Gene loci information

Transcript annotation

  • This transcript has been annotated as Double-strand break repair protein MRE11.

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_2 g8187 g8187.t1 TSS g8187.t1 28975470 28975470
chr_2 g8187 g8187.t1 isoform g8187.t1 28975551 28977884
chr_2 g8187 g8187.t1 exon g8187.t1.exon1 28975551 28975668
chr_2 g8187 g8187.t1 cds g8187.t1.CDS1 28975551 28975668
chr_2 g8187 g8187.t1 exon g8187.t1.exon2 28975757 28975880
chr_2 g8187 g8187.t1 cds g8187.t1.CDS2 28975757 28975880
chr_2 g8187 g8187.t1 exon g8187.t1.exon3 28975937 28976258
chr_2 g8187 g8187.t1 cds g8187.t1.CDS3 28975937 28976258
chr_2 g8187 g8187.t1 exon g8187.t1.exon4 28976325 28977884
chr_2 g8187 g8187.t1 cds g8187.t1.CDS4 28976325 28977884
chr_2 g8187 g8187.t1 TTS g8187.t1 28978013 28978013

Sequences

>g8187.t1 Gene=g8187 Length=2124
ATGTCAGGAGAAACTTTTGAAGATAATGCAAATGAAGGCATCGAACCTGAAAATATAATA
AAGATTCTCATTGCAACTGACATTCATTTAGGATACGATGAATCAAATGAAGAAACAGGT
AATGATTCCTTCAATACATTTGAAGAAATACTTATGCTTGCTAATAGTCGAAATGTGGAC
TTTATTCTTCTGGCTGGTGATCTGTTTCATAAAGCACAACCTTCAGCAAATTCACTCAAC
AAATGTATCCAGTTACTTCGTACATATACATTAGGACGTAAAGAGATTGAATTTGAGGTA
ACAGACATAGCAACAGGAGAACCTATGCAATTTCAAAGAAATCCCAATTTTGAAAATGAA
AGTCTTTCTGCAACTACTGCTCCAATTAATTATGAAGATGATAACATTAACGTCTCTTAT
CCTGTATTTACAATTCACGGTAACCACGATGATGTAGTTAACAGTCTTAGTGCAATCGAT
ATTCTCAGTTCAAGTGGTTTAGTTAACTATTTTGGCAAATGGGAAGATCTTTCTGAAATA
CATCTTCGTCCAATTATCATTCGTAAAAAAGCAACATCAATTGCTCTCTATGGACTAAGT
CACATTCCAGATCGTAGATTGTACAATTTACTTGAAAATGATAAAGTTTATGTTGAATAT
CCAGGTAAAGATATTGGAGAAACAGTCACTGATTATTTCAATATTCTTGCAATTCATCAA
AATCGAGTTGAACGAGGTCGTAATAATCACATTCCTGTTGATATGTTGCCTAATTTCATG
AATCTCATCGTTTGGGGACACGAACATGATTGCCGTATTCATCCTGAACAATATAGTAGA
ATGTTTGTTACGCAACCTGGCTCTTCAGTAGCAACCTCTCTATGCGAAGGTGAATCGATT
GAAAAACATGTAGGGATTTTGCAAGTTTGTTGCAATCCATTAAGTAATAACATAGCAAAA
CATCAATTTCTAATCACACCTGTTAAACTAAAAACTGTACGTCCTCTTATTTATAAATCG
ATTGATTTTAATGATTATATTGAAGAACTTGAGTTAAAAGAAAATAAAATCTCAGTTCAA
GTTGAAACTTTGCTCTCTAATTTAGTATTTGAAATGATTAGAGAAGCTAAAGAACGTCTC
ACAGGACATCCTCGTCAACCAAAAAGTCCTCTTCTACGTCTACGTGTTCAATACGATAAT
GTTGATCATCTGATCAACACACGACGCTTTGGACAACGCTTTGATGGTGTGGTTGCTAAG
AATGAAGATTTATTACTATTTAAGAAAAGTACTCGTCGAATTAGACTTGAAAAACCAAGC
ATTGATGATAAACTTTTAAAATCTACCAAAAAAGAAGATGATCTGAATAGAGTTGAAGAT
TTCGTTGATGATTATTTTGAAAAAGTTTCTGAAGACAAAGATAAACTCTCATTATTTAAT
TTCAAATGTATGAGTGATGTAGTACGTCTTCTTGTTGATAAAGATGATCAAGACGGAGCT
GAAAAAGTTCTTCAAGCTCAAGTTAATGCTGCAACGGATTATTTTTTGGAAACTTCTGAT
AATCTTGAACCCGAACAATTAATCGAATTAGCTTATTTGTATCGTGATGGAAAAAGTTTT
GTTGTACATGAAAAAACTGTTGAAAATATGATGATCCGTAAGAAAAGCTCACAAAGCATC
ACCCAAAGCAAAGATTTCATTCAGCCATCATCAACTTACAATGAGAGCAGTGAAGATGAA
AAATTATTCAAATCTAAAACACCAGTCCAATCAAAAAAGAAATTATCAGAATCTTCTCCA
TCAAGTGATTTTGAAATGGATGATGATCAAATTAATGATAGTTCTATGAAGCGGCAACAA
AATCAATCAGTTTCAACATCTAAACGAGGACGTGGTTCTCGTGGTGGAAAAAGTGCAGCA
TCTATGGCTTCTACGTCTAGAAATACAAGTACACGAAATAAATCAACTGCTTCTACAGCT
AAAAAAGGAAAAGCCAAGAATGATCAACCATCAATTGCGTCACAAATATCTCAGCTTCGA
GCAACCCGTAGCAAAGGACCCGCTGCGACATCTACACAAAAGCATTCTTTTCAATTTGTT
GTTTCATCATCTGATGATGAATAA

