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.t1 TSS g11742.t1 18201033 18201033
chr_1 g11742 g11742.t1 isoform g11742.t1 18201228 18203373
chr_1 g11742 g11742.t1 exon g11742.t1.exon1 18201228 18201458
chr_1 g11742 g11742.t1 cds g11742.t1.CDS1 18201228 18201458
chr_1 g11742 g11742.t1 exon g11742.t1.exon2 18201541 18201710
chr_1 g11742 g11742.t1 cds g11742.t1.CDS2 18201541 18201710
chr_1 g11742 g11742.t1 exon g11742.t1.exon3 18201786 18203373
chr_1 g11742 g11742.t1 cds g11742.t1.CDS3 18201786 18203373
chr_1 g11742 g11742.t1 TTS g11742.t1 18203415 18203415

Sequences

>g11742.t1 Gene=g11742 Length=1989
ATGGAGCAAAAAATTGAACATAAAAGTGAAATGCAGGCTCCTCAAATAATAAAACTTGAC
GATAGTGTTATAAATCGAATTGCAGCAGGTGAAATAATACAAAATCCATCAAATTGTGTC
AAAGAATTGATAGAAAACAGTATCGATGCAAAAGCTAAACAAATTCAAGTAAATACAAAG
CAAAATGGACTTTATATTCAAATTATTGATAATGGAACCGGTATTTTAAAGGAGAACTTA
GAAATTCTAGCAGAAAGATTTACTACGAGTAAACTAAGGAAATATGAGGATCTAGAAAAA
ATGTCAACTTATGGTTTTAGAGGAGAAGCTTTAGCCTCAATTGCAGAAATAAGCAGATTA
ACTGTTCAAACTAAAACCCGGGATCAATTATTTGCATATAAAGCACAATATATTGGGGGA
AAATTAATAGAAGAACCCACAACTTTAGCTGGAAATCAAGGGACAACTATTACTATTGAT
GACTTATTTTACAATGTTCCAATGAAGACAAAAACTATGACAAATGATCAATTTTCCAAA
ATATTTGATGTTGTTTCGAAATATGCAATACACAATCATAGAATATCATTTGGATTAAAA
AAGAATGATGAGAAAAATAATGTTATTAAAACACAGCCTTCAGATACTCCAATTAATGCC
ATAAGACTTATTTTTGGAAATAATGTAGCGAATGCTCTTATTAAAGTATTTATAGAAAAC
ATAGGACTAAAGTTTAACTTACAAGGATATGTATCTAAAACAGACTTTAATGCACTGAAA
AAGGGACAATTTATACTCTTTATCAACCATCGCAATGTTGAATCAAAGTCTTTAAAGAAA
GCATTGTTTGAAGATGTGTATCGAAAAATCCTTAATGTTAGTGTCATTCCATTCATTTAT
TTGTCACTTGAAGTTGATCCAAGGTCTGTTGATGTAAACGTATCGCCAACAAAGCATGAA
GTACATTTATTAAATGAAGACTTAATTGTAGAATCTATTAAGAATGTAGTTCATGAGACA
TTGATGAAAACAAATGAAACAAAAGTAATGTATGCACAAAAACTTCTTCCTGGAGCACCT
GAAATAATTTTTGAAACCCCAAAAATTGACAAGACATATGCAAAAGATATGATTAGAGTT
GATCCAAAAGTACAATCAATAACTAAATTTTTGAAGCATAATGAGGACAATCAATCAGCT
AACAGAAGTAGTTTGCAAATAATGCCATTTTCACCTGATAGCAGTTTAAGAAAATCAAAA
AACAATTATGAACAAACCAAATTGACGTCTGTTAAGGAACTATTAGCTGATGTAGAATCA
AACTGTGATGAAAATCTTAAGAAACAGATAAGAAACCTAAAATTTGTTGGAAATATCAAT
CAATTCAAGAGTGTAATTCAATCAGGTCACTTTCTATGGTGTGTCTCAAATCGCATTTTA
GCATGGCATCTTTTTTATCAATGTGCTCTAAAAGGTTTTTCGAATTTTGATGCTATAGTA
TTTAATGAACCTCTTAAATTACGTGAATTGACAAAAATTGGTTTGTGCGTAAAAAAAAGT
GAAACCCACAAGTCGAAGGATATTCTGATTGATAAAGTTGAACGAGTATTGGTTGAAAAA
AGTGAAATGTTAAAAGAATATTTCAGAATTTCTATAAATAAGAATGGTGAATTGGAATCA
CTTCCTATGTTAATTTCAAATTATGCACCGCTAATGAGCAGTTTACCAATTTTTATAATT
AGACTTGTAACACATGTCTCATATGAAAATGAAAAGCATTGTTTTAAAAGAATTTGTGAG
GAATTGGCGAAATTTTATTCTCAGTGGTCATTAAAGATTGACGAAAAAGATTATCATCGA
TTAATGGAAGATATTATTTTTCCAAAGATACGTTCATCATTATTGCCTCCAAAGGAATTT
CTTCATGATACAACATTTATAAAATTAACAAGCTTACAAGATTTGTATAAGATTTTCGAA
AGATGTTAA

