General information for g2506.t21
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.t21 | TSS | g2506.t21 | 18328889 | 18328889 |
| chr_3 | g2506 | g2506.t21 | isoform | g2506.t21 | 18329132 | 18332398 |
| chr_3 | g2506 | g2506.t21 | exon | g2506.t21.exon1 | 18329132 | 18329255 |
| chr_3 | g2506 | g2506.t21 | exon | g2506.t21.exon2 | 18330039 | 18330116 |
| chr_3 | g2506 | g2506.t21 | exon | g2506.t21.exon3 | 18330192 | 18330314 |
| chr_3 | g2506 | g2506.t21 | exon | g2506.t21.exon4 | 18330555 | 18330667 |
| chr_3 | g2506 | g2506.t21 | exon | g2506.t21.exon5 | 18331196 | 18331308 |
| chr_3 | g2506 | g2506.t21 | exon | g2506.t21.exon6 | 18331502 | 18331645 |
| chr_3 | g2506 | g2506.t21 | cds | g2506.t21.CDS1 | 18331508 | 18331645 |
| chr_3 | g2506 | g2506.t21 | exon | g2506.t21.exon7 | 18331872 | 18332398 |
| chr_3 | g2506 | g2506.t21 | cds | g2506.t21.CDS2 | 18331872 | 18332396 |
| chr_3 | g2506 | g2506.t21 | TTS | g2506.t21 | 18333069 | 18333069 |
Sequences
>g2506.t21 Gene=g2506 Length=1222
ATGCCAGAAACAACGACTAACATGAATGGTTATTCTAATGGACACAGTATTCACAATGGA
TATGAGCTTGAAGACAATTCTTCATTTCTCTTTACTTCAGAATCTGTCGGCGAAGGACAT
CCAGATAAAATGTGTGACCAAATTTCTGATGCTATCTTAGATGCTCATTTGAAACAAGAC
CCGAATGCAAAAGTTGCTTGTGAAACTGTCAGCAAGACTGGTATGATCCTCTTGTGCGGG
GAGATTACATCAAAAGCAAACGTCGACTATCAGAAAGTGGTTCGTGATACAGTCAAACAC
ATTGGATATGATGACTCCTCAAAGGGCTTCGACTGGAAGACTCTTAACTTGTTAGTGGCA
ATTGAACAGCAATCGCCTGATATCGCTCAAGGAGTACACTTAAATCGCGAAGAATATGAT
GTAGGAGCCGGTGATCAGGTTTTGATTACAAAACTTGTAGTCTTATGGTATGTCTTGAGC
AGCAAAGTCCAAATATTGCTGACGGGGTGCATGTTAATCGTAATGTCGAGGATATTGGAG
CTGGCGATCAGGGTTTGATGTTTGGATATGCTACAGACGAAACTGAAGAATGCATGCCTC
TTACAGTCGTCTTAGCACATCGTTTGAACCAAAAGATTGCTGAACTTCGCAGATCTGGAG
TTTTGAGCTGGGCACGTCCAGATTCTAAAACACAAGTTACAGCAGAATACATTTTCCAAA
AAGGAGCTTGCATTCCAAAGCGAGTTCACACGGTTGTCGTCTCTTTACAGCATTCTGAAA
AGGTTACATTGGAAGAATTACGAAAAGAGATTACTGAAAAAGTTGTTCGTGTCGTCATTC
CCGAAAAGTATTTGGATAATGAAACTATTGTTCACATCAATCCATGTGGAAATTTTGTAA
TTGGTGGACCACAAGGTGATGCAGGTTTAACTGGACGCAAAATTATTGTCGATACCTATG
GCGGATGGGGAGCTCATGGTGGTGGAGCATTTTCAGGAAAGGACTTTACAAAGGTCGATC
GCTCTGCTGCTTATGCTGCTCGTTGGGTTGCAAAATCATTGGTCAAAGCTGGTGTTTGCA
GAAGATGCTTGGTTCAAGTAAGCTACGCCATTGGTGTCGCTGAACCATTGTCAATAACAG
TCTTTGACTATGGAACATCAAGTTATACACAAAAACAACTTTTGGAAATCATTAAAAAGA
ACTTTGATCTTCGCCCAGGCAA
>g2506.t21 Gene=g2506 Length=221
MFGYATDETEECMPLTVVLAHRLNQKIAELRRSGVLSWARPDSKTQVTAEYIFQKGACIP
KRVHTVVVSLQHSEKVTLEELRKEITEKVVRVVIPEKYLDNETIVHINPCGNFVIGGPQG
DAGLTGRKIIVDTYGGWGAHGGGAFSGKDFTKVDRSAAYAARWVAKSLVKAGVCRRCLVQ
VSYAIGVAEPLSITVFDYGTSSYTQKQLLEIIKKNFDLRPG
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g2506.t21 | Gene3D | G3DSA:3.30.300.10 | - | 1 | 115 | 1.9E-42 |
| 9 | g2506.t21 | Gene3D | G3DSA:3.30.300.10 | - | 138 | 221 | 5.9E-36 |
| 3 | g2506.t21 | PANTHER | PTHR11964:SF11 | S-ADENOSYLMETHIONINE SYNTHASE ISOFORM TYPE-1 | 1 | 221 | 1.7E-120 |
| 4 | g2506.t21 | PANTHER | PTHR11964 | S-ADENOSYLMETHIONINE SYNTHETASE | 1 | 221 | 1.7E-120 |
| 1 | g2506.t21 | Pfam | PF02772 | S-adenosylmethionine synthetase, central domain | 1 | 113 | 9.3E-39 |
| 2 | g2506.t21 | Pfam | PF02773 | S-adenosylmethionine synthetase, C-terminal domain | 115 | 220 | 1.8E-53 |
| 7 | g2506.t21 | ProSitePatterns | PS00377 | S-adenosylmethionine synthase signature 2. | 141 | 149 | - |
| 5 | g2506.t21 | SUPERFAMILY | SSF55973 | S-adenosylmethionine synthetase | 1 | 114 | 6.67E-43 |
| 6 | g2506.t21 | SUPERFAMILY | SSF55973 | S-adenosylmethionine synthetase | 115 | 221 | 9.03E-51 |
| 10 | g2506.t21 | TIGRFAM | TIGR01034 | metK: methionine adenosyltransferase | 1 | 220 | 3.9E-101 |
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.
