Gene loci information

Transcript annotation

  • This transcript has been annotated as DNA mismatch repair protein Mlh1.

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 g11742 g11742.t2 TSS g11742.t2 18201033 18201033
chr_1 g11742 g11742.t2 isoform g11742.t2 18201228 18203373
chr_1 g11742 g11742.t2 exon g11742.t2.exon1 18201228 18201710
chr_1 g11742 g11742.t2 cds g11742.t2.CDS1 18201610 18201710
chr_1 g11742 g11742.t2 exon g11742.t2.exon2 18201786 18203373
chr_1 g11742 g11742.t2 cds g11742.t2.CDS2 18201786 18203373
chr_1 g11742 g11742.t2 TTS g11742.t2 18203415 18203415

Sequences

>g11742.t2 Gene=g11742 Length=2071
ATGGAGCAAAAAATTGAACATAAAAGTGAAATGCAGGCTCCTCAAATAATAAAACTTGAC
GATAGTGTTATAAATCGAATTGCAGCAGGTGAAATAATACAAAATCCATCAAATTGTGTC
AAAGAATTGATAGAAAACAGTATCGATGCAAAAGCTAAACAAATTCAAGTAAATACAAAG
CAAAATGGACTTTATATTCAAATTATTGATAATGGAACCGGTATTTTAAAGGTAATGATA
TAAAATAATGATTTAAATACTAGGATTTTGATATCATATTTTAAACATTTTTTTTTTTCC
ATATAATTTAAAGGAGAACTTAGAAATTCTAGCAGAAAGATTTACTACGAGTAAACTAAG
GAAATATGAGGATCTAGAAAAAATGTCAACTTATGGTTTTAGAGGAGAAGCTTTAGCCTC
AATTGCAGAAATAAGCAGATTAACTGTTCAAACTAAAACCCGGGATCAATTATTTGCATA
TAAAGCACAATATATTGGGGGAAAATTAATAGAAGAACCCACAACTTTAGCTGGAAATCA
AGGGACAACTATTACTATTGATGACTTATTTTACAATGTTCCAATGAAGACAAAAACTAT
GACAAATGATCAATTTTCCAAAATATTTGATGTTGTTTCGAAATATGCAATACACAATCA
TAGAATATCATTTGGATTAAAAAAGAATGATGAGAAAAATAATGTTATTAAAACACAGCC
TTCAGATACTCCAATTAATGCCATAAGACTTATTTTTGGAAATAATGTAGCGAATGCTCT
TATTAAAGTATTTATAGAAAACATAGGACTAAAGTTTAACTTACAAGGATATGTATCTAA
AACAGACTTTAATGCACTGAAAAAGGGACAATTTATACTCTTTATCAACCATCGCAATGT
TGAATCAAAGTCTTTAAAGAAAGCATTGTTTGAAGATGTGTATCGAAAAATCCTTAATGT
TAGTGTCATTCCATTCATTTATTTGTCACTTGAAGTTGATCCAAGGTCTGTTGATGTAAA
CGTATCGCCAACAAAGCATGAAGTACATTTATTAAATGAAGACTTAATTGTAGAATCTAT
TAAGAATGTAGTTCATGAGACATTGATGAAAACAAATGAAACAAAAGTAATGTATGCACA
AAAACTTCTTCCTGGAGCACCTGAAATAATTTTTGAAACCCCAAAAATTGACAAGACATA
TGCAAAAGATATGATTAGAGTTGATCCAAAAGTACAATCAATAACTAAATTTTTGAAGCA
TAATGAGGACAATCAATCAGCTAACAGAAGTAGTTTGCAAATAATGCCATTTTCACCTGA
TAGCAGTTTAAGAAAATCAAAAAACAATTATGAACAAACCAAATTGACGTCTGTTAAGGA
ACTATTAGCTGATGTAGAATCAAACTGTGATGAAAATCTTAAGAAACAGATAAGAAACCT
AAAATTTGTTGGAAATATCAATCAATTCAAGAGTGTAATTCAATCAGGTCACTTTCTATG
GTGTGTCTCAAATCGCATTTTAGCATGGCATCTTTTTTATCAATGTGCTCTAAAAGGTTT
TTCGAATTTTGATGCTATAGTATTTAATGAACCTCTTAAATTACGTGAATTGACAAAAAT
TGGTTTGTGCGTAAAAAAAAGTGAAACCCACAAGTCGAAGGATATTCTGATTGATAAAGT
TGAACGAGTATTGGTTGAAAAAAGTGAAATGTTAAAAGAATATTTCAGAATTTCTATAAA
TAAGAATGGTGAATTGGAATCACTTCCTATGTTAATTTCAAATTATGCACCGCTAATGAG
CAGTTTACCAATTTTTATAATTAGACTTGTAACACATGTCTCATATGAAAATGAAAAGCA
TTGTTTTAAAAGAATTTGTGAGGAATTGGCGAAATTTTATTCTCAGTGGTCATTAAAGAT
TGACGAAAAAGATTATCATCGATTAATGGAAGATATTATTTTTCCAAAGATACGTTCATC
ATTATTGCCTCCAAAGGAATTTCTTCATGATACAACATTTATAAAATTAACAAGCTTACA
AGATTTGTATAAGATTTTCGAAAGATGTTAA

