General information for g17418.t4
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.t4 | TSS | g17418.t4 | 13459725 | 13459725 |
| chr_4 | g17418 | g17418.t4 | isoform | g17418.t4 | 13459790 | 13462243 |
| chr_4 | g17418 | g17418.t4 | exon | g17418.t4.exon1 | 13459790 | 13459910 |
| chr_4 | g17418 | g17418.t4 | cds | g17418.t4.CDS1 | 13459790 | 13459910 |
| chr_4 | g17418 | g17418.t4 | exon | g17418.t4.exon2 | 13459967 | 13460090 |
| chr_4 | g17418 | g17418.t4 | cds | g17418.t4.CDS2 | 13459967 | 13460090 |
| chr_4 | g17418 | g17418.t4 | exon | g17418.t4.exon3 | 13460174 | 13460492 |
| chr_4 | g17418 | g17418.t4 | cds | g17418.t4.CDS3 | 13460174 | 13460492 |
| chr_4 | g17418 | g17418.t4 | exon | g17418.t4.exon4 | 13461054 | 13462243 |
| chr_4 | g17418 | g17418.t4 | cds | g17418.t4.CDS4 | 13461054 | 13461434 |
| chr_4 | g17418 | g17418.t4 | TTS | g17418.t4 | 13462454 | 13462454 |
Sequences
>g17418.t4 Gene=g17418 Length=1754
ATGTCTGAAGGAGAAACTTATCATGACAATCCATCTACAGACCAAGATGAAGAAAGCAAA
ATAAAGATTCTCATTGCAAGTGATATTCATCTGGGATATGATGAATTAAATCAAGAAACA
GGCAATGATTCTTTTAAAACATTTGAAGAAATTCTTATGATTGCAAATAGTCAAGATGTA
GATTTTATTCTATTGGCTGGTGATTTGTTTCATAAAGCACAACCATCAACTAATTCACTC
AATAGATGCATTCAATTACTTCGTACACACTCTCTTGGTAATAAAGAAATTCAATTTGAA
GTAAAAGATTCAAAAACAGGAGAAATAATGCAATTTCAAGTAATCACGAATGAAAATAAA
TCTGAAGAAAATTATAATTTTCCAATCAATATTGATGATGATAACATTAAAGTTTCTCAT
CCTGTCTTTGCAATTCATGGCTGTCATGATGATGTTGTTAATAATCTCAGTGCAATTGAT
GTTCTCAATTCAAGTGGTTTAGTCAATTATTTTGGAAAATGGAAAGATTTTTGTGAAGTT
AATTTGGAACCATTCATTATTTGTAAAGACAAAATAAAAATTGCTCTCTACGGCCTCAGT
CATATTCCAGATCGTAAACTTTTCGATTTATTTGCAAACGACAAAGTCAACGTAAAATTT
CCAGATCAAGTCAATGATTTTTACAACATTCTAACAATTCATCAAAATCGAATTGAAAAA
GGTAAAAATAATTTCATTCCGGTTGATATGCTGCCAAAATTTATGAATTTAATTATTTGG
GGACATGAACATGAATGTAAAATTGATATTGAACAATGCAATGACAAAATGTTTATTACA
CAACCTGGATCATCAATTGCAACATCTTTGAATCAAAGTGAAGCTGTTAGAAAGCATGTT
GGAATTTTAGAAATTAACAGTAATTCAATGAAATTCCTAAAATAACAAAAATTCCATTAA
AAACAGTTCGTCCTTTAATTTACAAATCGATTGAATTAAATTATGATGATGAAAATGTTG
AAGAATTTTTGACTAATTCAGTAATTGAAATGATTAATGAAGCTAAAGAGCTTCTTACAG
GACACTCTCATCAACCAACTAAACCACTGATTCGTTTGCGTGTTCAATATGTAAATCCCG
ATCATCTTATCAATACACGACGATTTGGACAAAAATTTGACGAATTAATCGCCAAGAGTG
AAGAAATATTGCAATTTAGAAAAGCAAGTCGTAGAAATAGACAGGAAAAATTAAGAATCG
ATGAAAATATTCTTAGAAATTCAAAAATTGATGACGACAATAATCGAGTTGAAGATTCAG
TTGATGAATATTTTGAAAAAGATAAAAATAAACTTTCATTATTTAATTTCAAATGCTTGA
GTGATGTTGTTCGTTTGCTTGTTGATAAAGATGATCAAGATGGTGCTGAAAAAGTAATTC
AAGCTCAAATTAATGCTGCTACTGAATATTTTATAGAAAAACTTGGTGATGAAGAATCAA
TTAATATTGCTCATGAATTTCGTGAAAATAAAAGTTTTGATGTGCATGAAAAGATTTTTG
AAAGTTTGAAAGTTCCAAAAAAGAATTCTAAAACTGCACAAAATGAAGATTCTGATAGTG
ATGAAGACAGTGATGTTGTTATGATTGATGGTGATAAAATCAAAAATCGAAGTTTATTAA
AACGACCACAAGATAAACCTGGAACTTCTTCTGCTTCTAAACGAGGTCGTGGATCATCAA
ATAACAAAAGATGA
>g17418.t4 Gene=g17418 Length=314
MSEGETYHDNPSTDQDEESKIKILIASDIHLGYDELNQETGNDSFKTFEEILMIANSQDV
DFILLAGDLFHKAQPSTNSLNRCIQLLRTHSLGNKEIQFEVKDSKTGEIMQFQVITNENK
SEENYNFPINIDDDNIKVSHPVFAIHGCHDDVVNNLSAIDVLNSSGLVNYFGKWKDFCEV
NLEPFIICKDKIKIALYGLSHIPDRKLFDLFANDKVNVKFPDQVNDFYNILTIHQNRIEK
GKNNFIPVDMLPKFMNLIIWGHEHECKIDIEQCNDKMFITQPGSSIATSLNQSEAVRKHV
GILEINSNSMKFLK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g17418.t4 | CDD | cd00840 | MPP_Mre11_N | 22 | 291 | 6.51789E-43 |
| 5 | g17418.t4 | Coils | Coil | Coil | 303 | 314 | - |
| 4 | g17418.t4 | Gene3D | G3DSA:3.60.21.10 | - | 9 | 314 | 1.3E-104 |
| 2 | g17418.t4 | PANTHER | PTHR10139 | DOUBLE-STRAND BREAK REPAIR PROTEIN MRE11 | 15 | 314 | 3.5E-97 |
| 1 | g17418.t4 | Pfam | PF00149 | Calcineurin-like phosphoesterase | 21 | 266 | 1.2E-9 |
| 3 | g17418.t4 | SUPERFAMILY | SSF56300 | Metallo-dependent phosphatases | 21 | 311 | 2.69E-40 |
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:0016787 | hydrolase 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.
