General information for g10246.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Mismatch repair endonuclease PMS2.
Parent gene
- The parent gene g10246 is located on chr_1: 8519482..8520421 (+ 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 | g10246 | g10246.t1 | TSS | g10246.t1 | 8516633 | 8516633 |
| chr_1 | g10246 | g10246.t1 | isoform | g10246.t1 | 8516709 | 8519482 |
| chr_1 | g10246 | g10246.t1 | exon | g10246.t1.exon1 | 8516709 | 8516810 |
| chr_1 | g10246 | g10246.t1 | cds | g10246.t1.CDS1 | 8516709 | 8516810 |
| chr_1 | g10246 | g10246.t1 | exon | g10246.t1.exon2 | 8516867 | 8517250 |
| chr_1 | g10246 | g10246.t1 | cds | g10246.t1.CDS2 | 8516867 | 8517250 |
| chr_1 | g10246 | g10246.t1 | exon | g10246.t1.exon3 | 8517317 | 8519482 |
| chr_1 | g10246 | g10246.t1 | cds | g10246.t1.CDS3 | 8517317 | 8519482 |
| chr_1 | g10246 | g10246.t1 | TTS | g10246.t1 | 8519510 | 8519510 |
Sequences
>g10246.t1 Gene=g10246 Length=2652
ATGACAGAAGAAATAGAAAAGTTTGATGAACCTACAACAAATGAGGCATCAGAAATAAAA
CGAATTTCAAAAGACAATGTGCTTAAAATCTGTTCTGCACAGGTCATTTTAAACTTGGGT
ATAGGTGTTAAGGAATTACTTGAAAATTCTGTTGATGCTGGTGCAACAGTGATTGAAATT
AAAATAAAAGAATATGGTTTAGAAGGATTTGAAGTGGTCGACAATGGTATTGGTGTTTTA
GAGTCTGATTTTGAAGGAATAACAGCAAAGCATCATACTTCCAAACTTAAAGAATTCAAT
GATTTAGAGACAATCAAAACACTTGGATTTCGTGGTGAAGCTTTATCTGCTCTTTGTTCT
TTATCAGATGTTACTATCTTCACTCGACACAAGAGTGCTACTTTTGGAACTTTTATTGAA
TATGGTAATGATGGAAAAATAATAAATAAATCTAACAAGGCACGTAATATTGGCACTACA
GTATCGGTTAAAAATTTCTTCAAGACATTACCTGTGCGAAAAACTGAGTTCCAAAAGAAT
TACAGAAGAGAGTACAATAAAATGATACAACTATTGCAAGAATATTGCTTAGTACTGATC
GGTGTCAAGATAATTTGCACAAACCAAACAAAAAATGGAACAAAGCAAACAGTTTTAACA
ACCGCTGGACTATCAATTAATGATAATATTACATCCATTTTTGGTGTAAAGCAATCACAA
GAAATTATAAAAATGAAATTACCTACAAATGACGGCACTGAAAACGGATTTTATACTCAA
GAATCGTTATTAGACATAAGCAGCTCTATCGATTTAAAAGAAAAGGATATAGAAACACTT
AATTCGATGAAATTCAGAATTGAAGGATTTATAAGCGATATAGATCATAAATGTGGACGA
ACAACTAAAGACCGTCAATTTACTTATGTCAATTCTAGACCAGTTGAGTTAAAAACAGCA
CTTAAAACCATCAATGAAGTTTATCAGATTTATAATTTGAAACAATATCCATTTGTGTTT
ATTAATTTTATGCTAGATCAATCTTGTATTGATGTTAATTTGAGTAAAGACAAACGTCAA
GTTGCAATCGTAAATGACACTGCTGTGCAGGTAGTTCTCAAGAAAAGCCTTTTAGAAACT
TTTGGTGAATTACCGACAAAATTCAAATTATCGAGTGTCAATAGTGTGATGAAAAAGTTT
TCTAACGATTCAGAAGAAAATGAAGATTCTTCTGAAGATGAAGATGATAAAATAATGGTT
ATTGAACCCAACAGTAATTTTGCAGCAAGTTTAAAACAATGGAAAATAAGTCCACATGCT
