General information for g11543.t1
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.t1 | TSS | g11543.t1 | 16951251 | 16951251 |
| chr_1 | g11543 | g11543.t1 | isoform | g11543.t1 | 16951347 | 16954445 |
| chr_1 | g11543 | g11543.t1 | exon | g11543.t1.exon1 | 16951347 | 16951380 |
| chr_1 | g11543 | g11543.t1 | cds | g11543.t1.CDS1 | 16951347 | 16951380 |
| chr_1 | g11543 | g11543.t1 | exon | g11543.t1.exon2 | 16951437 | 16952789 |
| chr_1 | g11543 | g11543.t1 | cds | g11543.t1.CDS2 | 16951437 | 16952789 |
| chr_1 | g11543 | g11543.t1 | exon | g11543.t1.exon3 | 16952858 | 16953457 |
| chr_1 | g11543 | g11543.t1 | cds | g11543.t1.CDS3 | 16952858 | 16953457 |
| chr_1 | g11543 | g11543.t1 | exon | g11543.t1.exon4 | 16953544 | 16953590 |
| chr_1 | g11543 | g11543.t1 | cds | g11543.t1.CDS4 | 16953544 | 16953590 |
| chr_1 | g11543 | g11543.t1 | exon | g11543.t1.exon5 | 16953645 | 16953840 |
| chr_1 | g11543 | g11543.t1 | cds | g11543.t1.CDS5 | 16953645 | 16953840 |
| chr_1 | g11543 | g11543.t1 | exon | g11543.t1.exon6 | 16953905 | 16953928 |
| chr_1 | g11543 | g11543.t1 | cds | g11543.t1.CDS6 | 16953905 | 16953928 |
| chr_1 | g11543 | g11543.t1 | exon | g11543.t1.exon7 | 16954054 | 16954445 |
| chr_1 | g11543 | g11543.t1 | cds | g11543.t1.CDS7 | 16954054 | 16954445 |
| chr_1 | g11543 | g11543.t1 | TTS | g11543.t1 | 16954516 | 16954516 |
Sequences
>g11543.t1 Gene=g11543 Length=2646
ATGAGTAAGCAAATACAAAAGGCATTGAATTTAGATCAAAAATCGCAAATTAATTTCATA
GAATTTTATCAAAAAATCACAGAAAAAACTTCAGAAGATACTCTTGTGTTTCGTGCATTT
GATAGAGGCGATTTTTATTCCATTCATGGCAAGGATATAAATATAGCTTTAAAAACTTCA
ATTAAATCGTCAATAGTTACAAAAATGATGTGTCCTCAAAAGAATTTCGAACTCAAATAT
GCTTCTTTAAATAGAACATTGGCCGAAAAAATGATTCGTGAGCTATTGCTGATTCATTTT
TATAGGGTTGAAGTCTATACTTGCAAAAGAGATGATTTTTCGGTAAAAAAAGGATCTCCT
GGAAATTTGGTTGAATTTGAAGATATTTTGACATCAGATGCAAATGAGATTGTGTTTTCT
AATTTGCTTGTATCTGTAGTGCTATCTACAAACAACAGAATTGGTTTGTGCTCTATAGAC
GTTGACGAATCAACTATTCAAGTAACAGAGTTTGAAGATTCTGATTTCTTTATGAATCTC
GAAGCTTGTCTTGTAGTTTTGGCGCCTAAAGAAATCATTCTACCATCTGTAACTAAGGAA
TATTCTAAAATTGGTGAAATACTGAATCGTAATCGTATTTTGTCAACTGTACTACAAAAA
GCTGATTTTGTTAAAAGTACAAACTTTCTACAAGATTTGGCTAAAGTATATAGATTTAGC
AAAGGACAACAAAAAAATGTTCATTTGATACCTGAAGTTAAAATGGATTTGGCCATGGGA
GCATTAGCAGCTGCTTTTAAATATATTGGCATCACAAAAGATGAAAGCAATGATAACAAA
TTTTCAATAAGCAATTTGAATTTCAATCAATTTGTTCGACTTGATACAGCAGCATTTTCA
GCATTGAACTTGTTTCCATCATCTGAGAGCAACAGTCGATCAAGTAATTACAAAACACAA
