General information for g17418.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Double-strand break repair protein MRE11.
Parent gene
- The parent gene g17418 is located on chr_4: 13459790..13462243 (+ 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_4 | g17418 | g17418.t1 | TSS | g17418.t1 | 13459725 | 13459725 |
| chr_4 | g17418 | g17418.t1 | isoform | g17418.t1 | 13459790 | 13462243 |
| chr_4 | g17418 | g17418.t1 | exon | g17418.t1.exon1 | 13459790 | 13459910 |
| chr_4 | g17418 | g17418.t1 | cds | g17418.t1.CDS1 | 13459790 | 13459910 |
| chr_4 | g17418 | g17418.t1 | exon | g17418.t1.exon2 | 13459967 | 13460090 |
| chr_4 | g17418 | g17418.t1 | cds | g17418.t1.CDS2 | 13459967 | 13460090 |
| chr_4 | g17418 | g17418.t1 | exon | g17418.t1.exon3 | 13460174 | 13460492 |
| chr_4 | g17418 | g17418.t1 | cds | g17418.t1.CDS3 | 13460174 | 13460492 |
| chr_4 | g17418 | g17418.t1 | exon | g17418.t1.exon4 | 13461054 | 13461408 |
| chr_4 | g17418 | g17418.t1 | cds | g17418.t1.CDS4 | 13461054 | 13461408 |
| chr_4 | g17418 | g17418.t1 | exon | g17418.t1.exon5 | 13461456 | 13462243 |
| chr_4 | g17418 | g17418.t1 | cds | g17418.t1.CDS5 | 13461456 | 13462243 |
| chr_4 | g17418 | g17418.t1 | TTS | g17418.t1 | 13462454 | 13462454 |
Sequences
>g17418.t1 Gene=g17418 Length=1707
ATGTCTGAAGGAGAAACTTATCATGACAATCCATCTACAGACCAAGATGAAGAAAGCAAA
ATAAAGATTCTCATTGCAAGTGATATTCATCTGGGATATGATGAATTAAATCAAGAAACA
GGCAATGATTCTTTTAAAACATTTGAAGAAATTCTTATGATTGCAAATAGTCAAGATGTA
GATTTTATTCTATTGGCTGGTGATTTGTTTCATAAAGCACAACCATCAACTAATTCACTC
AATAGATGCATTCAATTACTTCGTACACACTCTCTTGGTAATAAAGAAATTCAATTTGAA
GTAAAAGATTCAAAAACAGGAGAAATAATGCAATTTCAAGTAATCACGAATGAAAATAAA
TCTGAAGAAAATTATAATTTTCCAATCAATATTGATGATGATAACATTAAAGTTTCTCAT
CCTGTCTTTGCAATTCATGGCTGTCATGATGATGTTGTTAATAATCTCAGTGCAATTGAT
GTTCTCAATTCAAGTGGTTTAGTCAATTATTTTGGAAAATGGAAAGATTTTTGTGAAGTT
AATTTGGAACCATTCATTATTTGTAAAGACAAAATAAAAATTGCTCTCTACGGCCTCAGT
CATATTCCAGATCGTAAACTTTTCGATTTATTTGCAAACGACAAAGTCAACGTAAAATTT
CCAGATCAAGTCAATGATTTTTACAACATTCTAACAATTCATCAAAATCGAATTGAAAAA
GGTAAAAATAATTTCATTCCGGTTGATATGCTGCCAAAATTTATGAATTTAATTATTTGG
GGACATGAACATGAATGTAAAATTGATATTGAACAATGCAATGACAAAATGTTTATTACA
CAACCTGGATCATCAATTGCAACATCTTTGAATCAAAGTGAAGCTGTTAGAAAGCATGTT
GGAATTTTAGAAATTAACATTCGTCCTTTAATTTACAAATCGATTGAATTAAATTATGAT
GATGAAAATGTTGAAGAATTTTTGACTAATTCAGTAATTGAAATGATTAATGAAGCTAAA
GAGCTTCTTACAGGACACTCTCATCAACCAACTAAACCACTGATTCGTTTGCGTGTTCAA
TATGTAAATCCCGATCATCTTATCAATACACGACGATTTGGACAAAAATTTGACGAATTA
