General information for g2506.t29
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.t29 | TSS | g2506.t29 | 18328889 | 18328889 |
| chr_3 | g2506 | g2506.t29 | isoform | g2506.t29 | 18329132 | 18333574 |
| chr_3 | g2506 | g2506.t29 | exon | g2506.t29.exon1 | 18329132 | 18329255 |
| chr_3 | g2506 | g2506.t29 | exon | g2506.t29.exon2 | 18330039 | 18330120 |
| chr_3 | g2506 | g2506.t29 | cds | g2506.t29.CDS1 | 18330099 | 18330120 |
| chr_3 | g2506 | g2506.t29 | exon | g2506.t29.exon3 | 18330192 | 18330314 |
| chr_3 | g2506 | g2506.t29 | cds | g2506.t29.CDS2 | 18330192 | 18330314 |
| chr_3 | g2506 | g2506.t29 | exon | g2506.t29.exon4 | 18331196 | 18331308 |
| chr_3 | g2506 | g2506.t29 | cds | g2506.t29.CDS3 | 18331196 | 18331308 |
| chr_3 | g2506 | g2506.t29 | exon | g2506.t29.exon5 | 18331502 | 18331645 |
| chr_3 | g2506 | g2506.t29 | cds | g2506.t29.CDS4 | 18331502 | 18331645 |
| chr_3 | g2506 | g2506.t29 | exon | g2506.t29.exon6 | 18331872 | 18332377 |
| chr_3 | g2506 | g2506.t29 | cds | g2506.t29.CDS5 | 18331872 | 18332377 |
| chr_3 | g2506 | g2506.t29 | exon | g2506.t29.exon7 | 18332477 | 18333574 |
| chr_3 | g2506 | g2506.t29 | cds | g2506.t29.CDS6 | 18332477 | 18332582 |
| chr_3 | g2506 | g2506.t29 | TTS | g2506.t29 | 18333629 | 18333629 |
Sequences
>g2506.t29 Gene=g2506 Length=2190
ATGCCAGAAACAACGACTAACATGAATGGTTATTCTAATGGACACAGTATTCACAATGGA
TATGAGCTTGAAGACAATTCTTCATTTCTCTTTACTTCAGAATCTGTCGGCGAAGGACAT
CCAGATAAAATGTGTGACCAAATTTCTGATGCTATCTTAGATGCTCATTTGAAACAAGAC
CCGAATGCAAAAGTTGCTTGTGGTAAAAACTGTCAGCAAGACTGGTATGATCCTCTTGTG
CGGGGAGATTACATCAAAAGCAAACGTCGACTATCAGAAAGTGGTTCGTGATACAGTCAA
ACACATTGGATATGATGACTCCTCAAAGGGTTTTGATTACAAAACTTGTAGTCTTATGGT
ATGTCTTGAGCAGCAAAGTCCAAATATTGCTGACGGGGTGCATGTTAATCGTAATGTCGA
GGATATTGGAGCTGGCGATCAGGGTTTGATGTTTGGATATGCTACAGACGAAACTGAAGA
ATGCATGCCTCTTACAGTCGTCTTAGCACATCGTTTGAACCAAAAGATTGCTGAACTTCG
CAGATCTGGAGTTTTGAGCTGGGCACGTCCAGATTCTAAAACACAAGTTACAGCAGAATA
CATTTTCCAAAAAGGAGCTTGCATTCCAAAGCGAGTTCACACGGTTGTCGTCTCTTTACA
GCATTCTGAAAAGGTTACATTGGAAGAATTACGAAAAGAGATTACTGAAAAAGTTGTTCG
TGTCGTCATTCCCGAAAAGTATTTGGATAATGAAACTATTGTTCACATCAATCCATGTGG
AAATTTTGTAATTGGTGGACCACAAGGTGATGCAGGTTTAACTGGACGCAAAATTATTGT
CGATACCTATGGCGGATGGGGAGCTCATGGTGGTGGAGCATTTTCAGGAAAGGACTTTAC
AAAGGTCGATCGCTCTGCTGCTTATGCTGCTCGTTGGGTTGCAAAATCATTGGTCAAAGC
TGGTGTTTGCAGAAGATGCTTGGTTCAAGTAAGCTACGCCATTGGTGTCGCTGAACCATT
GTCAATAACAGTCTTTGACTATGGAACATCAAGTTATACACAAAAACAACTTTTGGAAAT
CATTAAAAAGAATGACTTAAATTTGCGCACACCATTTTACCAACAAACAAGCACATATGG
TCATTTTGGTCGTGAAGGTTTTCCATGGGAAAAACCAAAGACATTGATTCTTGAATGACT
GCCGCAACTTGTTGTTTCAGATGCATCCGAAAGTGATGATGAAAATCCCAATTGTTCTAA
AAAAATTAAATTAGCATAAGCCCACAAACAACATACTAAAAATTTTAAAATATGGTTCTT
AAAAATTCCCCACATGACGTTTAAAAAAATTAACATAGGACGTGACAAAAAGTTTAAATT