TCAGTAGTTGGTGTATTAGATTGTTGCAAGACTAACCAAGGTAAAAGACTTTTGAGACAG
TGGATAAAACAACCATTAAAAAATATTAATATGATACGACAACGTCTCGATGTTGTACAA
TGCTTTGTGGAGAATAAAGAAGTTCAATTCATTCTTCATAATCAATATCTCAACATTTTA
CCAGATGTTCTTCTCTTAACAAATAAGCTTCTTCGAAAACGTGGTTCTCTTTCAGATGTG
TATAAAATTTATCAAGTTGTCTCAAGAATTCCTGATATATTAAAGCTGTTAAAAAATCTT
GAATGTAATGCTATTAATTCGCTTCTTTTTACACCGTTGAATGAACTTAAAGATGAATTA
CATAAAATTTTGGAAATGGTCTTGGAAATAATCGATGGGGATGCTTTAAAGAAAGGCCTC
TTTCTAGTTCGTGCAAGTTTTGATGATGATTTAAATGAAATAAAGAAAAATATGAATGAC
ATTGAAGCAAAAATGAACAAAGAAACAAAATCCTCTGCGAGTAAATTAGGATTGGAAGAA
GGAAGCACATTAAAACTAGATTATGTTTCACATCTATCTTTTTTTCTCAGAGCATCTCGC
AAAGAAGATCAAACTATCCGAAAAAACAAACAATTTGAAATTATTGATACAGCGCGAGGA
TATTTGCGATTCACAACAGCAAAACTTAAGGAACTTAATGTTGAATATAATTCACTAAAA
GCATCCTATGAAGAGCACCAAAAGATGATTGTAGCTGAAATATGCAAAATTATTGTTGGA
TATTCCCTTCCTTTGACAAATTTAAATCATTGCATTGCGACACTCGATGTTTTTGTCAGT
TTTGCCCATGTTGTAGACAATTCGCCAGGCTCTTATGTTCGTCCTGAAATATTTTCCTCT
GAAGAGAAACGCATATTACAAATAGAAGAATTACGTCATCCATGTTTAGAGTGTCAAGAT
ATCGATTTCATACCAAATGACGTTAATTTTATAGAAAATGAAAGTGAGCTTTTAATTATT
ACTGGAGCTAATACATGCGGAAAGTCGACTTACATACGTAGTATCGGAATTGCTGTTTTG
CTTGCACATATAGGAATGTTTGTTCCATGTACTAGCGCTAAAATTTCAATGTGTGATTCA
ATTCTTGCTAGAATCGGCGCAGCAGATGATATACAAAAAAATTTAAGTACTTTCGCTGTT
GAAATGTGTGAGACAGCTGCTATACTTAGAACAGCTACAAAAAATTCATTGATTATCATT
GATGAATTAGGACGAGGCACTTCTACATTTGAAGGTCTTGGTTTAGCTTGGTCAATTTCT
GAACATCTCGCAAAAAATATTAAATGCTTTACGTTATTTGCAACGCATTTTCACGAAATC
ACAACTCTCGAAAATCAATTGTCAAATGTCAAAAATTATCATCTTGCTTCTGAAGTTAAA
AACGACAAGTTGTTATTGTTATTCCAAGTTATTCGTGGTCCAGTATTAAAATCATACGGT
ATTCATGTGGCAGATATTGCGCATTTACCAGAATCTGTAGTAGTAGCAGCTAAAAGTTAT
TTGAAGGAACTTGAGGCGAATGATGTTGATAAAGAAAATTCTGAGAAGTTATCAAAAATT
GAACGTTTATTAAAAAATATTGAGACTGATAAAAATCTTGATATTGATTTATTATCAATT
TTTTAA
>g11543.t1 Gene=g11543 Length=881
MSKQIQKALNLDQKSQINFIEFYQKITEKTSEDTLVFRAFDRGDFYSIHGKDINIALKTS
IKSSIVTKMMCPQKNFELKYASLNRTLAEKMIRELLLIHFYRVEVYTCKRDDFSVKKGSP
GNLVEFEDILTSDANEIVFSNLLVSVVLSTNNRIGLCSIDVDESTIQVTEFEDSDFFMNL
EACLVVLAPKEIILPSVTKEYSKIGEILNRNRILSTVLQKADFVKSTNFLQDLAKVYRFS
KGQQKNVHLIPEVKMDLAMGALAAAFKYIGITKDESNDNKFSISNLNFNQFVRLDTAAFS
ALNLFPSSESNSRSSNYKTQSVVGVLDCCKTNQGKRLLRQWIKQPLKNINMIRQRLDVVQ
CFVENKEVQFILHNQYLNILPDVLLLTNKLLRKRGSLSDVYKIYQVVSRIPDILKLLKNL
ECNAINSLLFTPLNELKDELHKILEMVLEIIDGDALKKGLFLVRASFDDDLNEIKKNMND
IEAKMNKETKSSASKLGLEEGSTLKLDYVSHLSFFLRASRKEDQTIRKNKQFEIIDTARG
YLRFTTAKLKELNVEYNSLKASYEEHQKMIVAEICKIIVGYSLPLTNLNHCIATLDVFVS
