General information for g2506.t39
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.t39 | isoform | g2506.t39 | 18331887 | 18333574 |
| chr_3 | g2506 | g2506.t39 | exon | g2506.t39.exon1 | 18331887 | 18332407 |
| chr_3 | g2506 | g2506.t39 | cds | g2506.t39.CDS1 | 18331887 | 18332407 |
| chr_3 | g2506 | g2506.t39 | exon | g2506.t39.exon2 | 18332477 | 18333574 |
| chr_3 | g2506 | g2506.t39 | cds | g2506.t39.CDS2 | 18332477 | 18332582 |
| chr_3 | g2506 | g2506.t39 | TTS | g2506.t39 | 18333629 | 18333629 |
| chr_3 | g2506 | g2506.t39 | TSS | g2506.t39 | NA | NA |
Sequences
>g2506.t39 Gene=g2506 Length=1619
ATTTTCCAAAAAGGAGCTTGCATTCCAAAGCGAGTTCACACGGTTGTCGTCTCTTTACAG
CATTCTGAAAAGGTTACATTGGAAGAATTACGAAAAGAGATTACTGAAAAAGTTGTTCGT
GTCGTCATTCCCGAAAAGTATTTGGATAATGAAACTATTGTTCACATCAATCCATGTGGA
AATTTTGTAATTGGTGGACCACAAGGTGATGCAGGTTTAACTGGACGCAAAATTATTGTC
GATACCTATGGCGGATGGGGAGCTCATGGTGGTGGAGCATTTTCAGGAAAGGACTTTACA
AAGGTCGATCGCTCTGCTGCTTATGCTGCTCGTTGGGTTGCAAAATCATTGGTCAAAGCT
GGTGTTTGCAGAAGATGCTTGGTTCAAGTAAGCTACGCCATTGGTGTCGCTGAACCATTG
TCAATAACAGTCTTTGACTATGGAACATCAAGTTATACACAAAAACAACTTTTGGAAATC
ATTAAAAAGAACTTTGATCTTCGCCCAGGCAAAATTGTTAATGACTTAAATTTGCGCACA
CCATTTTACCAACAAACAAGCACATATGGTCATTTTGGTCGTGAAGGTTTTCCATGGGAA
AAACCAAAGACATTGATTCTTGAATGACTGCCGCAACTTGTTGTTTCAGATGCATCCGAA
AGTGATGATGAAAATCCCAATTGTTCTAAAAAAATTAAATTAGCATAAGCCCACAAACAA
CATACTAAAAATTTTAAAATATGGTTCTTAAAAATTCCCCACATGACGTTTAAAAAAATT
AACATAGGACGTGACAAAAAGTTTAAATTCCTTTTAGTTTTATCCTCTATAAAAATAGTC
CATTTTCATGGGATTTTTGAATATTTTTCTTTATCGAGAAATCTACAAACATAACTTTTT
AGAAATACTTTTTTACTATCTTTAGTTGTTTAAGTAAATGTTCTACTACCTAACTCTTTT
TTTTTGTTAGTAGTTGCTTCTCAAAAAAACTTATAACTTTATCATAAAAGCTATTACATG
ATTAATGAGAAGATAAAAAAAATCAAAAAACCTTTGCTATTAGAGAAAGAGTGCTAGAAT
GATTTAGTCGAATCACGGCACCGAGTATCGTCGCAAAAAAAAAATAAATTGTAAAATTAT
CATTGCTCGATGTCGCAATACTTTCTTCATACATTATGACTCAGTGCTAATTGATTCTCG
AGAGACTTTCATGCGTTCTTTTTTGGCATGTAATATTATGTCTCAATAGTGACAATTTCG
CTCTCTATTAATTGTAATAAATGAAAATCTCACTATTGAGACTTGGACCATGAAATGCTT
TCCTGATTTTAAACTGTGATTACGATCTTTGAAGAAAGTCTTGTGTTGTGTTTCTGACTG
GAAAATGGAAAAGCGCGTTTGTCAAAAACACACCGGTTCACAAATCATTTGAAAAACATT
TGCAATGTGTGAAGATTTTTCTTAATAAACCTTAGATTATTAGGTAGATAAAGAAATAAA
AGTTGTAAGAAGGATTAGTAAGAATAGAAGCATTTGTCTGCACTTTAAATTCTCTAGCAT
TGGAAACAAAAAAATGGAATGTATTGATTTTTCTTTGAATAAATAGTTATAAACGAAAA
>g2506.t39 Gene=g2506 Length=208
IFQKGACIPKRVHTVVVSLQHSEKVTLEELRKEITEKVVRVVIPEKYLDNETIVHINPCG
NFVIGGPQGDAGLTGRKIIVDTYGGWGAHGGGAFSGKDFTKVDRSAAYAARWVAKSLVKA
GVCRRCLVQVSYAIGVAEPLSITVFDYGTSSYTQKQLLEIIKKNFDLRPGKIVNDLNLRT
PFYQQTSTYGHFGREGFPWEKPKTLILE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g2506.t39 | Gene3D | G3DSA:3.30.300.10 | - | 2 | 64 | 3.7E-21 |
| 9 | g2506.t39 | Gene3D | G3DSA:3.30.300.10 | - | 82 | 208 | 2.6E-53 |
| 3 | g2506.t39 | PANTHER | PTHR11964:SF11 | S-ADENOSYLMETHIONINE SYNTHASE ISOFORM TYPE-1 | 3 | 206 | 7.3E-104 |
| 4 | g2506.t39 | PANTHER | PTHR11964 | S-ADENOSYLMETHIONINE SYNTHETASE | 3 | 206 | 7.3E-104 |
| 1 | g2506.t39 | Pfam | PF02772 | S-adenosylmethionine synthetase, central domain | 6 | 62 | 1.2E-12 |
| 2 | g2506.t39 | Pfam | PF02773 | S-adenosylmethionine synthetase, C-terminal domain | 64 | 201 | 1.2E-68 |
| 7 | g2506.t39 | ProSitePatterns | PS00377 | S-adenosylmethionine synthase signature 2. | 90 | 98 | - |
| 5 | g2506.t39 | SUPERFAMILY | SSF55973 | S-adenosylmethionine synthetase | 4 | 63 | 3.77E-16 |
| 6 | g2506.t39 | SUPERFAMILY | SSF55973 | S-adenosylmethionine synthetase | 64 | 204 | 7.46E-67 |
| 10 | g2506.t39 | TIGRFAM | TIGR01034 | metK: methionine adenosyltransferase | 9 | 205 | 6.4E-96 |
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.