>g11742.t1 Gene=g11742 Length=662
MEQKIEHKSEMQAPQIIKLDDSVINRIAAGEIIQNPSNCVKELIENSIDAKAKQIQVNTK
QNGLYIQIIDNGTGILKENLEILAERFTTSKLRKYEDLEKMSTYGFRGEALASIAEISRL
TVQTKTRDQLFAYKAQYIGGKLIEEPTTLAGNQGTTITIDDLFYNVPMKTKTMTNDQFSK
IFDVVSKYAIHNHRISFGLKKNDEKNNVIKTQPSDTPINAIRLIFGNNVANALIKVFIEN
IGLKFNLQGYVSKTDFNALKKGQFILFINHRNVESKSLKKALFEDVYRKILNVSVIPFIY
LSLEVDPRSVDVNVSPTKHEVHLLNEDLIVESIKNVVHETLMKTNETKVMYAQKLLPGAP
EIIFETPKIDKTYAKDMIRVDPKVQSITKFLKHNEDNQSANRSSLQIMPFSPDSSLRKSK
NNYEQTKLTSVKELLADVESNCDENLKKQIRNLKFVGNINQFKSVIQSGHFLWCVSNRIL
AWHLFYQCALKGFSNFDAIVFNEPLKLRELTKIGLCVKKSETHKSKDILIDKVERVLVEK
SEMLKEYFRISINKNGELESLPMLISNYAPLMSSLPIFIIRLVTHVSYENEKHCFKRICE
ELAKFYSQWSLKIDEKDYHRLMEDIIFPKIRSSLLPPKEFLHDTTFIKLTSLQDLYKIFE
RC

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g11742.t1 CDD cd16926 HATPase_MutL-MLH-PMS-like 23 205 9.38618E-83
9 g11742.t1 Gene3D G3DSA:3.30.565.10 - 15 225 1.5E-67
8 g11742.t1 Gene3D G3DSA:3.30.230.10 - 226 354 2.9E-34
4 g11742.t1 PANTHER PTHR10073:SF12 DNA MISMATCH REPAIR PROTEIN MLH1 12 662 3.4E-173
5 g11742.t1 PANTHER PTHR10073 DNA MISMATCH REPAIR PROTEIN MLH, PMS, MUTL 12 662 3.4E-173
1 g11742.t1 Pfam PF13589 Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase 37 136 1.1E-13
2 g11742.t1 Pfam PF01119 DNA mismatch repair protein, C-terminal domain 222 341 1.4E-28
3 g11742.t1 Pfam PF16413 DNA mismatch repair protein Mlh1 C-terminus 427 662 3.7E-67
11 g11742.t1 ProSitePatterns PS00058 DNA mismatch repair proteins mutL / hexB / PMS1 signature. 105 111 -
12 g11742.t1 SMART SM01340 DNA_mis_repair_2 221 342 2.4E-34
7 g11742.t1 SUPERFAMILY SSF55874 ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase 14 227 8.25E-43
6 g11742.t1 SUPERFAMILY SSF54211 Ribosomal protein S5 domain 2-like 204 341 6.83E-29
13 g11742.t1 TIGRFAM TIGR00585 mutl: DNA mismatch repair protein MutL 15 322 6.2E-89

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

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.

Raw TPM values