FAHVVDNSPGSYVRPEIFSSEEKRILQIEELRHPCLECQDIDFIPNDVNFIENESELLII
TGANTCGKSTYIRSIGIAVLLAHIGMFVPCTSAKISMCDSILARIGAADDIQKNLSTFAV
EMCETAAILRTATKNSLIIIDELGRGTSTFEGLGLAWSISEHLAKNIKCFTLFATHFHEI
TTLENQLSNVKNYHLASEVKNDKLLLLFQVIRGPVLKSYGIHVADIAHLPESVVVAAKSY
LKELEANDVDKENSEKLSKIERLLKNIETDKNLDIDLLSIF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 16 | g11543.t1 | Coils | Coil | Coil | 464 | 491 | - |
| 17 | g11543.t1 | Coils | Coil | Coil | 542 | 569 | - |
| 12 | g11543.t1 | Gene3D | G3DSA:3.40.1170.10 | DNA repair protein MutS | 1 | 119 | 3.2E-22 |
| 15 | g11543.t1 | Gene3D | G3DSA:3.30.420.110 | DNA repair protein MutS | 120 | 289 | 2.4E-38 |
| 14 | g11543.t1 | Gene3D | G3DSA:1.10.1420.10 | - | 318 | 604 | 3.1E-83 |
| 13 | g11543.t1 | Gene3D | G3DSA:1.10.1420.10 | - | 464 | 546 | 3.1E-83 |
| 11 | g11543.t1 | Gene3D | G3DSA:3.40.50.300 | - | 613 | 877 | 2.5E-99 |
| 6 | g11543.t1 | PANTHER | PTHR11361 | DNA MISMATCH REPAIR PROTEIN MUTS FAMILY MEMBER | 29 | 867 | 3.4E-171 |
| 7 | g11543.t1 | PANTHER | PTHR11361:SF35 | DNA MISMATCH REPAIR PROTEIN MSH2 | 29 | 867 | 3.4E-171 |
| 18 | g11543.t1 | PIRSF | PIRSF005813 | MSH2 | 1 | 874 | 1.3E-259 |
| 2 | g11543.t1 | Pfam | PF01624 | MutS domain I | 19 | 108 | 3.5E-6 |
| 1 | g11543.t1 | Pfam | PF05188 | MutS domain II | 141 | 280 | 5.6E-16 |
| 4 | g11543.t1 | Pfam | PF05192 | MutS domain III | 298 | 602 | 4.6E-30 |
| 5 | g11543.t1 | Pfam | PF05190 | MutS family domain IV | 467 | 560 | 2.4E-15 |
| 3 | g11543.t1 | Pfam | PF00488 | MutS domain V | 658 | 845 | 2.8E-76 |
| 19 | g11543.t1 | ProSitePatterns | PS00486 | DNA mismatch repair proteins mutS family signature. | 736 | 752 | - |
| 20 | g11543.t1 | SMART | SM00533 | DNAend | 317 | 639 | 7.6E-66 |
| 21 | g11543.t1 | SMART | SM00534 | mutATP5 | 655 | 842 | 6.7E-104 |
| 8 | g11543.t1 | SUPERFAMILY | SSF53150 | DNA repair protein MutS, domain II | 140 | 306 | 2.62E-7 |
| 9 | g11543.t1 | SUPERFAMILY | SSF48334 | DNA repair protein MutS, domain III | 295 | 605 | 1.18E-60 |
| 10 | g11543.t1 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 612 | 845 | 3.72E-51 |
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 transcript has been annotated with K08735 (DNA mismatch repair protein MSH2)
Pathway
- This transcript belongs to the following pathways
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.
