General information for g2506.t13
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.t13 | TSS | g2506.t13 | 18328889 | 18328889 |
| chr_3 | g2506 | g2506.t13 | isoform | g2506.t13 | 18329132 | 18331309 |
| chr_3 | g2506 | g2506.t13 | exon | g2506.t13.exon1 | 18329132 | 18329255 |
| chr_3 | g2506 | g2506.t13 | cds | g2506.t13.CDS1 | 18329132 | 18329255 |
| chr_3 | g2506 | g2506.t13 | exon | g2506.t13.exon2 | 18330039 | 18330116 |
| chr_3 | g2506 | g2506.t13 | cds | g2506.t13.CDS2 | 18330039 | 18330116 |
| chr_3 | g2506 | g2506.t13 | exon | g2506.t13.exon3 | 18330192 | 18330314 |
| chr_3 | g2506 | g2506.t13 | cds | g2506.t13.CDS3 | 18330192 | 18330314 |
| chr_3 | g2506 | g2506.t13 | exon | g2506.t13.exon4 | 18331196 | 18331309 |
| chr_3 | g2506 | g2506.t13 | cds | g2506.t13.CDS4 | 18331196 | 18331308 |
| chr_3 | g2506 | g2506.t13 | TTS | g2506.t13 | NA | NA |
Sequences
>g2506.t13 Gene=g2506 Length=439
ATGCCAGAAACAACGACTAACATGAATGGTTATTCTAATGGACACAGTATTCACAATGGA
TATGAGCTTGAAGACAATTCTTCATTTCTCTTTACTTCAGAATCTGTCGGCGAAGGACAT
CCAGATAAAATGTGTGACCAAATTTCTGATGCTATCTTAGATGCTCATTTGAAACAAGAC
CCGAATGCAAAAGTTGCTTGTGAAACTGTCAGCAAGACTGGTATGATCCTCTTGTGCGGG
GAGATTACATCAAAAGCAAACGTCGACTATCAGAAAGTGGTTCGTGATACAGTCAAACAC
ATTGGATATGATGACTCCTCAAAGGGTTTTGATTACAAAACTTGTAGTCTTATGGTATGT
CTTGAGCAGCAAAGTCCAAATATTGCTGACGGGGTGCATGTTAATCGTAATGTCGAGGAT
ATTGGAGCTGGCGATCAGG
>g2506.t13 Gene=g2506 Length=146
MPETTTNMNGYSNGHSIHNGYELEDNSSFLFTSESVGEGHPDKMCDQISDAILDAHLKQD
PNAKVACETVSKTGMILLCGEITSKANVDYQKVVRDTVKHIGYDDSSKGFDYKTCSLMVC
LEQQSPNIADGVHVNRNVEDIGAGDQ
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g2506.t13 | Gene3D | G3DSA:3.30.300.10 | - | 36 | 146 | 0 |
| 2 | g2506.t13 | PANTHER | PTHR11964:SF11 | S-ADENOSYLMETHIONINE SYNTHASE ISOFORM TYPE-1 | 18 | 146 | 0 |
| 3 | g2506.t13 | PANTHER | PTHR11964 | S-ADENOSYLMETHIONINE SYNTHETASE | 18 | 146 | 0 |
| 1 | g2506.t13 | Pfam | PF00438 | S-adenosylmethionine synthetase, N-terminal domain | 29 | 126 | 0 |
| 4 | g2506.t13 | SUPERFAMILY | SSF55973 | S-adenosylmethionine synthetase | 28 | 135 | 0 |
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.