CCATTTCCTAAAATGTCAAAAGCAACTTCATCAAAAAGAAAACTTGAAAGTTCGGAATCA
TCTCAGTTAGAAAAACTCCAAAAAATTGACTCGTTTATGTTAAAAATGCCAAACGATGAA
GATTCTTATAATGAAAATGATACTTTTGTCAACACTTCACTCGTAGAAACATCAGAAAAG
ATCTCTCTCATTGAACCTTCCACAAGTAGTGTAAATGCAAATATATCAAAAATTTTAAAT
CGCACATCGAGCATTGAATCAATTGATGAAGAATATTTATCTCACATAGGGCGAACATCA
ACACAAAAAGGAATGGATGATATTTCTTTTAATATTGATTGTAAACCTGCATCAGATCAG
AATAGCACACTGAAACTAGAAATAATTAAGCCTCAAACAAGTATTAACACTTTAACAGAA
CAGATAAATGATGAAGAGGAATCCAATAATGAGACAAATGTAAATGACACATATTCACCA
CCAAAAAATTTCAACTTAACTGATACTATTGAAAATTTAGAGTACGATACCCCAAAATTA
AATGAAACTTTTAACCATAAAATAAGCATAACACTCGATCAAATCAAGACTAATGCTCTC
GAAGAAGAAGAAATTTTTCAAAACTTGAAAAAATCGTCTGCTAATAAATCATTTAAACTG
AAATTCAAGGAAAGTTTAGATCCATCAAAAAATAAGAAAGCTGAAATGGAATTGGAGACG
GAATTGAAAAAAGATATGTTTAAAAATATGAAAGTGATTGGTCAGTTCAATCTTGGATTC
ATTATAGCAAAATTAGATGATGATCTTTTCGTTATCGATCAACATGCTACAGATGAACGA
TATAATTTTGAAATGCTAAAGAAAAGTTTAATAATTGATTCACAAAAAATGGTAAATCCA
GAACAACTTGAACTAACAGCTATTCAAGAAGACACTATTATACAAAATCTTGATATATTT
GAAATGAACGGTTTCAAATTTGAGTACAATGAACATGCTTTGCCGACAAAAAGAATCAAA
CTAATTTCAAGACCTTATTTTGAAAACTGGGAATTTGGAAAAGAAGATGTCGAAGAAATG
ATTTTCATGCTTCAGGACGCACCAAAAATACATTGTCGCCCATCAAGAATAATTAAAATG
TTAGCATCCAAAGCGTGTAGAAAATCAGTCATGATTGGTACAGCACTTGATCATAAGCAA
ATGAAAGTATTATTAGAGCATATGGGAGATATGGTTCATCCCTGGAATTGCCCTCATAAT
CGGCCCACAATAAGATTTCTTCACAATTTAAGTATGATTGATCAAACAAACGGAAAATGT
TTAAATTCTTAA
>g10246.t1 Gene=g10246 Length=883
MTEEIEKFDEPTTNEASEIKRISKDNVLKICSAQVILNLGIGVKELLENSVDAGATVIEI
KIKEYGLEGFEVVDNGIGVLESDFEGITAKHHTSKLKEFNDLETIKTLGFRGEALSALCS
LSDVTIFTRHKSATFGTFIEYGNDGKIINKSNKARNIGTTVSVKNFFKTLPVRKTEFQKN
YRREYNKMIQLLQEYCLVLIGVKIICTNQTKNGTKQTVLTTAGLSINDNITSIFGVKQSQ
EIIKMKLPTNDGTENGFYTQESLLDISSSIDLKEKDIETLNSMKFRIEGFISDIDHKCGR
TTKDRQFTYVNSRPVELKTALKTINEVYQIYNLKQYPFVFINFMLDQSCIDVNLSKDKRQ
VAIVNDTAVQVVLKKSLLETFGELPTKFKLSSVNSVMKKFSNDSEENEDSSEDEDDKIMV
IEPNSNFAASLKQWKISPHAPFPKMSKATSSKRKLESSESSQLEKLQKIDSFMLKMPNDE
DSYNENDTFVNTSLVETSEKISLIEPSTSSVNANISKILNRTSSIESIDEEYLSHIGRTS
TQKGMDDISFNIDCKPASDQNSTLKLEIIKPQTSINTLTEQINDEEESNNETNVNDTYSP
PKNFNLTDTIENLEYDTPKLNETFNHKISITLDQIKTNALEEEEIFQNLKKSSANKSFKL
KFKESLDPSKNKKAEMELETELKKDMFKNMKVIGQFNLGFIIAKLDDDLFVIDQHATDER
YNFEMLKKSLIIDSQKMVNPEQLELTAIQEDTIIQNLDIFEMNGFKFEYNEHALPTKRIK
LISRPYFENWEFGKEDVEEMIFMLQDAPKIHCRPSRIIKMLASKACRKSVMIGTALDHKQ
