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.t23 TSS g2506.t23 18328889 18328889
chr_3 g2506 g2506.t23 isoform g2506.t23 18329132 18332582
chr_3 g2506 g2506.t23 exon g2506.t23.exon1 18329132 18329259
chr_3 g2506 g2506.t23 exon g2506.t23.exon2 18330039 18330116
chr_3 g2506 g2506.t23 cds g2506.t23.CDS1 18330044 18330116
chr_3 g2506 g2506.t23 exon g2506.t23.exon3 18330192 18330314
chr_3 g2506 g2506.t23 cds g2506.t23.CDS2 18330192 18330314
chr_3 g2506 g2506.t23 exon g2506.t23.exon4 18331196 18331308
chr_3 g2506 g2506.t23 cds g2506.t23.CDS3 18331196 18331308
chr_3 g2506 g2506.t23 exon g2506.t23.exon5 18331502 18331645
chr_3 g2506 g2506.t23 cds g2506.t23.CDS4 18331502 18331645
chr_3 g2506 g2506.t23 exon g2506.t23.exon6 18331872 18332407
chr_3 g2506 g2506.t23 cds g2506.t23.CDS5 18331872 18332407
chr_3 g2506 g2506.t23 exon g2506.t23.exon7 18332477 18332582
chr_3 g2506 g2506.t23 cds g2506.t23.CDS6 18332477 18332582
chr_3 g2506 g2506.t23 TTS g2506.t23 18333570 18333570

Sequences

>g2506.t23 Gene=g2506 Length=1228
ATGCCAGAAACAACGACTAACATGAATGGTTATTCTAATGGACACAGTATTCACAATGGA
TATGAGCTTGAAGACAATTCTTCATTTCTCTTTACTTCAGAATCTGTCGGCGAAGGACAT
CCAGGTAGATAAAATGTGTGACCAAATTTCTGATGCTATCTTAGATGCTCATTTGAAACA
AGACCCGAATGCAAAAGTTGCTTGTGAAACTGTCAGCAAGACTGGTATGATCCTCTTGTG
CGGGGAGATTACATCAAAAGCAAACGTCGACTATCAGAAAGTGGTTCGTGATACAGTCAA
ACACATTGGATATGATGACTCCTCAAAGGGTTTTGATTACAAAACTTGTAGTCTTATGGT
ATGTCTTGAGCAGCAAAGTCCAAATATTGCTGACGGGGTGCATGTTAATCGTAATGTCGA
GGATATTGGAGCTGGCGATCAGGGTTTGATGTTTGGATATGCTACAGACGAAACTGAAGA
ATGCATGCCTCTTACAGTCGTCTTAGCACATCGTTTGAACCAAAAGATTGCTGAACTTCG
CAGATCTGGAGTTTTGAGCTGGGCACGTCCAGATTCTAAAACACAAGTTACAGCAGAATA
CATTTTCCAAAAAGGAGCTTGCATTCCAAAGCGAGTTCACACGGTTGTCGTCTCTTTACA
GCATTCTGAAAAGGTTACATTGGAAGAATTACGAAAAGAGATTACTGAAAAAGTTGTTCG
TGTCGTCATTCCCGAAAAGTATTTGGATAATGAAACTATTGTTCACATCAATCCATGTGG
AAATTTTGTAATTGGTGGACCACAAGGTGATGCAGGTTTAACTGGACGCAAAATTATTGT
CGATACCTATGGCGGATGGGGAGCTCATGGTGGTGGAGCATTTTCAGGAAAGGACTTTAC
AAAGGTCGATCGCTCTGCTGCTTATGCTGCTCGTTGGGTTGCAAAATCATTGGTCAAAGC
TGGTGTTTGCAGAAGATGCTTGGTTCAAGTAAGCTACGCCATTGGTGTCGCTGAACCATT
GTCAATAACAGTCTTTGACTATGGAACATCAAGTTATACACAAAAACAACTTTTGGAAAT
CATTAAAAAGAACTTTGATCTTCGCCCAGGCAAAATTGTTAATGACTTAAATTTGCGCAC
ACCATTTTACCAACAAACAAGCACATATGGTCATTTTGGTCGTGAAGGTTTTCCATGGGA
AAAACCAAAGACATTGATTCTTGAATGA

>g2506.t23 Gene=g2506 Length=364
MCDQISDAILDAHLKQDPNAKVACETVSKTGMILLCGEITSKANVDYQKVVRDTVKHIGY
DDSSKGFDYKTCSLMVCLEQQSPNIADGVHVNRNVEDIGAGDQGLMFGYATDETEECMPL
TVVLAHRLNQKIAELRRSGVLSWARPDSKTQVTAEYIFQKGACIPKRVHTVVVSLQHSEK
VTLEELRKEITEKVVRVVIPEKYLDNETIVHINPCGNFVIGGPQGDAGLTGRKIIVDTYG
GWGAHGGGAFSGKDFTKVDRSAAYAARWVAKSLVKAGVCRRCLVQVSYAIGVAEPLSITV
FDYGTSSYTQKQLLEIIKKNFDLRPGKIVNDLNLRTPFYQQTSTYGHFGREGFPWEKPKT
LILE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g2506.t23 CDD cd18079 S-AdoMet_synt 1 359 0.0
10 g2506.t23 Gene3D G3DSA:3.30.300.10 - 1 259 2.1E-163
9 g2506.t23 Gene3D G3DSA:3.30.300.10 - 97 356 2.1E-163
11 g2506.t23 Gene3D G3DSA:3.30.300.10 - 120 222 2.1E-163
4 g2506.t23 PANTHER PTHR11964:SF11 S-ADENOSYLMETHIONINE SYNTHASE ISOFORM TYPE-1 1 362 1.6E-206
5 g2506.t23 PANTHER PTHR11964 S-ADENOSYLMETHIONINE SYNTHETASE 1 362 1.6E-206
12 g2506.t23 PIRSF PIRSF000497 MAT 1 363 3.9E-154
3 g2506.t23 Pfam PF00438 S-adenosylmethionine synthetase, N-terminal domain 1 83 1.4E-30
1 g2506.t23 Pfam PF02772 S-adenosylmethionine synthetase, central domain 98 218 1.2E-44
2 g2506.t23 Pfam PF02773 S-adenosylmethionine synthetase, C-terminal domain 220 357 5.0E-68
14 g2506.t23 ProSitePatterns PS00376 S-adenosylmethionine synthase signature 1. 99 109 -
15 g2506.t23 ProSitePatterns PS00377 S-adenosylmethionine synthase signature 2. 246 254 -
8 g2506.t23 SUPERFAMILY SSF55973 S-adenosylmethionine synthetase 1 92 5.1E-36
6 g2506.t23 SUPERFAMILY SSF55973 S-adenosylmethionine synthetase 96 219 1.06E-49
7 g2506.t23 SUPERFAMILY SSF55973 S-adenosylmethionine synthetase 220 360 3.18E-66
16 g2506.t23 TIGRFAM TIGR01034 metK: methionine adenosyltransferase 1 361 1.1E-169

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