfam PF00438 S-adenosylmethionine synthetase, N-terminal domain 29 124 1.4E-38
1 g2506.t22 Pfam PF02772 S-adenosylmethionine synthetase, central domain 139 259 1.5E-44
2 g2506.t22 Pfam PF02773 S-adenosylmethionine synthetase, C-terminal domain 261 398 6.3E-68
15 g2506.t22 ProSitePatterns PS00376 S-adenosylmethionine synthase signature 1. 140 150 -
16 g2506.t22 ProSitePatterns PS00377 S-adenosylmethionine synthase signature 2. 287 295 -
7 g2506.t22 SUPERFAMILY SSF55973 S-adenosylmethionine synthetase 28 133 1.14E-42
9 g2506.t22 SUPERFAMILY SSF55973 S-adenosylmethionine synthetase 137 260 1.29E-49
8 g2506.t22 SUPERFAMILY SSF55973 S-adenosylmethionine synthetase 261 401 3.92E-66
17 g2506.t22 TIGRFAM TIGR01034 metK: methionine adenosyltransferase 30 402 7.4E-176

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

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