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.t24 TSS g2506.t24 18328889 18328889
chr_3 g2506 g2506.t24 isoform g2506.t24 18329132 18333028
chr_3 g2506 g2506.t24 exon g2506.t24.exon1 18329132 18329255
chr_3 g2506 g2506.t24 exon g2506.t24.exon2 18330039 18330113
chr_3 g2506 g2506.t24 exon g2506.t24.exon3 18330192 18330314
chr_3 g2506 g2506.t24 cds g2506.t24.CDS1 18330212 18330314
chr_3 g2506 g2506.t24 exon g2506.t24.exon4 18331196 18331308
chr_3 g2506 g2506.t24 cds g2506.t24.CDS2 18331196 18331308
chr_3 g2506 g2506.t24 exon g2506.t24.exon5 18331502 18331649
chr_3 g2506 g2506.t24 cds g2506.t24.CDS3 18331502 18331649
chr_3 g2506 g2506.t24 exon g2506.t24.exon6 18331882 18332407
chr_3 g2506 g2506.t24 cds g2506.t24.CDS4 18331882 18332407
chr_3 g2506 g2506.t24 exon g2506.t24.exon7 18332477 18333028
chr_3 g2506 g2506.t24 cds g2506.t24.CDS5 18332477 18332582
chr_3 g2506 g2506.t24 TTS g2506.t24 18333629 18333629

Sequences

>g2506.t24 Gene=g2506 Length=1661
ATGCCAGAAACAACGACTAACATGAATGGTTATTCTAATGGACACAGTATTCACAATGGA
TATGAGCTTGAAGACAATTCTTCATTTCTCTTTACTTCAGAATCTGTCGGCGAAGGACAT
CCAGATAAAATGTGTGACCAAATTTCTGATGCTATCTTAGATGCTCATTTGAAACAAGAC
CCGAATGCAAAAGTTGCTTAAACTGTCAGCAAGACTGGTATGATCCTCTTGTGCGGGGAG
ATTACATCAAAAGCAAACGTCGACTATCAGAAAGTGGTTCGTGATACAGTCAAACACATT
GGATATGATGACTCCTCAAAGGGTTTTGATTACAAAACTTGTAGTCTTATGGTATGTCTT
GAGCAGCAAAGTCCAAATATTGCTGACGGGGTGCATGTTAATCGTAATGTCGAGGATATT
GGAGCTGGCGATCAGGGTTTGATGTTTGGATATGCTACAGACGAAACTGAAGAATGCATG
CCTCTTACAGTCGTCTTAGCACATCGTTTGAACCAAAAGATTGCTGAACTTCGCAGATCT
GGAGTTTTGAGCTGGGCACGTCCAGATTCTAAAACACAAGTGAAATACATTTTCCAAAAA
GGAGCTTGCATTCCAAAGCGAGTTCACACGGTTGTCGTCTCTTTACAGCATTCTGAAAAG
GTTACATTGGAAGAATTACGAAAAGAGATTACTGAAAAAGTTGTTCGTGTCGTCATTCCC
GAAAAGTATTTGGATAATGAAACTATTGTTCACATCAATCCATGTGGAAATTTTGTAATT
GGTGGACCACAAGGTGATGCAGGTTTAACTGGACGCAAAATTATTGTCGATACCTATGGC
GGATGGGGAGCTCATGGTGGTGGAGCATTTTCAGGAAAGGACTTTACAAAGGTCGATCGC
TCTGCTGCTTATGCTGCTCGTTGGGTTGCAAAATCATTGGTCAAAGCTGGTGTTTGCAGA
AGATGCTTGGTTCAAGTAAGCTACGCCATTGGTGTCGCTGAACCATTGTCAATAACAGTC
TTTGACTATGGAACATCAAGTTATACACAAAAACAACTTTTGGAAATCATTAAAAAGAAC
TTTGATCTTCGCCCAGGCAAAATTGTTAATGACTTAAATTTGCGCACACCATTTTACCAA
CAAACAAGCACATATGGTCATTTTGGTCGTGAAGGTTTTCCATGGGAAAAACCAAAGACA
TTGATTCTTGAATGACTGCCGCAACTTGTTGTTTCAGATGCATCCGAAAGTGATGATGAA
AATCCCAATTGTTCTAAAAAAATTAAATTAGCATAAGCCCACAAACAACATACTAAAAAT
TTTAAAATATGGTTCTTAAAAATTCCCCACATGACGTTTAAAAAAATTAACATAGGACGT
GACAAAAAGTTTAAATTCCTTTTAGTTTTATCCTCTATAAAAATAGTCCATTTTCATGGG
ATTTTTGAATATTTTTCTTTATCGAGAAATCTACAAACATAACTTTTTAGAAATACTTTT
TTACTATCTTTAGTTGTTTAAGTAAATGTTCTACTACCTAACTCTTTTTTTTTGTTAGTA
GTTGCTTCTCAAAAAAACTTATAACTTTATCATAAAAGCTATTACATGATTAATGAGAAG
ATAAAAAAAATCAAAAAACCTTTGCTATTAGAGAAAGAGTG

