General information for g2506.t17
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.t17 | TSS | g2506.t17 | 18328889 | 18328889 |
| chr_3 | g2506 | g2506.t17 | isoform | g2506.t17 | 18329132 | 18331945 |
| chr_3 | g2506 | g2506.t17 | exon | g2506.t17.exon1 | 18329132 | 18329255 |
| chr_3 | g2506 | g2506.t17 | exon | g2506.t17.exon2 | 18330039 | 18330120 |
| chr_3 | g2506 | g2506.t17 | cds | g2506.t17.CDS1 | 18330099 | 18330120 |
| chr_3 | g2506 | g2506.t17 | exon | g2506.t17.exon3 | 18330192 | 18330314 |
| chr_3 | g2506 | g2506.t17 | cds | g2506.t17.CDS2 | 18330192 | 18330314 |
| chr_3 | g2506 | g2506.t17 | exon | g2506.t17.exon4 | 18331196 | 18331308 |
| chr_3 | g2506 | g2506.t17 | cds | g2506.t17.CDS3 | 18331196 | 18331308 |
| chr_3 | g2506 | g2506.t17 | exon | g2506.t17.exon5 | 18331502 | 18331645 |
| chr_3 | g2506 | g2506.t17 | cds | g2506.t17.CDS4 | 18331502 | 18331645 |
| chr_3 | g2506 | g2506.t17 | exon | g2506.t17.exon6 | 18331872 | 18331945 |
| chr_3 | g2506 | g2506.t17 | cds | g2506.t17.CDS5 | 18331872 | 18331943 |
| chr_3 | g2506 | g2506.t17 | TTS | g2506.t17 | NA | NA |
Sequences
>g2506.t17 Gene=g2506 Length=660
ATGCCAGAAACAACGACTAACATGAATGGTTATTCTAATGGACACAGTATTCACAATGGA
TATGAGCTTGAAGACAATTCTTCATTTCTCTTTACTTCAGAATCTGTCGGCGAAGGACAT
CCAGATAAAATGTGTGACCAAATTTCTGATGCTATCTTAGATGCTCATTTGAAACAAGAC
CCGAATGCAAAAGTTGCTTGTGGTAAAAACTGTCAGCAAGACTGGTATGATCCTCTTGTG
CGGGGAGATTACATCAAAAGCAAACGTCGACTATCAGAAAGTGGTTCGTGATACAGTCAA
ACACATTGGATATGATGACTCCTCAAAGGGTTTTGATTACAAAACTTGTAGTCTTATGGT
ATGTCTTGAGCAGCAAAGTCCAAATATTGCTGACGGGGTGCATGTTAATCGTAATGTCGA
GGATATTGGAGCTGGCGATCAGGGTTTGATGTTTGGATATGCTACAGACGAAACTGAAGA
ATGCATGCCTCTTACAGTCGTCTTAGCACATCGTTTGAACCAAAAGATTGCTGAACTTCG
CAGATCTGGAGTTTTGAGCTGGGCACGTCCAGATTCTAAAACACAAGTTACAGCAGAATA
CATTTTCCAAAAAGGAGCTTGCATTCCAAAGCGAGTTCACACGGTTGTCGTCTCTTTACA
>g2506.t17 Gene=g2506 Length=158
MQKLLVVKTVSKTGMILLCGEITSKANVDYQKVVRDTVKHIGYDDSSKGFDYKTCSLMVC
LEQQSPNIADGVHVNRNVEDIGAGDQGLMFGYATDETEECMPLTVVLAHRLNQKIAELRR
SGVLSWARPDSKTQVTAEYIFQKGACIPKRVHTVVVSL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g2506.t17 | Gene3D | G3DSA:3.30.300.10 | - | 2 | 85 | 1.0E-21 |
| 8 | g2506.t17 | Gene3D | G3DSA:3.30.300.10 | - | 86 | 158 | 5.3E-30 |
| 3 | g2506.t17 | PANTHER | PTHR11964:SF11 | S-ADENOSYLMETHIONINE SYNTHASE ISOFORM TYPE-1 | 7 | 157 | 3.8E-81 |
| 4 | g2506.t17 | PANTHER | PTHR11964 | S-ADENOSYLMETHIONINE SYNTHETASE | 7 | 157 | 3.8E-81 |
| 2 | g2506.t17 | Pfam | PF00438 | S-adenosylmethionine synthetase, N-terminal domain | 7 | 66 | 4.4E-16 |
| 1 | g2506.t17 | Pfam | PF02772 | S-adenosylmethionine synthetase, central domain | 81 | 157 | 5.8E-31 |
| 7 | g2506.t17 | ProSitePatterns | PS00376 | S-adenosylmethionine synthase signature 1. | 82 | 92 | - |
| 6 | g2506.t17 | SUPERFAMILY | SSF55973 | S-adenosylmethionine synthetase | 6 | 75 | 9.03E-21 |
| 5 | g2506.t17 | SUPERFAMILY | SSF55973 | S-adenosylmethionine synthetase | 78 | 157 | 9.81E-34 |
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. There were no conditions that were differentially expressed