>g8187.t1 Gene=g8187 Length=707
MSGETFEDNANEGIEPENIIKILIATDIHLGYDESNEETGNDSFNTFEEILMLANSRNVD
FILLAGDLFHKAQPSANSLNKCIQLLRTYTLGRKEIEFEVTDIATGEPMQFQRNPNFENE
SLSATTAPINYEDDNINVSYPVFTIHGNHDDVVNSLSAIDILSSSGLVNYFGKWEDLSEI
HLRPIIIRKKATSIALYGLSHIPDRRLYNLLENDKVYVEYPGKDIGETVTDYFNILAIHQ
NRVERGRNNHIPVDMLPNFMNLIVWGHEHDCRIHPEQYSRMFVTQPGSSVATSLCEGESI
EKHVGILQVCCNPLSNNIAKHQFLITPVKLKTVRPLIYKSIDFNDYIEELELKENKISVQ
VETLLSNLVFEMIREAKERLTGHPRQPKSPLLRLRVQYDNVDHLINTRRFGQRFDGVVAK
NEDLLLFKKSTRRIRLEKPSIDDKLLKSTKKEDDLNRVEDFVDDYFEKVSEDKDKLSLFN
FKCMSDVVRLLVDKDDQDGAEKVLQAQVNAATDYFLETSDNLEPEQLIELAYLYRDGKSF
VVHEKTVENMMIRKKSSQSITQSKDFIQPSSTYNESSEDEKLFKSKTPVQSKKKLSESSP
SSDFEMDDDQINDSSMKRQQNQSVSTSKRGRGSRGGKSAASMASTSRNTSTRNKSTASTA
KKGKAKNDQPSIASQISQLRATRSKGPAATSTQKHSFQFVVSSSDDE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g8187.t1 CDD cd00840 MPP_Mre11_N 21 295 6.78036E-45
5 g8187.t1 Gene3D G3DSA:3.60.21.10 - 8 334 3.0E-114
6 g8187.t1 Gene3D G3DSA:3.30.110.110 - 336 438 3.4E-19
10 g8187.t1 MobiDBLite mobidb-lite consensus disorder prediction 558 707 -
11 g8187.t1 MobiDBLite mobidb-lite consensus disorder prediction 558 576 -
12 g8187.t1 MobiDBLite mobidb-lite consensus disorder prediction 577 591 -
13 g8187.t1 MobiDBLite mobidb-lite consensus disorder prediction 615 707 -
3 g8187.t1 PANTHER PTHR10139 DOUBLE-STRAND BREAK REPAIR PROTEIN MRE11 17 685 1.6E-146
7 g8187.t1 PIRSF PIRSF000882 DSB_repair_MRE11 5 706 4.5E-169
2 g8187.t1 Pfam PF00149 Calcineurin-like phosphoesterase 20 270 1.2E-11
1 g8187.t1 Pfam PF04152 Mre11 DNA-binding presumed domain 323 488 1.4E-28
9 g8187.t1 SMART SM01347 Mre11_DNA_bind_2 323 491 5.2E-37
4 g8187.t1 SUPERFAMILY SSF56300 Metallo-dependent phosphatases 20 380 2.28E-46

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:0006302 double-strand break repair BP
GO:0008408 3’-5’ exonuclease activity MF
GO:0005634 nucleus CC
GO:0016787 hydrolase activity MF
GO:0030870 Mre11 complex CC
GO:0004519 endonuclease activity MF
GO:0030145 manganese ion binding 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