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.t5 isoform g2506.t5 18328331 18332582
chr_3 g2506 g2506.t5 exon g2506.t5.exon1 18328331 18328458
chr_3 g2506 g2506.t5 TSS g2506.t5 18328343 18328343
chr_3 g2506 g2506.t5 exon g2506.t5.exon2 18329059 18329255
chr_3 g2506 g2506.t5 exon g2506.t5.exon3 18330039 18330116
chr_3 g2506 g2506.t5 exon g2506.t5.exon4 18330192 18330318
chr_3 g2506 g2506.t5 exon g2506.t5.exon5 18330555 18330667
chr_3 g2506 g2506.t5 exon g2506.t5.exon6 18331502 18331645
chr_3 g2506 g2506.t5 cds g2506.t5.CDS1 18331508 18331645
chr_3 g2506 g2506.t5 exon g2506.t5.exon7 18331872 18332407
chr_3 g2506 g2506.t5 cds g2506.t5.CDS2 18331872 18332407
chr_3 g2506 g2506.t5 exon g2506.t5.exon8 18332477 18332582
chr_3 g2506 g2506.t5 cds g2506.t5.CDS3 18332477 18332582
chr_3 g2506 g2506.t5 TTS g2506.t5 18333570 18333570

Sequences

>g2506.t5 Gene=g2506 Length=1429
CATTTCGCATTCATCATTCGTTCGGGAACCTTCAATTAGAGAAGCATCTCTCTCACCCTT
AGTCTTTCGACTTTAAGATTTAGAAGTAAAGTTTTTAACATTTTTATAAAACTAGTTTAA
CATTTCGTAAAATCTAAAGTGAAAAAAATTCAATCGGCCCAAAAGTGAAAAATAAGAAGA
GAGTTCTTAGCCTGAATTAAAATGCCAGAAACAACGACTAACATGAATGGTTATTCTAAT
GGACACAGTATTCACAATGGATATGAGCTTGAAGACAATTCTTCATTTCTCTTTACTTCA
GAATCTGTCGGCGAAGGACATCCAGATAAAATGTGTGACCAAATTTCTGATGCTATCTTA
GATGCTCATTTGAAACAAGACCCGAATGCAAAAGTTGCTTGTGAAACTGTCAGCAAGACT
GGTATGATCCTCTTGTGCGGGGAGATTACATCAAAAGCAAACGTCGACTATCAGAAAGTG
GTTCGTGATACAGTCAAACACATTGGATATGATGACTCCTCAAAGGGTAAGCTTCGACTG
GAAGACTCTTAACTTGTTAGTGGCAATTGAACAGCAATCGCCTGATATCGCTCAAGGAGT
ACACTTAAATCGCGAAGAATATGATGTAGGAGCCGGTGATCAGGGTTTGATGTTTGGATA
TGCTACAGACGAAACTGAAGAATGCATGCCTCTTACAGTCGTCTTAGCACATCGTTTGAA
CCAAAAGATTGCTGAACTTCGCAGATCTGGAGTTTTGAGCTGGGCACGTCCAGATTCTAA
AACACAAGTTACAGCAGAATACATTTTCCAAAAAGGAGCTTGCATTCCAAAGCGAGTTCA
CACGGTTGTCGTCTCTTTACAGCATTCTGAAAAGGTTACATTGGAAGAATTACGAAAAGA
GATTACTGAAAAAGTTGTTCGTGTCGTCATTCCCGAAAAGTATTTGGATAATGAAACTAT
TGTTCACATCAATCCATGTGGAAATTTTGTAATTGGTGGACCACAAGGTGATGCAGGTTT
AACTGGACGCAAAATTATTGTCGATACCTATGGCGGATGGGGAGCTCATGGTGGTGGAGC
ATTTTCAGGAAAGGACTTTACAAAGGTCGATCGCTCTGCTGCTTATGCTGCTCGTTGGGT
TGCAAAATCATTGGTCAAAGCTGGTGTTTGCAGAAGATGCTTGGTTCAAGTAAGCTACGC
CATTGGTGTCGCTGAACCATTGTCAATAACAGTCTTTGACTATGGAACATCAAGTTATAC
ACAAAAACAACTTTTGGAAATCATTAAAAAGAACTTTGATCTTCGCCCAGGCAAAATTGT
TAATGACTTAAATTTGCGCACACCATTTTACCAACAAACAAGCACATATGGTCATTTTGG
TCGTGAAGGTTTTCCATGGGAAAAACCAAAGACATTGATTCTTGAATGA

>g2506.t5 Gene=g2506 Length=259
MFGYATDETEECMPLTVVLAHRLNQKIAELRRSGVLSWARPDSKTQVTAEYIFQKGACIP
KRVHTVVVSLQHSEKVTLEELRKEITEKVVRVVIPEKYLDNETIVHINPCGNFVIGGPQG
DAGLTGRKIIVDTYGGWGAHGGGAFSGKDFTKVDRSAAYAARWVAKSLVKAGVCRRCLVQ
VSYAIGVAEPLSITVFDYGTSSYTQKQLLEIIKKNFDLRPGKIVNDLNLRTPFYQQTSTY
GHFGREGFPWEKPKTLILE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g2506.t5 CDD cd18079 S-AdoMet_synt 1 254 9.38842E-163
8 g2506.t5 Gene3D G3DSA:3.30.300.10 - 1 115 2.8E-42
9 g2506.t5 Gene3D G3DSA:3.30.300.10 - 133 259 4.7E-53
3 g2506.t5 PANTHER PTHR11964:SF11 S-ADENOSYLMETHIONINE SYNTHASE ISOFORM TYPE-1 1 257 5.7E-137
4 g2506.t5 PANTHER PTHR11964 S-ADENOSYLMETHIONINE SYNTHETASE 1 257 5.7E-137
1 g2506.t5 Pfam PF02772 S-adenosylmethionine synthetase, central domain 1 113 1.4E-38
2 g2506.t5 Pfam PF02773 S-adenosylmethionine synthetase, C-terminal domain 115 252 2.2E-68
7 g2506.t5 ProSitePatterns PS00377 S-adenosylmethionine synthase signature 2. 141 149 -
6 g2506.t5 SUPERFAMILY SSF55973 S-adenosylmethionine synthetase 1 114 1.02E-42
5 g2506.t5 SUPERFAMILY SSF55973 S-adenosylmethionine synthetase 115 255 1.37E-66
10 g2506.t5 TIGRFAM TIGR01034 metK: methionine adenosyltransferase 1 256 4.8E-119

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