General information for g11543.t6
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative DNA mismatch repair protein spellchecker 1.
Parent gene
- The parent gene g11543 is located on chr_1: 16953532..16954445 (+ 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_1 | g11543 | g11543.t6 | isoform | g11543.t6 | 16953378 | 16954445 |
| chr_1 | g11543 | g11543.t6 | exon | g11543.t6.exon1 | 16953378 | 16953457 |
| chr_1 | g11543 | g11543.t6 | exon | g11543.t6.exon2 | 16953544 | 16953590 |
| chr_1 | g11543 | g11543.t6 | exon | g11543.t6.exon3 | 16953645 | 16953840 |
| chr_1 | g11543 | g11543.t6 | cds | g11543.t6.CDS1 | 16953666 | 16953840 |
| chr_1 | g11543 | g11543.t6 | exon | g11543.t6.exon4 | 16954038 | 16954445 |
| chr_1 | g11543 | g11543.t6 | cds | g11543.t6.CDS2 | 16954038 | 16954081 |
| chr_1 | g11543 | g11543.t6 | TTS | g11543.t6 | 16954516 | 16954516 |
| chr_1 | g11543 | g11543.t6 | TSS | g11543.t6 | NA | NA |
Sequences
>g11543.t6 Gene=g11543 Length=731
AGAGTGTCAAGATATCGATTTCATACCAAATGACGTTAATTTTATAGAAAATGAAAGTGA
GCTTTTAATTATTACTGGAGCTAATACATGCGGAAAGTCGACTTACATACGTAGTATCGG
AATTGCTGTTTTGCTTGCACATATAGGAATGTTTGTTCCATGTACTAGCGCTAAAATTTC
AATGTGTGATTCAATTCTTGCTAGAATCGGCGCAGCAGATGATATACAAAAAAATTTAAG
TACTTTCGCTGTTGAAATGTGTGAGACAGCTGCTATACTTAGAACAGCTACAAAAAATTC
ATTGATTATCATTGATGAATTAGGTAATTTCTCATTTAGGTCTTGGTTTAGCTTGGTCAA
TTTCTGAACATCTCGCAAAAAATATTAAATGCTTTACGTTATTTGCAACGCATTTTCACG
AAATCACAACTCTCGAAAATCAATTGTCAAATGTCAAAAATTATCATCTTGCTTCTGAAG
TTAAAAACGACAAGTTGTTATTGTTATTCCAAGTTATTCGTGGTCCAGTATTAAAATCAT
ACGGTATTCATGTGGCAGATATTGCGCATTTACCAGAATCTGTAGTAGTAGCAGCTAAAA
GTTATTTGAAGGAACTTGAGGCGAATGATGTTGATAAAGAAAATTCTGAGAAGTTATCAA
AAATTGAACGTTTATTAAAAAATATTGAGACTGATAAAAATCTTGATATTGATTTATTAT
CAATTTTTTAA
>g11543.t6 Gene=g11543 Length=72
MFVPCTSAKISMCDSILARIGAADDIQKNLSTFAVEMCETAAILRTATKNSLIIIDELGN
FSFRSWFSLVNF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g11543.t6 | Gene3D | G3DSA:3.40.50.300 | - | 1 | 60 | 0.00000 |
| 2 | g11543.t6 | PANTHER | PTHR11361 | DNA MISMATCH REPAIR PROTEIN MUTS FAMILY MEMBER | 1 | 59 | 0.00000 |
| 3 | g11543.t6 | PANTHER | PTHR11361:SF35 | DNA MISMATCH REPAIR PROTEIN MSH2 | 1 | 59 | 0.00000 |
| 1 | g11543.t6 | Pfam | PF00488 | MutS domain V | 2 | 59 | 0.00000 |
| 5 | g11543.t6 | SMART | SM00534 | mutATP5 | 1 | 72 | 0.00026 |
| 4 | g11543.t6 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 2 | 60 | 0.00000 |
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:0003677 | DNA binding | MF |
| GO:0005524 | ATP binding | MF |
| GO:0032300 | mismatch repair complex | CC |
| GO:0006298 | mismatch repair | BP |
| GO:0030983 | mismatched DNA binding | MF |
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.
