General information for g1177.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Probable DNA mismatch repair protein Msh6.
Parent gene
- The parent gene g1177 is located on chr_3: 8496442..8497740 (+ 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 | g1177 | g1177.t1 | isoform | g1177.t1 | 8492761 | 8496442 |
| chr_3 | g1177 | g1177.t1 | exon | g1177.t1.exon1 | 8492761 | 8492929 |
| chr_3 | g1177 | g1177.t1 | cds | g1177.t1.CDS1 | 8492761 | 8492929 |
| chr_3 | g1177 | g1177.t1 | exon | g1177.t1.exon2 | 8492995 | 8493504 |
| chr_3 | g1177 | g1177.t1 | cds | g1177.t1.CDS2 | 8492995 | 8493504 |
| chr_3 | g1177 | g1177.t1 | exon | g1177.t1.exon3 | 8493559 | 8493692 |
| chr_3 | g1177 | g1177.t1 | cds | g1177.t1.CDS3 | 8493559 | 8493692 |
| chr_3 | g1177 | g1177.t1 | exon | g1177.t1.exon4 | 8493756 | 8496269 |
| chr_3 | g1177 | g1177.t1 | cds | g1177.t1.CDS4 | 8493756 | 8496269 |
| chr_3 | g1177 | g1177.t1 | exon | g1177.t1.exon5 | 8496323 | 8496442 |
| chr_3 | g1177 | g1177.t1 | cds | g1177.t1.CDS5 | 8496323 | 8496442 |
| chr_3 | g1177 | g1177.t1 | TSS | g1177.t1 | NA | NA |
| chr_3 | g1177 | g1177.t1 | TTS | g1177.t1 | NA | NA |
Sequences
>g1177.t1 Gene=g1177 Length=3447
ATGTCGCAAAAATTTAAAGCATCACCAAAACCGTCACCTAAGAATACATTGTTTAATTAT
TTCTCAAAAAATCCAGGAAACACACCACAAAGTCAAAATTCAGCAGAGGAAATTAATGTT
TCTAAAAAAGATAATGAACAAAAATTGAGCGCTAAAAAACTTGAATTTGGAAAAAGGCCA
ACTTCCATACAAGATTCAAGTGACGAAGATGAAATCAAATTGACTACTAGTTCAAAGAAA
CGCAAAGTTATTGAATCCGATGAAGACGACAATACAGAAAATACTGATTCAAATTTAAAT
TCACCAAAGAAAACTACTTCTGCTATTAAAAAACGTCCAATAATTGAATCTGATGAAGAA
ACTGAAAAGAAAAATCAAAATACAAGTAAGTCTGCCTCTAAATTAGCAAAATTTACCGAA
ACTTACAGCAGTTCCAATGAAGAAAAAGTTCAAGATGATAAAGTGTTAAAAACTTTAAGT
ATAAAGAATGATGATGATGATGAAGACTCATGTGATGGTGTTGGTATTGAGAATGAAGCA
AAAGTATGGGCACATGAGAAGTTAGAATTCTTAAAACCAGAAAATATTCGTGATGCAAAC
AAGAACAGACCAAATCACCCAGATTATGATCCAAGAACTCTTTATGTACCTCCTGAATTT
CTTAAAAATCAAACTCCTGGACATTTACAATGGTGGACACTCAAGTCATTATATTTTGAT
TGTGTGTTCTTTTTCAAAGTTGGAAAATTTTATGAACTTTACCATCAAGATGCAGTGATT
GGAGTAAAAGAATTAGGATTCACATTCATGAAGGGAGATTTCGCGCACTCGGGTTTTCCT
GAAAGTGCTTATGACAAAATGGCAAGTACATTAGTTGATAAAGGATATAAAGTGGCTAGA
