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.t1 TSS g2506.t1 18328889 18328889
chr_3 g2506 g2506.t1 isoform g2506.t1 18329132 18332582
chr_3 g2506 g2506.t1 exon g2506.t1.exon1 18329132 18329255
chr_3 g2506 g2506.t1 cds g2506.t1.CDS1 18329132 18329255
chr_3 g2506 g2506.t1 exon g2506.t1.exon2 18330039 18330116
chr_3 g2506 g2506.t1 cds g2506.t1.CDS2 18330039 18330116
chr_3 g2506 g2506.t1 exon g2506.t1.exon3 18330192 18330314
chr_3 g2506 g2506.t1 cds g2506.t1.CDS3 18330192 18330314
chr_3 g2506 g2506.t1 exon g2506.t1.exon4 18331196 18331308
chr_3 g2506 g2506.t1 cds g2506.t1.CDS4 18331196 18331308
chr_3 g2506 g2506.t1 exon g2506.t1.exon5 18331502 18331645
chr_3 g2506 g2506.t1 cds g2506.t1.CDS5 18331502 18331645
chr_3 g2506 g2506.t1 exon g2506.t1.exon6 18331872 18332407
chr_3 g2506 g2506.t1 cds g2506.t1.CDS6 18331872 18332407
chr_3 g2506 g2506.t1 exon g2506.t1.exon7 18332477 18332582
chr_3 g2506 g2506.t1 cds g2506.t1.CDS7 18332477 18332582
chr_3 g2506 g2506.t1 TTS g2506.t1 18333570 18333570

Sequences

>g2506.t1 Gene=g2506 Length=1224
ATGCCAGAAACAACGACTAACATGAATGGTTATTCTAATGGACACAGTATTCACAATGGA
TATGAGCTTGAAGACAATTCTTCATTTCTCTTTACTTCAGAATCTGTCGGCGAAGGACAT
CCAGATAAAATGTGTGACCAAATTTCTGATGCTATCTTAGATGCTCATTTGAAACAAGAC
CCGAATGCAAAAGTTGCTTGTGAAACTGTCAGCAAGACTGGTATGATCCTCTTGTGCGGG
GAGATTACATCAAAAGCAAACGTCGACTATCAGAAAGTGGTTCGTGATACAGTCAAACAC
ATTGGATATGATGACTCCTCAAAGGGTTTTGATTACAAAACTTGTAGTCTTATGGTATGT
CTTGAGCAGCAAAGTCCAAATATTGCTGACGGGGTGCATGTTAATCGTAATGTCGAGGAT
ATTGGAGCTGGCGATCAGGGTTTGATGTTTGGATATGCTACAGACGAAACTGAAGAATGC
ATGCCTCTTACAGTCGTCTTAGCACATCGTTTGAACCAAAAGATTGCTGAACTTCGCAGA
TCTGGAGTTTTGAGCTGGGCACGTCCAGATTCTAAAACACAAGTTACAGCAGAATACATT
TTCCAAAAAGGAGCTTGCATTCCAAAGCGAGTTCACACGGTTGTCGTCTCTTTACAGCAT
TCTGAAAAGGTTACATTGGAAGAATTACGAAAAGAGATTACTGAAAAAGTTGTTCGTGTC
GTCATTCCCGAAAAGTATTTGGATAATGAAACTATTGTTCACATCAATCCATGTGGAAAT
TTTGTAATTGGTGGACCACAAGGTGATGCAGGTTTAACTGGACGCAAAATTATTGTCGAT
ACCTATGGCGGATGGGGAGCTCATGGTGGTGGAGCATTTTCAGGAAAGGACTTTACAAAG
GTCGATCGCTCTGCTGCTTATGCTGCTCGTTGGGTTGCAAAATCATTGGTCAAAGCTGGT
GTTTGCAGAAGATGCTTGGTTCAAGTAAGCTACGCCATTGGTGTCGCTGAACCATTGTCA
ATAACAGTCTTTGACTATGGAACATCAAGTTATACACAAAAACAACTTTTGGAAATCATT
AAAAAGAACTTTGATCTTCGCCCAGGCAAAATTGTTAATGACTTAAATTTGCGCACACCA
TTTTACCAACAAACAAGCACATATGGTCATTTTGGTCGTGAAGGTTTTCCATGGGAAAAA
CCAAAGACATTGATTCTTGAATGA

>g2506.t1 Gene=g2506 Length=407
MPETTTNMNGYSNGHSIHNGYELEDNSSFLFTSESVGEGHPDKMCDQISDAILDAHLKQD
PNAKVACETVSKTGMILLCGEITSKANVDYQKVVRDTVKHIGYDDSSKGFDYKTCSLMVC
LEQQSPNIADGVHVNRNVEDIGAGDQGLMFGYATDETEECMPLTVVLAHRLNQKIAELRR
SGVLSWARPDSKTQVTAEYIFQKGACIPKRVHTVVVSLQHSEKVTLEELRKEITEKVVRV
VIPEKYLDNETIVHINPCGNFVIGGPQGDAGLTGRKIIVDTYGGWGAHGGGAFSGKDFTK
VDRSAAYAARWVAKSLVKAGVCRRCLVQVSYAIGVAEPLSITVFDYGTSSYTQKQLLEII
KKNFDLRPGKIVNDLNLRTPFYQQTSTYGHFGREGFPWEKPKTLILE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g2506.t1 CDD cd18079 S-AdoMet_synt 30 402 0.0
11 g2506.t1 Gene3D G3DSA:3.30.300.10 - 30 265 4.6E-174
12 g2506.t1 Gene3D G3DSA:3.30.300.10 - 36 302 4.6E-174
10 g2506.t1 Gene3D G3DSA:3.30.300.10 - 140 399 4.6E-174
6 g2506.t1 Hamap MF_00086 S-adenosylmethionine synthase [metK]. 27 405 49.960907
4 g2506.t1 PANTHER PTHR11964:SF11 S-ADENOSYLMETHIONINE SYNTHASE ISOFORM TYPE-1 18 405 9.2E-221
5 g2506.t1 PANTHER PTHR11964 S-ADENOSYLMETHIONINE SYNTHETASE 18 405 9.2E-221
13 g2506.t1 PIRSF PIRSF000497 MAT 23 406 5.2E-166
3 g2506.t1 Pfam PF00438 S-adenosylmethionine synthetase, N-terminal domain 29 126 4.2E-43
1 g2506.t1 Pfam PF02772 S-adenosylmethionine synthetase, central domain 141 261 1.5E-44
2 g2506.t1 Pfam PF02773 S-adenosylmethionine synthetase, C-terminal domain 263 400 6.4E-68
15 g2506.t1 ProSitePatterns PS00376 S-adenosylmethionine synthase signature 1. 142 152 -
16 g2506.t1 ProSitePatterns PS00377 S-adenosylmethionine synthase signature 2. 289 297 -
7 g2506.t1 SUPERFAMILY SSF55973 S-adenosylmethionine synthetase 28 135 3.69E-47
8 g2506.t1 SUPERFAMILY SSF55973 S-adenosylmethionine synthetase 139 262 1.32E-49
9 g2506.t1 SUPERFAMILY SSF55973 S-adenosylmethionine synthetase 263 403 3.92E-66
17 g2506.t1 TIGRFAM TIGR01034 metK: methionine adenosyltransferase 30 404 3.7E-180

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