MKVLLEHMGDMVHPWNCPHNRPTIRFLHNLSMIDQTNGKCLNS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 14 | g10246.t1 | CDD | cd16926 | HATPase_MutL-MLH-PMS-like | 29 | 209 | 2.11113E-66 |
| 15 | g10246.t1 | CDD | cd03484 | MutL_Trans_hPMS_2_like | 225 | 382 | 1.80063E-39 |
| 13 | g10246.t1 | Coils | Coil | Coil | 575 | 595 | - |
| 11 | g10246.t1 | Gene3D | G3DSA:3.30.565.10 | - | 15 | 234 | 9.2E-67 |
| 9 | g10246.t1 | Gene3D | G3DSA:3.30.230.10 | - | 258 | 387 | 2.0E-33 |
| 12 | g10246.t1 | Gene3D | G3DSA:2.30.42.20 | - | 693 | 867 | 6.4E-37 |
| 10 | g10246.t1 | Gene3D | G3DSA:3.30.1370.100 | - | 731 | 829 | 6.4E-37 |
| 19 | g10246.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 442 | 462 | - |
| 4 | g10246.t1 | PANTHER | PTHR10073:SF52 | MISMATCH REPAIR ENDONUCLEASE PMS2-RELATED | 15 | 865 | 1.1E-195 |
| 5 | g10246.t1 | PANTHER | PTHR10073 | DNA MISMATCH REPAIR PROTEIN MLH, PMS, MUTL | 15 | 865 | 1.1E-195 |
| 1 | g10246.t1 | Pfam | PF13589 | Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase | 43 | 141 | 8.7E-10 |
| 2 | g10246.t1 | Pfam | PF01119 | DNA mismatch repair protein, C-terminal domain | 281 | 379 | 3.2E-18 |
| 3 | g10246.t1 | Pfam | PF08676 | MutL C terminal dimerisation domain | 691 | 836 | 1.4E-28 |
| 16 | g10246.t1 | ProSitePatterns | PS00058 | DNA mismatch repair proteins mutL / hexB / PMS1 signature. | 109 | 115 | - |
| 18 | g10246.t1 | SMART | SM01340 | DNA_mis_repair_2 | 230 | 382 | 7.5E-24 |
| 17 | g10246.t1 | SMART | SM00853 | MutL_C_2 | 692 | 836 | 1.2E-31 |
| 7 | g10246.t1 | SUPERFAMILY | SSF55874 | ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | 35 | 220 | 3.72E-42 |
| 6 | g10246.t1 | SUPERFAMILY | SSF54211 | Ribosomal protein S5 domain 2-like | 213 | 382 | 1.21E-25 |
| 8 | g10246.t1 | SUPERFAMILY | SSF118116 | DNA mismatch repair protein MutL | 689 | 867 | 3.14E-22 |
| 20 | g10246.t1 | TIGRFAM | TIGR00585 | mutl: DNA mismatch repair protein MutL | 18 | 361 | 8.3E-80 |
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:0032300 | mismatch repair complex | CC |
| GO:0006298 | mismatch repair | BP |
| GO:0030983 | mismatched DNA binding | MF |
| GO:0016887 | ATP hydrolysis activity | MF |
KEGG
Orthology
- This transcript has been annotated with K10858 (DNA mismatch repair protein PMS2)
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.
