Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Mismatch repair endonuclease PMS2.

Parent gene

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.t7 TSS g10246.t7 8516806 8516806
chr_1 g10246 g10246.t7 isoform g10246.t7 8517590 8518651
chr_1 g10246 g10246.t7 exon g10246.t7.exon1 8517590 8518651
chr_1 g10246 g10246.t7 cds g10246.t7.CDS1 8517677 8518651
chr_1 g10246 g10246.t7 TTS g10246.t7 8519510 8519510

Sequences

>g10246.t7 Gene=g10246 Length=1062
GAAAACGGATTTTATACTCAAGAATCGTTATTAGACATAAGCAGCTCTATCGATTTAAAA
GAAAAGGATATAGAAACACTTAATTCGATGAAATTCAGAATTGAAGGATTTATAAGCGAT
ATAGATCATAAATGTGGACGAACAACTAAAGACCGTCAATTTACTTATGTCAATTCTAGA
CCAGTTGAGTTAAAAACAGCACTTAAAACCATCAATGAAGTTTATCAGATTTATAATTTG
AAACAATATCCATTTGTGTTTATTAATTTTATGCTAGATCAATCTTGTATTGATGTTAAT
TTGAGTAAAGACAAACGTCAAGTTGCAATCGTAAATGACACTGCTGTGCAGGTAGTTCTC
AAGAAAAGCCTTTTAGAAACTTTTGGTGAATTACCGACAAAATTCAAATTATCGAGTGTC
AATAGTGTGATGAAAAAGTTTTCTAACGATTCAGAAGAAAATGAAGATTCTTCTGAAGAT
GAAGATGATAAAATAATGGTTATTGAACCCAACAGTAATTTTGCAGCAAGTTTAAAACAA
TGGAAAATAAGTCCACATGCTCCATTTCCTAAAATGTCAAAAGCAACTTCATCAAAAAGA
AAACTTGAAAGTTCGGAATCATCTCAGTTAGAAAAACTCCAAAAAATTGACTCGTTTATG
TTAAAAATGCCAAACGATGAAGATTCTTATAATGAAAATGATACTTTTGTCAACACTTCA
CTCGTAGAAACATCAGAAAAGATCTCTCTCATTGAACCTTCCACAAGTAGTGTAAATGCA
AATATATCAAAAATTTTAAATCGCACATCGAGCATTGAATCAATTGATGAAGAATATTTA
TCTCACATAGGGCGAACATCAACACAAAAAGGAATGGATGATATTTCTTTTAATATTGAT
TGTAAACCTGCATCAGATCAGAATAGCACACTGAAACTAGAAATAATTAAGCCTCAAACA
AGTATTAACACTTTAACAGAACAGATAAATGATGAAGAGGAATCCAATAATGAGACAAAT
GTAAATGACACATATTCACCACCAAAAAATTTCAACTTAACT

>g10246.t7 Gene=g10246 Length=325
MKFRIEGFISDIDHKCGRTTKDRQFTYVNSRPVELKTALKTINEVYQIYNLKQYPFVFIN
FMLDQSCIDVNLSKDKRQVAIVNDTAVQVVLKKSLLETFGELPTKFKLSSVNSVMKKFSN
DSEENEDSSEDEDDKIMVIEPNSNFAASLKQWKISPHAPFPKMSKATSSKRKLESSESSQ
LEKLQKIDSFMLKMPNDEDSYNENDTFVNTSLVETSEKISLIEPSTSSVNANISKILNRT
SSIESIDEEYLSHIGRTSTQKGMDDISFNIDCKPASDQNSTLKLEIIKPQTSINTLTEQI
NDEEESNNETNVNDTYSPPKNFNLT

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g10246.t7 CDD cd03484 MutL_Trans_hPMS_2_like 2 100 1.75561E-36
6 g10246.t7 Coils Coil Coil 293 313 -
5 g10246.t7 Gene3D G3DSA:3.30.230.10 - 1 106 6.3E-33
9 g10246.t7 MobiDBLite mobidb-lite consensus disorder prediction 160 180 -
11 g10246.t7 MobiDBLite mobidb-lite consensus disorder prediction 299 325 -
10 g10246.t7 MobiDBLite mobidb-lite consensus disorder prediction 310 325 -
2 g10246.t7 PANTHER PTHR10073:SF52 MISMATCH REPAIR ENDONUCLEASE PMS2-RELATED 3 304 7.2E-25
3 g10246.t7 PANTHER PTHR10073 DNA MISMATCH REPAIR PROTEIN MLH, PMS, MUTL 3 304 7.2E-25
1 g10246.t7 Pfam PF01119 DNA mismatch repair protein, C-terminal domain 3 97 3.8E-18
8 g10246.t7 SMART SM01340 DNA_mis_repair_2 1 100 3.8E-14
4 g10246.t7 SUPERFAMILY SSF54211 Ribosomal protein S5 domain 2-like 3 100 6.45E-23

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 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.

Raw TPM values