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.t8 TSS g2506.t8 18328343 18328343
chr_3 g2506 g2506.t8 isoform g2506.t8 18328646 18333574
chr_3 g2506 g2506.t8 exon g2506.t8.exon1 18328646 18328991
chr_3 g2506 g2506.t8 exon g2506.t8.exon2 18329059 18329255
chr_3 g2506 g2506.t8 cds g2506.t8.CDS1 18329132 18329255
chr_3 g2506 g2506.t8 exon g2506.t8.exon3 18330039 18330116
chr_3 g2506 g2506.t8 cds g2506.t8.CDS2 18330039 18330116
chr_3 g2506 g2506.t8 exon g2506.t8.exon4 18330192 18330314
chr_3 g2506 g2506.t8 cds g2506.t8.CDS3 18330192 18330314
chr_3 g2506 g2506.t8 exon g2506.t8.exon5 18330555 18330667
chr_3 g2506 g2506.t8 cds g2506.t8.CDS4 18330555 18330667
chr_3 g2506 g2506.t8 exon g2506.t8.exon6 18331502 18331645
chr_3 g2506 g2506.t8 cds g2506.t8.CDS5 18331502 18331645
chr_3 g2506 g2506.t8 exon g2506.t8.exon7 18331879 18332407
chr_3 g2506 g2506.t8 cds g2506.t8.CDS6 18331879 18332076
chr_3 g2506 g2506.t8 exon g2506.t8.exon8 18332477 18333574
chr_3 g2506 g2506.t8 TTS g2506.t8 18333629 18333629

Sequences

>g2506.t8 Gene=g2506 Length=2628
TGTTTGACTACTACTTTGATAATCAGTAAAAAAGCCATTATCTCGTTGCCTTGAGACTTT
GATTATATAATTGCAAGTGAACTTGATTCATTATCATTCTATTTGCTTTTTAAAATACTC
TTCCCGTTCATTGTTTTCTTTAATATGATAGAGTATGCTGGGATGTTAATTATCAAAGTA
TGAATCGACCATAAAGTGACATAGTCGAAAACAGTATAAATACAACTTGCAAGCAAGTCT
CAACGCGCTTTTCCTTTGAAAATTTAAGACATACACATCGTATTTAAAGAAATTATTAAA
TAAGTCTTAAAGTTGATTTTAAATAACCATAAAAATCATTAAAATTAAAATCTAAAGTGA
AAAAAATTCAATCGGCCCAAAAGTGAAAAATAAGAAGAGAGTTCTTAGCCTGAATTAAAA
TGCCAGAAACAACGACTAACATGAATGGTTATTCTAATGGACACAGTATTCACAATGGAT
ATGAGCTTGAAGACAATTCTTCATTTCTCTTTACTTCAGAATCTGTCGGCGAAGGACATC
CAGATAAAATGTGTGACCAAATTTCTGATGCTATCTTAGATGCTCATTTGAAACAAGACC
CGAATGCAAAAGTTGCTTGTGAAACTGTCAGCAAGACTGGTATGATCCTCTTGTGCGGGG
AGATTACATCAAAAGCAAACGTCGACTATCAGAAAGTGGTTCGTGATACAGTCAAACACA
TTGGATATGATGACTCCTCAAAGGGCTTCGACTGGAAGACTCTTAACTTGTTAGTGGCAA
TTGAACAGCAATCGCCTGATATCGCTCAAGGAGTACACTTAAATCGCGAAGAATATGATG
TAGGAGCCGGTGATCAGGGTTTGATGTTTGGATATGCTACAGACGAAACTGAAGAATGCA
TGCCTCTTACAGTCGTCTTAGCACATCGTTTGAACCAAAAGATTGCTGAACTTCGCAGAT
CTGGAGTTTTGAGCTGGGCACGTCCAGATTCTAAAACACAACAGAATACATTTTCCAAAA
AGGAGCTTGCATTCCAAAGCGAGTTCACACGGTTGTCGTCTCTTTACAGCATTCTGAAAA
GGTTACATTGGAAGAATTACGAAAAGAGATTACTGAAAAAGTTGTTCGTGTCGTCATTCC
CGAAAAGTATTTGGATAATGAAACTATTGTTCACATCAATCCATGTGGAAATTTTGTAAT
TGGTGGACCACAAGGTGATGCAGGTTTAACTGGACGCAAAATTATTGTCGATACCTATGG
CGGATGGGGAGCTCATGGTGGTGGAGCATTTTCAGGAAAGGACTTTACAAAGGTCGATCG
CTCTGCTGCTTATGCTGCTCGTTGGGTTGCAAAATCATTGGTCAAAGCTGGTGTTTGCAG
AAGATGCTTGGTTCAAGTAAGCTACGCCATTGGTGTCGCTGAACCATTGTCAATAACAGT
CTTTGACTATGGAACATCAAGTTATACACAAAAACAACTTTTGGAAATCATTAAAAAGAA
CTTTGATCTTCGCCCAGGCAAAATTGTTAATGACTTAAATTTGCGCACACCATTTTACCA
ACAAACAAGCACATATGGTCATTTTGGTCGTGAAGGTTTTCCATGGGAAAAACCAAAGAC
ATTGATTCTTGAATGACTGCCGCAACTTGTTGTTTCAGATGCATCCGAAAGTGATGATGA
AAATCCCAATTGTTCTAAAAAAATTAAATTAGCATAAGCCCACAAACAACATACTAAAAA
TTTTAAAATATGGTTCTTAAAAATTCCCCACATGACGTTTAAAAAAATTAACATAGGACG
TGACAAAAAGTTTAAATTCCTTTTAGTTTTATCCTCTATAAAAATAGTCCATTTTCATGG
GATTTTTGAATATTTTTCTTTATCGAGAAATCTACAAACATAACTTTTTAGAAATACTTT
TTTACTATCTTTAGTTGTTTAAGTAAATGTTCTACTACCTAACTCTTTTTTTTTGTTAGT
AGTTGCTTCTCAAAAAAACTTATAACTTTATCATAAAAGCTATTACATGATTAATGAGAA
GATAAAAAAAATCAAAAAACCTTTGCTATTAGAGAAAGAGTGCTAGAATGATTTAGTCGA
ATCACGGCACCGAGTATCGTCGCAAAAAAAAAATAAATTGTAAAATTATCATTGCTCGAT
GTCGCAATACTTTCTTCATACATTATGACTCAGTGCTAATTGATTCTCGAGAGACTTTCA
TGCGTTCTTTTTTGGCATGTAATATTATGTCTCAATAGTGACAATTTCGCTCTCTATTAA
TTGTAATAAATGAAAATCTCACTATTGAGACTTGGACCATGAAATGCTTTCCTGATTTTA
AACTGTGATTACGATCTTTGAAGAAAGTCTTGTGTTGTGTTTCTGACTGGAAAATGGAAA
AGCGCGTTTGTCAAAAACACACCGGTTCACAAATCATTTGAAAAACATTTGCAATGTGTG
AAGATTTTTCTTAATAAACCTTAGATTATTAGGTAGATAAAGAAATAAAAGTTGTAAGAA
GGATTAGTAAGAATAGAAGCATTTGTCTGCACTTTAAATTCTCTAGCATTGGAAACAAAA
AAATGGAATGTATTGATTTTTCTTTGAATAAATAGTTATAAACGAAAA

