General information for g11543.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 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.t3 | TSS | g11543.t3 | 16951251 | 16951251 |
| chr_1 | g11543 | g11543.t3 | isoform | g11543.t3 | 16951347 | 16952789 |
| chr_1 | g11543 | g11543.t3 | exon | g11543.t3.exon1 | 16951347 | 16951380 |
| chr_1 | g11543 | g11543.t3 | cds | g11543.t3.CDS1 | 16951347 | 16951380 |
| chr_1 | g11543 | g11543.t3 | exon | g11543.t3.exon2 | 16951437 | 16952789 |
| chr_1 | g11543 | g11543.t3 | cds | g11543.t3.CDS2 | 16951437 | 16952788 |
| chr_1 | g11543 | g11543.t3 | TTS | g11543.t3 | NA | NA |
Sequences
>g11543.t3 Gene=g11543 Length=1387
ATGAGTAAGCAAATACAAAAGGCATTGAATTTAGATCAAAAATCGCAAATTAATTTCATA
GAATTTTATCAAAAAATCACAGAAAAAACTTCAGAAGATACTCTTGTGTTTCGTGCATTT
GATAGAGGCGATTTTTATTCCATTCATGGCAAGGATATAAATATAGCTTTAAAAACTTCA
ATTAAATCGTCAATAGTTACAAAAATGATGTGTCCTCAAAAGAATTTCGAACTCAAATAT
GCTTCTTTAAATAGAACATTGGCCGAAAAAATGATTCGTGAGCTATTGCTGATTCATTTT
TATAGGGTTGAAGTCTATACTTGCAAAAGAGATGATTTTTCGGTAAAAAAAGGATCTCCT
GGAAATTTGGTTGAATTTGAAGATATTTTGACATCAGATGCAAATGAGATTGTGTTTTCT
AATTTGCTTGTATCTGTAGTGCTATCTACAAACAACAGAATTGGTTTGTGCTCTATAGAC
GTTGACGAATCAACTATTCAAGTAACAGAGTTTGAAGATTCTGATTTCTTTATGAATCTC
GAAGCTTGTCTTGTAGTTTTGGCGCCTAAAGAAATCATTCTACCATCTGTAACTAAGGAA
TATTCTAAAATTGGTGAAATACTGAATCGTAATCGTATTTTGTCAACTGTACTACAAAAA
GCTGATTTTGTTAAAAGTACAAACTTTCTACAAGATTTGGCTAAAGTATATAGATTTAGC
AAAGGACAACAAAAAAATGTTCATTTGATACCTGAAGTTAAAATGGATTTGGCCATGGGA
GCATTAGCAGCTGCTTTTAAATATATTGGCATCACAAAAGATGAAAGCAATGATAACAAA
TTTTCAATAAGCAATTTGAATTTCAATCAATTTGTTCGACTTGATACAGCAGCATTTTCA
GCATTGAACTTGTTTCCATCATCTGAGAGCAACAGTCGATCAAGTAATTACAAAACACAA
TCAGTAGTTGGTGTATTAGATTGTTGCAAGACTAACCAAGGTAAAAGACTTTTGAGACAG
TGGATAAAACAACCATTAAAAAATATTAATATGATACGACAACGTCTCGATGTTGTACAA
TGCTTTGTGGAGAATAAAGAAGTTCAATTCATTCTTCATAATCAATATCTCAACATTTTA
CCAGATGTTCTTCTCTTAACAAATAAGCTTCTTCGAAAACGTGGTTCTCTTTCAGATGTG
TATAAAATTTATCAAGTTGTCTCAAGAATTCCTGATATATTAAAGCTGTTAAAAAATCTT
GAATGTAATGCTATTAATTCGCTTCTTTTTACACCGTTGAATGAACTTAAAGATGAATTA
CATAAAATTTTGGAAATGGTCTTGGAAATAATCGATGGGGATGCTTTAAAGAAAGGCCTC
TTTCTAG
>g11543.t3 Gene=g11543 Length=462
MSKQIQKALNLDQKSQINFIEFYQKITEKTSEDTLVFRAFDRGDFYSIHGKDINIALKTS
IKSSIVTKMMCPQKNFELKYASLNRTLAEKMIRELLLIHFYRVEVYTCKRDDFSVKKGSP
GNLVEFEDILTSDANEIVFSNLLVSVVLSTNNRIGLCSIDVDESTIQVTEFEDSDFFMNL
EACLVVLAPKEIILPSVTKEYSKIGEILNRNRILSTVLQKADFVKSTNFLQDLAKVYRFS
KGQQKNVHLIPEVKMDLAMGALAAAFKYIGITKDESNDNKFSISNLNFNQFVRLDTAAFS
ALNLFPSSESNSRSSNYKTQSVVGVLDCCKTNQGKRLLRQWIKQPLKNINMIRQRLDVVQ
CFVENKEVQFILHNQYLNILPDVLLLTNKLLRKRGSLSDVYKIYQVVSRIPDILKLLKNL
ECNAINSLLFTPLNELKDELHKILEMVLEIIDGDALKKGLFL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g11543.t3 | Gene3D | G3DSA:3.40.1170.10 | DNA repair protein MutS | 1 | 119 | 0.0e+00 |
| 10 | g11543.t3 | Gene3D | G3DSA:3.30.420.110 | DNA repair protein MutS | 120 | 289 | 0.0e+00 |
| 9 | g11543.t3 | Gene3D | G3DSA:1.10.1420.10 | - | 292 | 462 | 0.0e+00 |
| 4 | g11543.t3 | PANTHER | PTHR11361 | DNA MISMATCH REPAIR PROTEIN MUTS FAMILY MEMBER | 27 | 426 | 0.0e+00 |
| 5 | g11543.t3 | PANTHER | PTHR11361:SF35 | DNA MISMATCH REPAIR PROTEIN MSH2 | 27 | 426 | 0.0e+00 |
| 2 | g11543.t3 | Pfam | PF01624 | MutS domain I | 19 | 108 | 1.3e-06 |
| 1 | g11543.t3 | Pfam | PF05188 | MutS domain II | 141 | 280 | 0.0e+00 |
| 3 | g11543.t3 | Pfam | PF05192 | MutS domain III | 298 | 442 | 0.0e+00 |
| 6 | g11543.t3 | SUPERFAMILY | SSF53150 | DNA repair protein MutS, domain II | 140 | 306 | 1.0e-07 |
| 7 | g11543.t3 | SUPERFAMILY | SSF48334 | DNA repair protein MutS, domain III | 295 | 456 | 0.0e+00 |
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.