ATCGCCAAGAGTGAAGAAATATTGCAATTTAGAAAAGCAAGTCGTAGAAATAGACAGGAA
AAATTAAGAATCGATGAAAATATTCTTAGAAATTCAAAAATTGATGACGACAATAATCGA
GTTGAAGATTCAGTTGATGAATATTTTGAAAAAGATAAAAATAAACTTTCATTATTTAAT
TTCAAATGCTTGAGTGATGTTGTTCGTTTGCTTGTTGATAAAGATGATCAAGATGGTGCT
GAAAAAGTAATTCAAGCTCAAATTAATGCTGCTACTGAATATTTTATAGAAAAACTTGGT
GATGAAGAATCAATTAATATTGCTCATGAATTTCGTGAAAATAAAAGTTTTGATGTGCAT
GAAAAGATTTTTGAAAGTTTGAAAGTTCCAAAAAAGAATTCTAAAACTGCACAAAATGAA
GATTCTGATAGTGATGAAGACAGTGATGTTGTTATGATTGATGGTGATAAAATCAAAAAT
CGAAGTTTATTAAAACGACCACAAGATAAACCTGGAACTTCTTCTGCTTCTAAACGAGGT
CGTGGATCATCAAATAACAAAAGATGA
>g17418.t1 Gene=g17418 Length=568
MSEGETYHDNPSTDQDEESKIKILIASDIHLGYDELNQETGNDSFKTFEEILMIANSQDV
DFILLAGDLFHKAQPSTNSLNRCIQLLRTHSLGNKEIQFEVKDSKTGEIMQFQVITNENK
SEENYNFPINIDDDNIKVSHPVFAIHGCHDDVVNNLSAIDVLNSSGLVNYFGKWKDFCEV
NLEPFIICKDKIKIALYGLSHIPDRKLFDLFANDKVNVKFPDQVNDFYNILTIHQNRIEK
GKNNFIPVDMLPKFMNLIIWGHEHECKIDIEQCNDKMFITQPGSSIATSLNQSEAVRKHV
GILEINIRPLIYKSIELNYDDENVEEFLTNSVIEMINEAKELLTGHSHQPTKPLIRLRVQ
YVNPDHLINTRRFGQKFDELIAKSEEILQFRKASRRNRQEKLRIDENILRNSKIDDDNNR
VEDSVDEYFEKDKNKLSLFNFKCLSDVVRLLVDKDDQDGAEKVIQAQINAATEYFIEKLG
DEESINIAHEFRENKSFDVHEKIFESLKVPKKNSKTAQNEDSDSDEDSDVVMIDGDKIKN
RSLLKRPQDKPGTSSASKRGRGSSNNKR
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g17418.t1 | CDD | cd00840 | MPP_Mre11_N | 22 | 291 | 3.68193E-41 |
| 5 | g17418.t1 | Gene3D | G3DSA:3.60.21.10 | - | 9 | 314 | 1.3E-103 |
| 6 | g17418.t1 | Gene3D | G3DSA:3.30.110.110 | - | 315 | 402 | 4.4E-19 |
| 10 | g17418.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 510 | 568 | - |
| 12 | g17418.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 531 | 546 | - |
| 11 | g17418.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 547 | 561 | - |
| 3 | g17418.t1 | PANTHER | PTHR10139 | DOUBLE-STRAND BREAK REPAIR PROTEIN MRE11 | 16 | 566 | 1.7E-124 |
| 7 | g17418.t1 | PIRSF | PIRSF000882 | DSB_repair_MRE11 | 8 | 568 | 6.8E-140 |
| 2 | g17418.t1 | Pfam | PF00149 | Calcineurin-like phosphoesterase | 21 | 266 | 4.6E-9 |
| 1 | g17418.t1 | Pfam | PF04152 | Mre11 DNA-binding presumed domain | 307 | 448 | 2.8E-23 |
| 9 | g17418.t1 | SMART | SM01347 | Mre11_DNA_bind_2 | 300 | 451 | 2.2E-23 |
| 4 | g17418.t1 | SUPERFAMILY | SSF56300 | Metallo-dependent phosphatases | 21 | 345 | 1.05E-38 |
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
- This transcript has been annotated with K10865 (double-strand break repair protein MRE11)
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.
