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.t4 isoform g2506.t4 18328331 18332582
chr_3 g2506 g2506.t4 exon g2506.t4.exon1 18328331 18328458
chr_3 g2506 g2506.t4 TSS g2506.t4 18328343 18328343
chr_3 g2506 g2506.t4 exon g2506.t4.exon2 18329059 18329255
chr_3 g2506 g2506.t4 exon g2506.t4.exon3 18330039 18330113
chr_3 g2506 g2506.t4 exon g2506.t4.exon4 18330192 18330314
chr_3 g2506 g2506.t4 cds g2506.t4.CDS1 18330212 18330314
chr_3 g2506 g2506.t4 exon g2506.t4.exon5 18330555 18330667
chr_3 g2506 g2506.t4 cds g2506.t4.CDS2 18330555 18330667
chr_3 g2506 g2506.t4 exon g2506.t4.exon6 18331502 18331645
chr_3 g2506 g2506.t4 cds g2506.t4.CDS3 18331502 18331645
chr_3 g2506 g2506.t4 exon g2506.t4.exon7 18331872 18332582
chr_3 g2506 g2506.t4 cds g2506.t4.CDS4 18331872 18332411
chr_3 g2506 g2506.t4 TTS g2506.t4 18333570 18333570

Sequences

>g2506.t4 Gene=g2506 Length=1491
CATTTCGCATTCATCATTCGTTCGGGAACCTTCAATTAGAGAAGCATCTCTCTCACCCTT
AGTCTTTCGACTTTAAGATTTAGAAGTAAAGTTTTTAACATTTTTATAAAACTAGTTTAA
CATTTCGTAAAATCTAAAGTGAAAAAAATTCAATCGGCCCAAAAGTGAAAAATAAGAAGA
GAGTTCTTAGCCTGAATTAAAATGCCAGAAACAACGACTAACATGAATGGTTATTCTAAT
GGACACAGTATTCACAATGGATATGAGCTTGAAGACAATTCTTCATTTCTCTTTACTTCA
GAATCTGTCGGCGAAGGACATCCAGATAAAATGTGTGACCAAATTTCTGATGCTATCTTA
GATGCTCATTTGAAACAAGACCCGAATGCAAAAGTTGCTTAAACTGTCAGCAAGACTGGT
ATGATCCTCTTGTGCGGGGAGATTACATCAAAAGCAAACGTCGACTATCAGAAAGTGGTT
CGTGATACAGTCAAACACATTGGATATGATGACTCCTCAAAGGGCTTCGACTGGAAGACT
CTTAACTTGTTAGTGGCAATTGAACAGCAATCGCCTGATATCGCTCAAGGAGTACACTTA
AATCGCGAAGAATATGATGTAGGAGCCGGTGATCAGGGTTTGATGTTTGGATATGCTACA
GACGAAACTGAAGAATGCATGCCTCTTACAGTCGTCTTAGCACATCGTTTGAACCAAAAG
ATTGCTGAACTTCGCAGATCTGGAGTTTTGAGCTGGGCACGTCCAGATTCTAAAACACAA
GTTACAGCAGAATACATTTTCCAAAAAGGAGCTTGCATTCCAAAGCGAGTTCACACGGTT
GTCGTCTCTTTACAGCATTCTGAAAAGGTTACATTGGAAGAATTACGAAAAGAGATTACT
GAAAAAGTTGTTCGTGTCGTCATTCCCGAAAAGTATTTGGATAATGAAACTATTGTTCAC
ATCAATCCATGTGGAAATTTTGTAATTGGTGGACCACAAGGTGATGCAGGTTTAACTGGA
CGCAAAATTATTGTCGATACCTATGGCGGATGGGGAGCTCATGGTGGTGGAGCATTTTCA
GGAAAGGACTTTACAAAGGTCGATCGCTCTGCTGCTTATGCTGCTCGTTGGGTTGCAAAA
TCATTGGTCAAAGCTGGTGTTTGCAGAAGATGCTTGGTTCAAGTAAGCTACGCCATTGGT
GTCGCTGAACCATTGTCAATAACAGTCTTTGACTATGGAACATCAAGTTATACACAAAAA
CAACTTTTGGAAATCATTAAAAAGAACTTTGATCTTCGCCCAGGCAAAATTGTTAAGTAA
GTTGTAGAGAGAATTTTTTATTCTGCTAAATATAAATAATTAATGATATTATTTTTTTTC
TTTAGTGACTTAAATTTGCGCACACCATTTTACCAACAAACAAGCACATATGGTCATTTT
GGTCGTGAAGGTTTTCCATGGGAAAAACCAAAGACATTGATTCTTGAATGA

>g2506.t4 Gene=g2506 Length=299
MILLCGEITSKANVDYQKVVRDTVKHIGYDDSSKGFDWKTLNLLVAIEQQSPDIAQGVHL
NREEYDVGAGDQGLMFGYATDETEECMPLTVVLAHRLNQKIAELRRSGVLSWARPDSKTQ
VTAEYIFQKGACIPKRVHTVVVSLQHSEKVTLEELRKEITEKVVRVVIPEKYLDNETIVH
INPCGNFVIGGPQGDAGLTGRKIIVDTYGGWGAHGGGAFSGKDFTKVDRSAAYAARWVAK
SLVKAGVCRRCLVQVSYAIGVAEPLSITVFDYGTSSYTQKQLLEIIKKNFDLRPGKIVK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g2506.t4 CDD cd18079 S-AdoMet_synt 1 299 0.0
11 g2506.t4 Gene3D G3DSA:3.30.300.10 - 1 228 3.3E-131
13 g2506.t4 Gene3D G3DSA:3.30.300.10 - 66 299 3.3E-131
12 g2506.t4 Gene3D G3DSA:3.30.300.10 - 89 191 3.3E-131
4 g2506.t4 PANTHER PTHR11964:SF11 S-ADENOSYLMETHIONINE SYNTHASE ISOFORM TYPE-1 1 299 6.7E-170
5 g2506.t4 PANTHER PTHR11964 S-ADENOSYLMETHIONINE SYNTHETASE 1 299 6.7E-170
3 g2506.t4 Pfam PF00438 S-adenosylmethionine synthetase, N-terminal domain 1 52 7.2E-13
1 g2506.t4 Pfam PF02772 S-adenosylmethionine synthetase, central domain 67 187 1.2E-44
2 g2506.t4 Pfam PF02773 S-adenosylmethionine synthetase, C-terminal domain 189 299 1.6E-54
9 g2506.t4 ProSitePatterns PS00376 S-adenosylmethionine synthase signature 1. 68 78 -
10 g2506.t4 ProSitePatterns PS00377 S-adenosylmethionine synthase signature 2. 215 223 -
6 g2506.t4 SUPERFAMILY SSF55973 S-adenosylmethionine synthetase 1 61 1.33E-18
8 g2506.t4 SUPERFAMILY SSF55973 S-adenosylmethionine synthetase 66 188 2.63E-49
7 g2506.t4 SUPERFAMILY SSF55973 S-adenosylmethionine synthetase 189 299 1.02E-51
14 g2506.t4 TIGRFAM TIGR01034 metK: methionine adenosyltransferase 1 299 3.6E-135

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