CCTTTTAGTTTTATCCTCTATAAAAATAGTCCATTTTCATGGGATTTTTGAATATTTTTC
TTTATCGAGAAATCTACAAACATAACTTTTTAGAAATACTTTTTTACTATCTTTAGTTGT
TTAAGTAAATGTTCTACTACCTAACTCTTTTTTTTTGTTAGTAGTTGCTTCTCAAAAAAA
CTTATAACTTTATCATAAAAGCTATTACATGATTAATGAGAAGATAAAAAAAATCAAAAA
ACCTTTGCTATTAGAGAAAGAGTGCTAGAATGATTTAGTCGAATCACGGCACCGAGTATC
GTCGCAAAAAAAAAATAAATTGTAAAATTATCATTGCTCGATGTCGCAATACTTTCTTCA
TACATTATGACTCAGTGCTAATTGATTCTCGAGAGACTTTCATGCGTTCTTTTTTGGCAT
GTAATATTATGTCTCAATAGTGACAATTTCGCTCTCTATTAATTGTAATAAATGAAAATC
TCACTATTGAGACTTGGACCATGAAATGCTTTCCTGATTTTAAACTGTGATTACGATCTT
TGAAGAAAGTCTTGTGTTGTGTTTCTGACTGGAAAATGGAAAAGCGCGTTTGTCAAAAAC
ACACCGGTTCACAAATCATTTGAAAAACATTTGCAATGTGTGAAGATTTTTCTTAATAAA
CCTTAGATTATTAGGTAGATAAAGAAATAAAAGTTGTAAGAAGGATTAGTAAGAATAGAA
GCATTTGTCTGCACTTTAAATTCTCTAGCATTGGAAACAAAAAAATGGAATGTATTGATT
TTTCTTTGAATAAATAGTTATAAACGAAAA
>g2506.t29 Gene=g2506 Length=337
MQKLLVVKTVSKTGMILLCGEITSKANVDYQKVVRDTVKHIGYDDSSKGFDYKTCSLMVC
LEQQSPNIADGVHVNRNVEDIGAGDQGLMFGYATDETEECMPLTVVLAHRLNQKIAELRR
SGVLSWARPDSKTQVTAEYIFQKGACIPKRVHTVVVSLQHSEKVTLEELRKEITEKVVRV
VIPEKYLDNETIVHINPCGNFVIGGPQGDAGLTGRKIIVDTYGGWGAHGGGAFSGKDFTK
VDRSAAYAARWVAKSLVKAGVCRRCLVQVSYAIGVAEPLSITVFDYGTSSYTQKQLLEII
KKNDLNLRTPFYQQTSTYGHFGREGFPWEKPKTLILE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 15 | g2506.t29 | CDD | cd18079 | S-AdoMet_synt | 9 | 332 | 0.0 |
| 11 | g2506.t29 | Gene3D | G3DSA:3.30.300.10 | - | 7 | 242 | 3.7E-137 |
| 13 | g2506.t29 | Gene3D | G3DSA:3.30.300.10 | - | 80 | 329 | 3.7E-137 |
| 12 | g2506.t29 | Gene3D | G3DSA:3.30.300.10 | - | 103 | 205 | 3.7E-137 |
| 4 | g2506.t29 | PANTHER | PTHR11964:SF11 | S-ADENOSYLMETHIONINE SYNTHASE ISOFORM TYPE-1 | 7 | 335 | 3.3E-176 |
| 5 | g2506.t29 | PANTHER | PTHR11964 | S-ADENOSYLMETHIONINE SYNTHETASE | 7 | 335 | 3.3E-176 |
| 3 | g2506.t29 | Pfam | PF00438 | S-adenosylmethionine synthetase, N-terminal domain | 7 | 66 | 1.8E-15 |
| 1 | g2506.t29 | Pfam | PF02772 | S-adenosylmethionine synthetase, central domain | 81 | 201 | 1.0E-44 |
| 2 | g2506.t29 | Pfam | PF02773 | S-adenosylmethionine synthetase, C-terminal domain | 203 | 330 | 1.4E-57 |
| 9 | g2506.t29 | ProSitePatterns | PS00376 | S-adenosylmethionine synthase signature 1. | 82 | 92 | - |
| 10 | g2506.t29 | ProSitePatterns | PS00377 | S-adenosylmethionine synthase signature 2. | 229 | 237 | - |
| 6 | g2506.t29 | SUPERFAMILY | SSF55973 | S-adenosylmethionine synthetase | 6 | 75 | 4.32E-20 |
| 8 | g2506.t29 | SUPERFAMILY | SSF55973 | S-adenosylmethionine synthetase | 79 | 202 | 8.83E-50 |
| 7 | g2506.t29 | SUPERFAMILY | SSF55973 | S-adenosylmethionine synthetase | 203 | 333 | 8.24E-59 |
| 14 | g2506.t29 | TIGRFAM | TIGR01034 | metK: methionine adenosyltransferase | 7 | 334 | 2.4E-143 |
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