General information for g2506.t28
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as S-adenosylmethionine synthase.
Parent gene
- The parent gene g2506 is located on chr_3: 18332519..18333574 (+ strand)
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.t28 | TSS | g2506.t28 | 18328889 | 18328889 |
| chr_3 | g2506 | g2506.t28 | isoform | g2506.t28 | 18329132 | 18333574 |
| chr_3 | g2506 | g2506.t28 | exon | g2506.t28.exon1 | 18329132 | 18329255 |
| chr_3 | g2506 | g2506.t28 | cds | g2506.t28.CDS1 | 18329132 | 18329255 |
| chr_3 | g2506 | g2506.t28 | exon | g2506.t28.exon2 | 18330039 | 18330116 |
| chr_3 | g2506 | g2506.t28 | cds | g2506.t28.CDS2 | 18330039 | 18330116 |
| chr_3 | g2506 | g2506.t28 | exon | g2506.t28.exon3 | 18330192 | 18330314 |
| chr_3 | g2506 | g2506.t28 | cds | g2506.t28.CDS3 | 18330192 | 18330314 |
| chr_3 | g2506 | g2506.t28 | exon | g2506.t28.exon4 | 18331196 | 18331308 |
| chr_3 | g2506 | g2506.t28 | cds | g2506.t28.CDS4 | 18331196 | 18331308 |
| chr_3 | g2506 | g2506.t28 | exon | g2506.t28.exon5 | 18331502 | 18331645 |
| chr_3 | g2506 | g2506.t28 | cds | g2506.t28.CDS5 | 18331502 | 18331645 |
| chr_3 | g2506 | g2506.t28 | exon | g2506.t28.exon6 | 18331872 | 18332402 |
| chr_3 | g2506 | g2506.t28 | cds | g2506.t28.CDS6 | 18331872 | 18332402 |
| chr_3 | g2506 | g2506.t28 | exon | g2506.t28.exon7 | 18332477 | 18333574 |
| chr_3 | g2506 | g2506.t28 | cds | g2506.t28.CDS7 | 18332477 | 18332479 |
| chr_3 | g2506 | g2506.t28 | TTS | g2506.t28 | 18333629 | 18333629 |
Sequences
>g2506.t28 Gene=g2506 Length=2211
ATGCCAGAAACAACGACTAACATGAATGGTTATTCTAATGGACACAGTATTCACAATGGA
TATGAGCTTGAAGACAATTCTTCATTTCTCTTTACTTCAGAATCTGTCGGCGAAGGACAT
CCAGATAAAATGTGTGACCAAATTTCTGATGCTATCTTAGATGCTCATTTGAAACAAGAC
CCGAATGCAAAAGTTGCTTGTGAAACTGTCAGCAAGACTGGTATGATCCTCTTGTGCGGG
GAGATTACATCAAAAGCAAACGTCGACTATCAGAAAGTGGTTCGTGATACAGTCAAACAC
ATTGGATATGATGACTCCTCAAAGGGTTTTGATTACAAAACTTGTAGTCTTATGGTATGT
CTTGAGCAGCAAAGTCCAAATATTGCTGACGGGGTGCATGTTAATCGTAATGTCGAGGAT
ATTGGAGCTGGCGATCAGGGTTTGATGTTTGGATATGCTACAGACGAAACTGAAGAATGC
ATGCCTCTTACAGTCGTCTTAGCACATCGTTTGAACCAAAAGATTGCTGAACTTCGCAGA
TCTGGAGTTTTGAGCTGGGCACGTCCAGATTCTAAAACACAAGTTACAGCAGAATACATT
TTCCAAAAAGGAGCTTGCATTCCAAAGCGAGTTCACACGGTTGTCGTCTCTTTACAGCAT
TCTGAAAAGGTTACATTGGAAGAATTACGAAAAGAGATTACTGAAAAAGTTGTTCGTGTC
GTCATTCCCGAAAAGTATTTGGATAATGAAACTATTGTTCACATCAATCCATGTGGAAAT
TTTGTAATTGGTGGACCACAAGGTGATGCAGGTTTAACTGGACGCAAAATTATTGTCGAT
ACCTATGGCGGATGGGGAGCTCATGGTGGTGGAGCATTTTCAGGAAAGGACTTTACAAAG
GTCGATCGCTCTGCTGCTTATGCTGCTCGTTGGGTTGCAAAATCATTGGTCAAAGCTGGT
GTTTGCAGAAGATGCTTGGTTCAAGTAAGCTACGCCATTGGTGTCGCTGAACCATTGTCA
ATAACAGTCTTTGACTATGGAACATCAAGTTATACACAAAAACAACTTTTGGAAATCATT
AAAAAGAACTTTGATCTTCGCCCAGGCAAAATTTGACTTAAATTTGCGCACACCATTTTA
CCAACAAACAAGCACATATGGTCATTTTGGTCGTGAAGGTTTTCCATGGGAAAAACCAAA
GACATTGATTCTTGAATGACTGCCGCAACTTGTTGTTTCAGATGCATCCGAAAGTGATGA
TGAAAATCCCAATTGTTCTAAAAAAATTAAATTAGCATAAGCCCACAAACAACATACTAA
AAATTTTAAAATATGGTTCTTAAAAATTCCCCACATGACGTTTAAAAAAATTAACATAGG
