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.t6 isoform g2506.t6 18328331 18333574
chr_3 g2506 g2506.t6 exon g2506.t6.exon1 18328331 18328458
chr_3 g2506 g2506.t6 TSS g2506.t6 18328343 18328343
chr_3 g2506 g2506.t6 exon g2506.t6.exon2 18329059 18329255
chr_3 g2506 g2506.t6 cds g2506.t6.CDS1 18329132 18329255
chr_3 g2506 g2506.t6 exon g2506.t6.exon3 18330039 18330116
chr_3 g2506 g2506.t6 cds g2506.t6.CDS2 18330039 18330116
chr_3 g2506 g2506.t6 exon g2506.t6.exon4 18330192 18330314
chr_3 g2506 g2506.t6 cds g2506.t6.CDS3 18330192 18330314
chr_3 g2506 g2506.t6 exon g2506.t6.exon5 18330555 18330667
chr_3 g2506 g2506.t6 cds g2506.t6.CDS4 18330555 18330667
chr_3 g2506 g2506.t6 exon g2506.t6.exon6 18331502 18331645
chr_3 g2506 g2506.t6 cds g2506.t6.CDS5 18331502 18331645
chr_3 g2506 g2506.t6 exon g2506.t6.exon7 18331872 18332407
chr_3 g2506 g2506.t6 cds g2506.t6.CDS6 18331872 18332407
chr_3 g2506 g2506.t6 exon g2506.t6.exon8 18332477 18333574
chr_3 g2506 g2506.t6 cds g2506.t6.CDS7 18332477 18332582
chr_3 g2506 g2506.t6 TTS g2506.t6 18333629 18333629

Sequences

>g2506.t6 Gene=g2506 Length=2417
CATTTCGCATTCATCATTCGTTCGGGAACCTTCAATTAGAGAAGCATCTCTCTCACCCTT
AGTCTTTCGACTTTAAGATTTAGAAGTAAAGTTTTTAACATTTTTATAAAACTAGTTTAA
CATTTCGTAAAATCTAAAGTGAAAAAAATTCAATCGGCCCAAAAGTGAAAAATAAGAAGA
GAGTTCTTAGCCTGAATTAAAATGCCAGAAACAACGACTAACATGAATGGTTATTCTAAT
GGACACAGTATTCACAATGGATATGAGCTTGAAGACAATTCTTCATTTCTCTTTACTTCA
GAATCTGTCGGCGAAGGACATCCAGATAAAATGTGTGACCAAATTTCTGATGCTATCTTA
GATGCTCATTTGAAACAAGACCCGAATGCAAAAGTTGCTTGTGAAACTGTCAGCAAGACT
GGTATGATCCTCTTGTGCGGGGAGATTACATCAAAAGCAAACGTCGACTATCAGAAAGTG
GTTCGTGATACAGTCAAACACATTGGATATGATGACTCCTCAAAGGGCTTCGACTGGAAG
ACTCTTAACTTGTTAGTGGCAATTGAACAGCAATCGCCTGATATCGCTCAAGGAGTACAC
TTAAATCGCGAAGAATATGATGTAGGAGCCGGTGATCAGGGTTTGATGTTTGGATATGCT
ACAGACGAAACTGAAGAATGCATGCCTCTTACAGTCGTCTTAGCACATCGTTTGAACCAA
AAGATTGCTGAACTTCGCAGATCTGGAGTTTTGAGCTGGGCACGTCCAGATTCTAAAACA
CAAGTTACAGCAGAATACATTTTCCAAAAAGGAGCTTGCATTCCAAAGCGAGTTCACACG
GTTGTCGTCTCTTTACAGCATTCTGAAAAGGTTACATTGGAAGAATTACGAAAAGAGATT
ACTGAAAAAGTTGTTCGTGTCGTCATTCCCGAAAAGTATTTGGATAATGAAACTATTGTT
CACATCAATCCATGTGGAAATTTTGTAATTGGTGGACCACAAGGTGATGCAGGTTTAACT
GGACGCAAAATTATTGTCGATACCTATGGCGGATGGGGAGCTCATGGTGGTGGAGCATTT
TCAGGAAAGGACTTTACAAAGGTCGATCGCTCTGCTGCTTATGCTGCTCGTTGGGTTGCA
AAATCATTGGTCAAAGCTGGTGTTTGCAGAAGATGCTTGGTTCAAGTAAGCTACGCCATT
GGTGTCGCTGAACCATTGTCAATAACAGTCTTTGACTATGGAACATCAAGTTATACACAA
AAACAACTTTTGGAAATCATTAAAAAGAACTTTGATCTTCGCCCAGGCAAAATTGTTAAT
GACTTAAATTTGCGCACACCATTTTACCAACAAACAAGCACATATGGTCATTTTGGTCGT
GAAGGTTTTCCATGGGAAAAACCAAAGACATTGATTCTTGAATGACTGCCGCAACTTGTT
GTTTCAGATGCATCCGAAAGTGATGATGAAAATCCCAATTGTTCTAAAAAAATTAAATTA
GCATAAGCCCACAAACAACATACTAAAAATTTTAAAATATGGTTCTTAAAAATTCCCCAC
ATGACGTTTAAAAAAATTAACATAGGACGTGACAAAAAGTTTAAATTCCTTTTAGTTTTA
TCCTCTATAAAAATAGTCCATTTTCATGGGATTTTTGAATATTTTTCTTTATCGAGAAAT
CTACAAACATAACTTTTTAGAAATACTTTTTTACTATCTTTAGTTGTTTAAGTAAATGTT
CTACTACCTAACTCTTTTTTTTTGTTAGTAGTTGCTTCTCAAAAAAACTTATAACTTTAT
CATAAAAGCTATTACATGATTAATGAGAAGATAAAAAAAATCAAAAAACCTTTGCTATTA
GAGAAAGAGTGCTAGAATGATTTAGTCGAATCACGGCACCGAGTATCGTCGCAAAAAAAA
AATAAATTGTAAAATTATCATTGCTCGATGTCGCAATACTTTCTTCATACATTATGACTC
AGTGCTAATTGATTCTCGAGAGACTTTCATGCGTTCTTTTTTGGCATGTAATATTATGTC
TCAATAGTGACAATTTCGCTCTCTATTAATTGTAATAAATGAAAATCTCACTATTGAGAC
TTGGACCATGAAATGCTTTCCTGATTTTAAACTGTGATTACGATCTTTGAAGAAAGTCTT
GTGTTGTGTTTCTGACTGGAAAATGGAAAAGCGCGTTTGTCAAAAACACACCGGTTCACA
AATCATTTGAAAAACATTTGCAATGTGTGAAGATTTTTCTTAATAAACCTTAGATTATTA
GGTAGATAAAGAAATAAAAGTTGTAAGAAGGATTAGTAAGAATAGAAGCATTTGTCTGCA
CTTTAAATTCTCTAGCATTGGAAACAAAAAAATGGAATGTATTGATTTTTCTTTGAATAA
ATAGTTATAAACGAAAA

