General information for g2506.t16
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.t16 | TSS | g2506.t16 | 18328889 | 18328889 |
| chr_3 | g2506 | g2506.t16 | isoform | g2506.t16 | 18329132 | 18331647 |
| chr_3 | g2506 | g2506.t16 | exon | g2506.t16.exon1 | 18329132 | 18329255 |
| chr_3 | g2506 | g2506.t16 | cds | g2506.t16.CDS1 | 18329132 | 18329255 |
| chr_3 | g2506 | g2506.t16 | exon | g2506.t16.exon2 | 18330039 | 18330116 |
| chr_3 | g2506 | g2506.t16 | cds | g2506.t16.CDS2 | 18330039 | 18330116 |
| chr_3 | g2506 | g2506.t16 | exon | g2506.t16.exon3 | 18330192 | 18330314 |
| chr_3 | g2506 | g2506.t16 | cds | g2506.t16.CDS3 | 18330192 | 18330314 |
| chr_3 | g2506 | g2506.t16 | exon | g2506.t16.exon4 | 18331202 | 18331308 |
| chr_3 | g2506 | g2506.t16 | cds | g2506.t16.CDS4 | 18331202 | 18331308 |
| chr_3 | g2506 | g2506.t16 | exon | g2506.t16.exon5 | 18331502 | 18331647 |
| chr_3 | g2506 | g2506.t16 | cds | g2506.t16.CDS5 | 18331502 | 18331645 |
| chr_3 | g2506 | g2506.t16 | TTS | g2506.t16 | NA | NA |
Sequences
>g2506.t16 Gene=g2506 Length=578
ATGCCAGAAACAACGACTAACATGAATGGTTATTCTAATGGACACAGTATTCACAATGGA
TATGAGCTTGAAGACAATTCTTCATTTCTCTTTACTTCAGAATCTGTCGGCGAAGGACAT
CCAGATAAAATGTGTGACCAAATTTCTGATGCTATCTTAGATGCTCATTTGAAACAAGAC
CCGAATGCAAAAGTTGCTTGTGAAACTGTCAGCAAGACTGGTATGATCCTCTTGTGCGGG
GAGATTACATCAAAAGCAAACGTCGACTATCAGAAAGTGGTTCGTGATACAGTCAAACAC
ATTGGATATGATGACTCCTCAAAGGATTACAAAACTTGTAGTCTTATGGTATGTCTTGAG
CAGCAAAGTCCAAATATTGCTGACGGGGTGCATGTTAATCGTAATGTCGAGGATATTGGA
GCTGGCGATCAGGGTTTGATGTTTGGATATGCTACAGACGAAACTGAAGAATGCATGCCT
CTTACAGTCGTCTTAGCACATCGTTTGAACCAAAAGATTGCTGAACTTCGCAGATCTGGA
GTTTTGAGCTGGGCACGTCCAGATTCTAAAACACAAGT
>g2506.t16 Gene=g2506 Length=192
MPETTTNMNGYSNGHSIHNGYELEDNSSFLFTSESVGEGHPDKMCDQISDAILDAHLKQD
PNAKVACETVSKTGMILLCGEITSKANVDYQKVVRDTVKHIGYDDSSKDYKTCSLMVCLE
QQSPNIADGVHVNRNVEDIGAGDQGLMFGYATDETEECMPLTVVLAHRLNQKIAELRRSG
VLSWARPDSKTQ
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g2506.t16 | Gene3D | G3DSA:3.30.300.10 | - | 38 | 143 | 4.3E-41 |
| 9 | g2506.t16 | Gene3D | G3DSA:3.30.300.10 | - | 144 | 192 | 8.8E-22 |
| 3 | g2506.t16 | PANTHER | PTHR11964:SF11 | S-ADENOSYLMETHIONINE SYNTHASE ISOFORM TYPE-1 | 18 | 192 | 4.6E-100 |
| 4 | g2506.t16 | PANTHER | PTHR11964 | S-ADENOSYLMETHIONINE SYNTHETASE | 18 | 192 | 4.6E-100 |
| 2 | g2506.t16 | Pfam | PF00438 | S-adenosylmethionine synthetase, N-terminal domain | 29 | 124 | 1.9E-40 |
| 1 | g2506.t16 | Pfam | PF02772 | S-adenosylmethionine synthetase, central domain | 139 | 192 | 8.5E-23 |
| 7 | g2506.t16 | ProSitePatterns | PS00376 | S-adenosylmethionine synthase signature 1. | 140 | 150 | - |
| 6 | g2506.t16 | SUPERFAMILY | SSF55973 | S-adenosylmethionine synthetase | 28 | 133 | 5.89E-45 |
| 5 | g2506.t16 | SUPERFAMILY | SSF55973 | S-adenosylmethionine synthetase | 134 | 192 | 1.88E-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.