ATTGAACAAACAGAGACACCTGCTATGATGGAAAAGAGATGTGAGAGAGAAAACAAGAGA
AGTAAATTTGACAAAGTTGTAAAACGTGAAGTATGTCAAATAACAAATTTGGGTACACAA
ATTTATTCTACTGGTCAATCTTCAATGTCTATGGGACAAATTTCATCTGATGCCAATTAT
TTGCTCTCAATAACTGAAGCAAAAGAATCGTCTACTGTGAAACGTTTTGGGATAGCTTTT
GTTGAAACAACTCTCGGAAATTTCACAATCGGTGAATTTGATGACGATCAGCAATGTTCA
AGATTACTCACTCTTCTTTCACTTTATACTCCTGTTGTTGTGCTTCACGAAAAAACAGAA
CTTAGTGAATTTACAGCTAAAATTATCAAAAATATCAATGCACAAAAGGAGAAATTGATA
AATGAAAAACAATTTTGGAGTGGAAAGAAGGCGCTTCAATTTCTGGCAGAAAATATATAC
GATAACAATTTCGATAAATTTCCAGATGTATTAAAAGAAATGCAAAGTGGTGATTTTCAA
CCAGCGCCAAATGGTTTATTAGCTTTGAAAGCATTAGGTGGTTGTTTATGGTATTTGAAT
CATAATTTATTAGATCAGCATGTACTTTCACTTGCAACTTTCAACAAATATACACCACCT
GATGAAATAATTGAAGCAGACGCATCAAAAATTAGTAAAGATAAGAAAAGACATCCTAAA
CATATGATGCTCGATGCGATTACACTCCGAAATCTTAACATTAATGGTAAAGAAGGCTCT
CTTTTTATGAAACTCGATTACTGTTGTACTCAATTTGGTAAACGTCTTTTGATGGAATTT
TTATGTAATCCAAGTTGTGACATTCATGAAATTCGTTCACGACAGGAGGCAGTGAATGAA
TTATCTCTGAATACTGAACTTCTTACTGATTGTCGTGCTCTTCTTTCTACGTTAAATATT
GATCTTGAACGAAGTATTGCACAAATTCATCAACTTGGCAATAAGAAAGTTATGAAGAAT
CATCCAAGCTCTCGAGCGATTCTTTATGAAGCAGAAACTTATGGTAAAAATAAGATAACT
GATTTTGTTGCTGCACTTAATGCTCTCGAACAATTGATGAATATTCCAAAAATTTTCGAA
GATTGTAATTCACACTTGTTACGATTATTAACTCAAACTAATACAAATGGTGGCGAATTC
ATAGACATGTCTGAAAATATTGAGAAATTTAAAAAGTCTTTTGATATTGATCATGCAAAA
AAGACTGGCTATATAATACCAGGCAGAAATGTAGATGATGAATACGATGAAGTTTTGAAT
GAAATAGATGAGCTTGAGGCTGAAATCAAGAATTACTTGAAGCAGCAAGAAAAAATTATT
GGCACAAAACTTGTCTATTTTGGATCTGATAGAAAACGATATCAAATTGAAGTACCAGAA
AGTTATTGCAAAAAAGTTCCGAGCGATTTTACAATGGAGAGTTCAAAAGGAAAAGGAAAG
AATGCTGTCGTACGTTATACAAGTGAAGAAACAAAAGATTTTTTGAGACGCATGCAAGAA
TTGGAGGATAAGAAAAAGCATGTGTTGGATGATTTTGGAAGAAAAACTTTTGAAAAATTC
TCTAATGATTATTTCAAATACAAAAAGATTGTCAATTTAGTTGCAAAACTAGATGTTATT
GCATCACTTGCTGAATATTCTAGAAATCTCTCATCATCCTGTGTTCCCGAATGTTTTGAC
ATTACAGATAAGCCTGGTGAAAGTTTCTTAATTATTGAAAATGGTTTGCATCCTCTTATG
AGTGCAAATGATTATATACCAAATAGTATTAACACTGGCATGTATTCTAAATGCTTTTTT
GAGCTAATTACCGGATCTAATATGTCCGGCAAATCCACTTTAATGAGACAAGTTGCTTTA
CTCAGTGTATTAGCTCAAATTGGATCGTTAGTTCCAGCCGAATCAATGAAATTTACATTA
ATTGATCGCATATTTACACGATTAGGTGCAAATGATAACATCATGGAAAATCAAAGTACA
TTCCTTGTTGAATTAAATGAAACAGCTATTATTTTAAAGCATTGTACATTCAACAGTCTT