>g2506.t24 Gene=g2506 Length=331
MILLCGEITSKANVDYQKVVRDTVKHIGYDDSSKGFDYKTCSLMVCLEQQSPNIADGVHV
NRNVEDIGAGDQGLMFGYATDETEECMPLTVVLAHRLNQKIAELRRSGVLSWARPDSKTQ
VKYIFQKGACIPKRVHTVVVSLQHSEKVTLEELRKEITEKVVRVVIPEKYLDNETIVHIN
PCGNFVIGGPQGDAGLTGRKIIVDTYGGWGAHGGGAFSGKDFTKVDRSAAYAARWVAKSL
VKAGVCRRCLVQVSYAIGVAEPLSITVFDYGTSSYTQKQLLEIIKKNFDLRPGKIVNDLN
LRTPFYQQTSTYGHFGREGFPWEKPKTLILE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g2506.t24 CDD cd18079 S-AdoMet_synt 1 326 0.0
13 g2506.t24 Gene3D G3DSA:3.30.300.10 - 1 226 8.1E-144
11 g2506.t24 Gene3D G3DSA:3.30.300.10 - 66 323 8.1E-144
12 g2506.t24 Gene3D G3DSA:3.30.300.10 - 89 189 8.1E-144
4 g2506.t24 PANTHER PTHR11964:SF11 S-ADENOSYLMETHIONINE SYNTHASE ISOFORM TYPE-1 1 329 3.6E-181
5 g2506.t24 PANTHER PTHR11964 S-ADENOSYLMETHIONINE SYNTHETASE 1 329 3.6E-181
3 g2506.t24 Pfam PF00438 S-adenosylmethionine synthetase, N-terminal domain 1 52 6.6E-13
1 g2506.t24 Pfam PF02772 S-adenosylmethionine synthetase, central domain 67 185 8.0E-43
2 g2506.t24 Pfam PF02773 S-adenosylmethionine synthetase, C-terminal domain 187 324 4.1E-68
9 g2506.t24 ProSitePatterns PS00376 S-adenosylmethionine synthase signature 1. 68 78 -
10 g2506.t24 ProSitePatterns PS00377 S-adenosylmethionine synthase signature 2. 213 221 -
7 g2506.t24 SUPERFAMILY SSF55973 S-adenosylmethionine synthetase 1 61 1.96E-17
8 g2506.t24 SUPERFAMILY SSF55973 S-adenosylmethionine synthetase 65 186 1.12E-46
6 g2506.t24 SUPERFAMILY SSF55973 S-adenosylmethionine synthetase 187 327 2.55E-66
14 g2506.t24 TIGRFAM TIGR01034 metK: methionine adenosyltransferase 1 328 3.7E-150

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