ACGTGACAAAAAGTTTAAATTCCTTTTAGTTTTATCCTCTATAAAAATAGTCCATTTTCA
TGGGATTTTTGAATATTTTTCTTTATCGAGAAATCTACAAACATAACTTTTTAGAAATAC
TTTTTTACTATCTTTAGTTGTTTAAGTAAATGTTCTACTACCTAACTCTTTTTTTTTGTT
AGTAGTTGCTTCTCAAAAAAACTTATAACTTTATCATAAAAGCTATTACATGATTAATGA
GAAGATAAAAAAAATCAAAAAACCTTTGCTATTAGAGAAAGAGTGCTAGAATGATTTAGT
CGAATCACGGCACCGAGTATCGTCGCAAAAAAAAAATAAATTGTAAAATTATCATTGCTC
GATGTCGCAATACTTTCTTCATACATTATGACTCAGTGCTAATTGATTCTCGAGAGACTT
TCATGCGTTCTTTTTTGGCATGTAATATTATGTCTCAATAGTGACAATTTCGCTCTCTAT
TAATTGTAATAAATGAAAATCTCACTATTGAGACTTGGACCATGAAATGCTTTCCTGATT
TTAAACTGTGATTACGATCTTTGAAGAAAGTCTTGTGTTGTGTTTCTGACTGGAAAATGG
AAAAGCGCGTTTGTCAAAAACACACCGGTTCACAAATCATTTGAAAAACATTTGCAATGT
GTGAAGATTTTTCTTAATAAACCTTAGATTATTAGGTAGATAAAGAAATAAAAGTTGTAA
GAAGGATTAGTAAGAATAGAAGCATTTGTCTGCACTTTAAATTCTCTAGCATTGGAAACA
AAAAAATGGAATGTATTGATTTTTCTTTGAATAAATAGTTATAAACGAAAA
>g2506.t28 Gene=g2506 Length=371
MPETTTNMNGYSNGHSIHNGYELEDNSSFLFTSESVGEGHPDKMCDQISDAILDAHLKQD
PNAKVACETVSKTGMILLCGEITSKANVDYQKVVRDTVKHIGYDDSSKGFDYKTCSLMVC
LEQQSPNIADGVHVNRNVEDIGAGDQGLMFGYATDETEECMPLTVVLAHRLNQKIAELRR
SGVLSWARPDSKTQVTAEYIFQKGACIPKRVHTVVVSLQHSEKVTLEELRKEITEKVVRV
VIPEKYLDNETIVHINPCGNFVIGGPQGDAGLTGRKIIVDTYGGWGAHGGGAFSGKDFTK
VDRSAAYAARWVAKSLVKAGVCRRCLVQVSYAIGVAEPLSITVFDYGTSSYTQKQLLEII
KKNFDLRPGKI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 13 | g2506.t28 | CDD | cd18079 | S-AdoMet_synt | 30 | 371 | 0.0 |
| 10 | g2506.t28 | Gene3D | G3DSA:3.30.300.10 | - | 30 | 265 | 8.0E-159 |
| 11 | g2506.t28 | Gene3D | G3DSA:3.30.300.10 | - | 36 | 302 | 8.0E-159 |
| 9 | g2506.t28 | Gene3D | G3DSA:3.30.300.10 | - | 140 | 371 | 8.0E-159 |
| 4 | g2506.t28 | PANTHER | PTHR11964:SF11 | S-ADENOSYLMETHIONINE SYNTHASE ISOFORM TYPE-1 | 18 | 371 | 1.5E-204 |
| 5 | g2506.t28 | PANTHER | PTHR11964 | S-ADENOSYLMETHIONINE SYNTHETASE | 18 | 371 | 1.5E-204 |
| 12 | g2506.t28 | PIRSF | PIRSF000497 | MAT | 23 | 371 | 9.1E-152 |
| 3 | g2506.t28 | Pfam | PF00438 | S-adenosylmethionine synthetase, N-terminal domain | 29 | 126 | 3.5E-43 |
| 1 | g2506.t28 | Pfam | PF02772 | S-adenosylmethionine synthetase, central domain | 141 | 261 | 1.3E-44 |
| 2 | g2506.t28 | Pfam | PF02773 | S-adenosylmethionine synthetase, C-terminal domain | 263 | 371 | 1.2E-53 |
| 14 | g2506.t28 | ProSitePatterns | PS00376 | S-adenosylmethionine synthase signature 1. | 142 | 152 | - |
| 15 | g2506.t28 | ProSitePatterns | PS00377 | S-adenosylmethionine synthase signature 2. | 289 | 297 | - |
| 6 | g2506.t28 | SUPERFAMILY | SSF55973 | S-adenosylmethionine synthetase | 28 | 135 | 3.1E-47 |
| 8 | g2506.t28 | SUPERFAMILY | SSF55973 | S-adenosylmethionine synthetase | 139 | 262 | 1.09E-49 |
| 7 | g2506.t28 | SUPERFAMILY | SSF55973 | S-adenosylmethionine synthetase | 263 | 371 | 6.28E-51 |
| 16 | g2506.t28 | TIGRFAM | TIGR01034 | metK: methionine adenosyltransferase | 30 | 371 | 7.3E-163 |
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 transcript has been annotated with K00789 (S-adenosylmethionine synthetase)
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.