GTAATTTTGGACGAATTAGGAAGAGGAACGAGTACATATGATGGCACGGCAATTGCTAGA
GCAGTTTGTGATTTTTTGGCAGAAAAGAAATGTCGTTCACTCTTTTCAACACATTATCAT
AGTTTAGTAGAAGATTTTCAAGATGATGAACGCATTCACTTAGGTCATATGGCATGTGTC
GTAGAAAATGAAAATTCTGAAGACATTATTAAGGAAAATGTAACATTTTTATACAAATAT
ATTTCTGGAAGTAGTTCACGTTCATTTGGATTCAATGCTGCTAAACTTGCCGGCATCGAT
CATGATATTATTCGTCGAGCATTTGAAGTTTCGAAAAAAGTTGAAGCAGAGAGCCTTAAG
CTTCGCATAAAATCAAAAATTTTACTTGGCGCAAAAGACGATGAAATTAAAAAGCTCATT
GTTAAGTTCAAAAAATGTTTATCTTAA
>g1177.t1 Gene=g1177 Length=1148
MSQKFKASPKPSPKNTLFNYFSKNPGNTPQSQNSAEEINVSKKDNEQKLSAKKLEFGKRP
TSIQDSSDEDEIKLTTSSKKRKVIESDEDDNTENTDSNLNSPKKTTSAIKKRPIIESDEE
TEKKNQNTSKSASKLAKFTETYSSSNEEKVQDDKVLKTLSIKNDDDDEDSCDGVGIENEA
KVWAHEKLEFLKPENIRDANKNRPNHPDYDPRTLYVPPEFLKNQTPGHLQWWTLKSLYFD
CVFFFKVGKFYELYHQDAVIGVKELGFTFMKGDFAHSGFPESAYDKMASTLVDKGYKVAR
IEQTETPAMMEKRCERENKRSKFDKVVKREVCQITNLGTQIYSTGQSSMSMGQISSDANY
LLSITEAKESSTVKRFGIAFVETTLGNFTIGEFDDDQQCSRLLTLLSLYTPVVVLHEKTE
LSEFTAKIIKNINAQKEKLINEKQFWSGKKALQFLAENIYDNNFDKFPDVLKEMQSGDFQ
PAPNGLLALKALGGCLWYLNHNLLDQHVLSLATFNKYTPPDEIIEADASKISKDKKRHPK
HMMLDAITLRNLNINGKEGSLFMKLDYCCTQFGKRLLMEFLCNPSCDIHEIRSRQEAVNE
LSLNTELLTDCRALLSTLNIDLERSIAQIHQLGNKKVMKNHPSSRAILYEAETYGKNKIT
DFVAALNALEQLMNIPKIFEDCNSHLLRLLTQTNTNGGEFIDMSENIEKFKKSFDIDHAK
KTGYIIPGRNVDDEYDEVLNEIDELEAEIKNYLKQQEKIIGTKLVYFGSDRKRYQIEVPE
SYCKKVPSDFTMESSKGKGKNAVVRYTSEETKDFLRRMQELEDKKKHVLDDFGRKTFEKF
SNDYFKYKKIVNLVAKLDVIASLAEYSRNLSSSCVPECFDITDKPGESFLIIENGLHPLM
SANDYIPNSINTGMYSKCFFELITGSNMSGKSTLMRQVALLSVLAQIGSLVPAESMKFTL
IDRIFTRLGANDNIMENQSTFLVELNETAIILKHCTFNSLVILDELGRGTSTYDGTAIAR
AVCDFLAEKKCRSLFSTHYHSLVEDFQDDERIHLGHMACVVENENSEDIIKENVTFLYKY
ISGSSSRSFGFNAAKLAGIDHDIIRRAFEVSKKVEAESLKLRIKSKILLGAKDDEIKKLI
VKFKKCLS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 17 | g1177.t1 | Coils | Coil | Coil | 429 | 449 | - |
| 18 | g1177.t1 | Coils | Coil | Coil | 728 | 762 | - |
| 13 | g1177.t1 | Gene3D | G3DSA:3.40.1170.10 | DNA repair protein MutS | 180 | 348 | 4.2E-67 |
| 16 | g1177.t1 | Gene3D | G3DSA:3.30.420.110 | DNA repair protein MutS | 358 | 537 | 9.1E-46 |
| 15 | g1177.t1 | Gene3D | G3DSA:1.10.1420.10 | - | 542 | 864 | 6.9E-88 |