>g2506.t6 Gene=g2506 Length=407
MPETTTNMNGYSNGHSIHNGYELEDNSSFLFTSESVGEGHPDKMCDQISDAILDAHLKQD
PNAKVACETVSKTGMILLCGEITSKANVDYQKVVRDTVKHIGYDDSSKGFDWKTLNLLVA
IEQQSPDIAQGVHLNREEYDVGAGDQGLMFGYATDETEECMPLTVVLAHRLNQKIAELRR
SGVLSWARPDSKTQVTAEYIFQKGACIPKRVHTVVVSLQHSEKVTLEELRKEITEKVVRV
VIPEKYLDNETIVHINPCGNFVIGGPQGDAGLTGRKIIVDTYGGWGAHGGGAFSGKDFTK
VDRSAAYAARWVAKSLVKAGVCRRCLVQVSYAIGVAEPLSITVFDYGTSSYTQKQLLEII
KKNFDLRPGKIVNDLNLRTPFYQQTSTYGHFGREGFPWEKPKTLILE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g2506.t6 CDD cd18079 S-AdoMet_synt 30 402 0.0
11 g2506.t6 Gene3D G3DSA:3.30.300.10 - 30 265 1.2E-174
12 g2506.t6 Gene3D G3DSA:3.30.300.10 - 36 302 1.2E-174
10 g2506.t6 Gene3D G3DSA:3.30.300.10 - 140 399 1.2E-174
6 g2506.t6 Hamap MF_00086 S-adenosylmethionine synthase [metK]. 27 405 49.988564
4 g2506.t6 PANTHER PTHR11964:SF11 S-ADENOSYLMETHIONINE SYNTHASE ISOFORM TYPE-1 18 405 6.6E-222
5 g2506.t6 PANTHER PTHR11964 S-ADENOSYLMETHIONINE SYNTHETASE 18 405 6.6E-222
13 g2506.t6 PIRSF PIRSF000497 MAT 23 406 1.2E-166
3 g2506.t6 Pfam PF00438 S-adenosylmethionine synthetase, N-terminal domain 29 126 4.9E-43
1 g2506.t6 Pfam PF02772 S-adenosylmethionine synthetase, central domain 141 261 2.2E-44
2 g2506.t6 Pfam PF02773 S-adenosylmethionine synthetase, C-terminal domain 263 400 6.4E-68
15 g2506.t6 ProSitePatterns PS00376 S-adenosylmethionine synthase signature 1. 142 152 -
16 g2506.t6 ProSitePatterns PS00377 S-adenosylmethionine synthase signature 2. 289 297 -
7 g2506.t6 SUPERFAMILY SSF55973 S-adenosylmethionine synthetase 28 135 2.83E-48
9 g2506.t6 SUPERFAMILY SSF55973 S-adenosylmethionine synthetase 140 262 3.83E-49
8 g2506.t6 SUPERFAMILY SSF55973 S-adenosylmethionine synthetase 263 403 3.92E-66
17 g2506.t6 TIGRFAM TIGR01034 metK: methionine adenosyltransferase 30 404 2.1E-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