>g11742.t2 Gene=g11742 Length=562
MSTYGFRGEALASIAEISRLTVQTKTRDQLFAYKAQYIGGKLIEEPTTLAGNQGTTITID
DLFYNVPMKTKTMTNDQFSKIFDVVSKYAIHNHRISFGLKKNDEKNNVIKTQPSDTPINA
IRLIFGNNVANALIKVFIENIGLKFNLQGYVSKTDFNALKKGQFILFINHRNVESKSLKK
ALFEDVYRKILNVSVIPFIYLSLEVDPRSVDVNVSPTKHEVHLLNEDLIVESIKNVVHET
LMKTNETKVMYAQKLLPGAPEIIFETPKIDKTYAKDMIRVDPKVQSITKFLKHNEDNQSA
NRSSLQIMPFSPDSSLRKSKNNYEQTKLTSVKELLADVESNCDENLKKQIRNLKFVGNIN
QFKSVIQSGHFLWCVSNRILAWHLFYQCALKGFSNFDAIVFNEPLKLRELTKIGLCVKKS
ETHKSKDILIDKVERVLVEKSEMLKEYFRISINKNGELESLPMLISNYAPLMSSLPIFII
RLVTHVSYENEKHCFKRICEELAKFYSQWSLKIDEKDYHRLMEDIIFPKIRSSLLPPKEF
LHDTTFIKLTSLQDLYKIFERC

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g11742.t2 Gene3D G3DSA:3.30.565.10 - 1 125 2.5E-29
9 g11742.t2 Gene3D G3DSA:3.30.230.10 - 126 254 2.2E-34
3 g11742.t2 PANTHER PTHR10073:SF12 DNA MISMATCH REPAIR PROTEIN MLH1 2 562 3.4E-132
4 g11742.t2 PANTHER PTHR10073 DNA MISMATCH REPAIR PROTEIN MLH, PMS, MUTL 2 562 3.4E-132
1 g11742.t2 Pfam PF01119 DNA mismatch repair protein, C-terminal domain 122 241 1.1E-28
2 g11742.t2 Pfam PF16413 DNA mismatch repair protein Mlh1 C-terminus 327 562 2.5E-67
8 g11742.t2 ProSitePatterns PS00058 DNA mismatch repair proteins mutL / hexB / PMS1 signature. 5 11 -
7 g11742.t2 SMART SM01340 DNA_mis_repair_2 121 242 2.4E-34
6 g11742.t2 SUPERFAMILY SSF55874 ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase 3 108 6.77E-17
5 g11742.t2 SUPERFAMILY SSF54211 Ribosomal protein S5 domain 2-like 104 241 4.93E-29

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. There were no conditions that were differentially expressed