| 14 | g1177.t1 | Gene3D | G3DSA:1.10.1420.10 | - | 706 | 840 | 6.9E-88 |
| 12 | g1177.t1 | Gene3D | G3DSA:3.40.50.300 | - | 872 | 1125 | 1.5E-90 |
| 26 | g1177.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 149 | - |
| 27 | g1177.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 38 | - |
| 25 | g1177.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 39 | 88 | - |
| 24 | g1177.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 109 | 127 | - |
| 23 | g1177.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 128 | 145 | - |
| 6 | g1177.t1 | PANTHER | PTHR11361:SF34 | DNA MISMATCH REPAIR PROTEIN MSH6 | 130 | 1126 | 8.7E-272 |
| 7 | g1177.t1 | PANTHER | PTHR11361 | DNA MISMATCH REPAIR PROTEIN MUTS FAMILY MEMBER | 130 | 1126 | 8.7E-272 |
| 19 | g1177.t1 | PIRSF | PIRSF037677 | Msh6 | 4 | 1145 | 0.0 |
| 2 | g1177.t1 | Pfam | PF01624 | MutS domain I | 225 | 342 | 4.5E-30 |
| 1 | g1177.t1 | Pfam | PF05188 | MutS domain II | 359 | 505 | 7.0E-7 |
| 4 | g1177.t1 | Pfam | PF05192 | MutS domain III | 548 | 864 | 5.9E-27 |
| 5 | g1177.t1 | Pfam | PF05190 | MutS family domain IV | 730 | 823 | 2.7E-14 |
| 3 | g1177.t1 | Pfam | PF00488 | MutS domain V | 922 | 1114 | 9.0E-66 |
| 20 | g1177.t1 | ProSitePatterns | PS00486 | DNA mismatch repair proteins mutS family signature. | 999 | 1015 | - |
| 21 | g1177.t1 | SMART | SM00533 | DNAend | 556 | 903 | 4.3E-38 |
| 22 | g1177.t1 | SMART | SM00534 | mutATP5 | 918 | 1112 | 8.0E-101 |
| 8 | g1177.t1 | SUPERFAMILY | SSF55271 | DNA repair protein MutS, domain I | 213 | 339 | 1.05E-31 |
| 9 | g1177.t1 | SUPERFAMILY | SSF53150 | DNA repair protein MutS, domain II | 356 | 505 | 6.15E-6 |
| 10 | g1177.t1 | SUPERFAMILY | SSF48334 | DNA repair protein MutS, domain III | 556 | 869 | 1.19E-51 |
| 11 | g1177.t1 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 886 | 1115 | 3.86E-47 |
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:0006298 | mismatch repair | BP |
| GO:0030983 | mismatched DNA binding | MF |
KEGG
Orthology
- This transcript has been annotated with K08737 (DNA mismatch repair protein MSH6)
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.