>g2506.t8 Gene=g2506 Length=259
MPETTTNMNGYSNGHSIHNGYELEDNSSFLFTSESVGEGHPDKMCDQISDAILDAHLKQD
PNAKVACETVSKTGMILLCGEITSKANVDYQKVVRDTVKHIGYDDSSKGFDWKTLNLLVA
IEQQSPDIAQGVHLNREEYDVGAGDQGLMFGYATDETEECMPLTVVLAHRLNQKIAELRR
SGVLSWARPDSKTQQNTFSKKELAFQSEFTRLSSLYSILKRLHWKNYEKRLLKKLFVSSF
PKSIWIMKLLFTSIHVEIL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g2506.t8 Gene3D G3DSA:3.30.300.10 - 30 232 1.6E-74
8 g2506.t8 Gene3D G3DSA:3.30.300.10 - 36 139 1.6E-74
9 g2506.t8 Gene3D G3DSA:3.30.300.10 - 140 162 1.6E-74
3 g2506.t8 PANTHER PTHR11964:SF11 S-ADENOSYLMETHIONINE SYNTHASE ISOFORM TYPE-1 18 197 6.6E-106
4 g2506.t8 PANTHER PTHR11964 S-ADENOSYLMETHIONINE SYNTHETASE 18 197 6.6E-106
2 g2506.t8 Pfam PF00438 S-adenosylmethionine synthetase, N-terminal domain 29 126 2.0E-43
1 g2506.t8 Pfam PF02772 S-adenosylmethionine synthetase, central domain 141 194 9.2E-23
7 g2506.t8 ProSitePatterns PS00376 S-adenosylmethionine synthase signature 1. 142 152 -
5 g2506.t8 SUPERFAMILY SSF55973 S-adenosylmethionine synthetase 28 135 1.1E-48
6 g2506.t8 SUPERFAMILY SSF55973 S-adenosylmethionine synthetase 137 194 7.46E-24

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