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.t3 isoform g2506.t3 18328331 18332398
chr_3 g2506 g2506.t3 exon g2506.t3.exon1 18328331 18328458
chr_3 g2506 g2506.t3 TSS g2506.t3 18328343 18328343
chr_3 g2506 g2506.t3 exon g2506.t3.exon2 18329059 18329255
chr_3 g2506 g2506.t3 cds g2506.t3.CDS1 18329132 18329255
chr_3 g2506 g2506.t3 exon g2506.t3.exon3 18330039 18330120
chr_3 g2506 g2506.t3 cds g2506.t3.CDS2 18330039 18330120
chr_3 g2506 g2506.t3 exon g2506.t3.exon4 18330202 18330314
chr_3 g2506 g2506.t3 cds g2506.t3.CDS3 18330202 18330314
chr_3 g2506 g2506.t3 exon g2506.t3.exon5 18330555 18330667
chr_3 g2506 g2506.t3 cds g2506.t3.CDS4 18330555 18330667
chr_3 g2506 g2506.t3 exon g2506.t3.exon6 18331502 18331645
chr_3 g2506 g2506.t3 cds g2506.t3.CDS5 18331502 18331645
chr_3 g2506 g2506.t3 exon g2506.t3.exon7 18331872 18332398
chr_3 g2506 g2506.t3 cds g2506.t3.CDS6 18331872 18332396
chr_3 g2506 g2506.t3 TTS g2506.t3 18333069 18333069

Sequences

>g2506.t3 Gene=g2506 Length=1304
CATTTCGCATTCATCATTCGTTCGGGAACCTTCAATTAGAGAAGCATCTCTCTCACCCTT
AGTCTTTCGACTTTAAGATTTAGAAGTAAAGTTTTTAACATTTTTATAAAACTAGTTTAA
CATTTCGTAAAATCTAAAGTGAAAAAAATTCAATCGGCCCAAAAGTGAAAAATAAGAAGA
GAGTTCTTAGCCTGAATTAAAATGCCAGAAACAACGACTAACATGAATGGTTATTCTAAT
GGACACAGTATTCACAATGGATATGAGCTTGAAGACAATTCTTCATTTCTCTTTACTTCA
GAATCTGTCGGCGAAGGACATCCAGATAAAATGTGTGACCAAATTTCTGATGCTATCTTA
GATGCTCATTTGAAACAAGACCCGAATGCAAAAGTTGCTTGTGGTAACAAGACTGGTATG
ATCCTCTTGTGCGGGGAGATTACATCAAAAGCAAACGTCGACTATCAGAAAGTGGTTCGT
GATACAGTCAAACACATTGGATATGATGACTCCTCAAAGGGCTTCGACTGGAAGACTCTT
AACTTGTTAGTGGCAATTGAACAGCAATCGCCTGATATCGCTCAAGGAGTACACTTAAAT
CGCGAAGAATATGATGTAGGAGCCGGTGATCAGGGTTTGATGTTTGGATATGCTACAGAC
GAAACTGAAGAATGCATGCCTCTTACAGTCGTCTTAGCACATCGTTTGAACCAAAAGATT
GCTGAACTTCGCAGATCTGGAGTTTTGAGCTGGGCACGTCCAGATTCTAAAACACAAGTT
ACAGCAGAATACATTTTCCAAAAAGGAGCTTGCATTCCAAAGCGAGTTCACACGGTTGTC
GTCTCTTTACAGCATTCTGAAAAGGTTACATTGGAAGAATTACGAAAAGAGATTACTGAA
AAAGTTGTTCGTGTCGTCATTCCCGAAAAGTATTTGGATAATGAAACTATTGTTCACATC
AATCCATGTGGAAATTTTGTAATTGGTGGACCACAAGGTGATGCAGGTTTAACTGGACGC
AAAATTATTGTCGATACCTATGGCGGATGGGGAGCTCATGGTGGTGGAGCATTTTCAGGA
AAGGACTTTACAAAGGTCGATCGCTCTGCTGCTTATGCTGCTCGTTGGGTTGCAAAATCA
TTGGTCAAAGCTGGTGTTTGCAGAAGATGCTTGGTTCAAGTAAGCTACGCCATTGGTGTC
GCTGAACCATTGTCAATAACAGTCTTTGACTATGGAACATCAAGTTATACACAAAAACAA
CTTTTGGAAATCATTAAAAAGAACTTTGATCTTCGCCCAGGCAA

>g2506.t3 Gene=g2506 Length=367
MPETTTNMNGYSNGHSIHNGYELEDNSSFLFTSESVGEGHPDKMCDQISDAILDAHLKQD
PNAKVACGNKTGMILLCGEITSKANVDYQKVVRDTVKHIGYDDSSKGFDWKTLNLLVAIE
QQSPDIAQGVHLNREEYDVGAGDQGLMFGYATDETEECMPLTVVLAHRLNQKIAELRRSG
VLSWARPDSKTQVTAEYIFQKGACIPKRVHTVVVSLQHSEKVTLEELRKEITEKVVRVVI
PEKYLDNETIVHINPCGNFVIGGPQGDAGLTGRKIIVDTYGGWGAHGGGAFSGKDFTKVD
RSAAYAARWVAKSLVKAGVCRRCLVQVSYAIGVAEPLSITVFDYGTSSYTQKQLLEIIKK
NFDLRPG

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g2506.t3 CDD cd18079 S-AdoMet_synt 30 367 0.0
11 g2506.t3 Gene3D G3DSA:3.30.300.10 - 30 263 3.9E-154
10 g2506.t3 Gene3D G3DSA:3.30.300.10 - 36 300 3.9E-154
9 g2506.t3 Gene3D G3DSA:3.30.300.10 - 138 366 3.9E-154
4 g2506.t3 PANTHER PTHR11964:SF11 S-ADENOSYLMETHIONINE SYNTHASE ISOFORM TYPE-1 18 367 1.3E-200
5 g2506.t3 PANTHER PTHR11964 S-ADENOSYLMETHIONINE SYNTHETASE 18 367 1.3E-200
12 g2506.t3 PIRSF PIRSF000497 MAT 23 367 1.7E-147
3 g2506.t3 Pfam PF00438 S-adenosylmethionine synthetase, N-terminal domain 29 124 1.4E-38
1 g2506.t3 Pfam PF02772 S-adenosylmethionine synthetase, central domain 139 259 1.8E-44
2 g2506.t3 Pfam PF02773 S-adenosylmethionine synthetase, C-terminal domain 261 366 5.5E-53
14 g2506.t3 ProSitePatterns PS00376 S-adenosylmethionine synthase signature 1. 140 150 -
15 g2506.t3 ProSitePatterns PS00377 S-adenosylmethionine synthase signature 2. 287 295 -
6 g2506.t3 SUPERFAMILY SSF55973 S-adenosylmethionine synthetase 28 133 7.46E-44
8 g2506.t3 SUPERFAMILY SSF55973 S-adenosylmethionine synthetase 138 260 4.32E-49
7 g2506.t3 SUPERFAMILY SSF55973 S-adenosylmethionine synthetase 261 367 2.71E-50
16 g2506.t3 TIGRFAM TIGR01034 metK: methionine adenosyltransferase 30 366 3.9E-158

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. There were no conditions that were differentially expressed