General information for g17418.t3
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.t3 | TSS | g17418.t3 | 13459725 | 13459725 |
| chr_4 | g17418 | g17418.t3 | isoform | g17418.t3 | 13459790 | 13461456 |
| chr_4 | g17418 | g17418.t3 | exon | g17418.t3.exon1 | 13459790 | 13459902 |
| chr_4 | g17418 | g17418.t3 | exon | g17418.t3.exon2 | 13459967 | 13460090 |
| chr_4 | g17418 | g17418.t3 | cds | g17418.t3.CDS1 | 13460002 | 13460090 |
| chr_4 | g17418 | g17418.t3 | exon | g17418.t3.exon3 | 13460174 | 13460492 |
| chr_4 | g17418 | g17418.t3 | cds | g17418.t3.CDS2 | 13460174 | 13460492 |
| chr_4 | g17418 | g17418.t3 | exon | g17418.t3.exon4 | 13461054 | 13461456 |
| chr_4 | g17418 | g17418.t3 | cds | g17418.t3.CDS3 | 13461054 | 13461434 |
| chr_4 | g17418 | g17418.t3 | TTS | g17418.t3 | 13462454 | 13462454 |
Sequences
>g17418.t3 Gene=g17418 Length=959
ATGTCTGAAGGAGAAACTTATCATGACAATCCATCTACAGACCAAGATGAAGAAAGCAAA
ATAAAGATTCTCATTGCAAGTGATATTCATCTGGGATATGATGAATTAAATCAGCAATGA
TTCTTTTAAAACATTTGAAGAAATTCTTATGATTGCAAATAGTCAAGATGTAGATTTTAT
TCTATTGGCTGGTGATTTGTTTCATAAAGCACAACCATCAACTAATTCACTCAATAGATG
CATTCAATTACTTCGTACACACTCTCTTGGTAATAAAGAAATTCAATTTGAAGTAAAAGA
TTCAAAAACAGGAGAAATAATGCAATTTCAAGTAATCACGAATGAAAATAAATCTGAAGA
AAATTATAATTTTCCAATCAATATTGATGATGATAACATTAAAGTTTCTCATCCTGTCTT
TGCAATTCATGGCTGTCATGATGATGTTGTTAATAATCTCAGTGCAATTGATGTTCTCAA
TTCAAGTGGTTTAGTCAATTATTTTGGAAAATGGAAAGATTTTTGTGAAGTTAATTTGGA
ACCATTCATTATTTGTAAAGACAAAATAAAAATTGCTCTCTACGGCCTCAGTCATATTCC
AGATCGTAAACTTTTCGATTTATTTGCAAACGACAAAGTCAACGTAAAATTTCCAGATCA
AGTCAATGATTTTTACAACATTCTAACAATTCATCAAAATCGAATTGAAAAAGGTAAAAA
TAATTTCATTCCGGTTGATATGCTGCCAAAATTTATGAATTTAATTATTTGGGGACATGA
ACATGAATGTAAAATTGATATTGAACAATGCAATGACAAAATGTTTATTACACAACCTGG
ATCATCAATTGCAACATCTTTGAATCAAAGTGAAGCTGTTAGAAAGCATGTTGGAATTTT
AGAAATTAACAGTAATTCAATGAAATTCCTAAAATAACAAAAATTCCATTAAAAACAGT
>g17418.t3 Gene=g17418 Length=262
MIANSQDVDFILLAGDLFHKAQPSTNSLNRCIQLLRTHSLGNKEIQFEVKDSKTGEIMQF
QVITNENKSEENYNFPINIDDDNIKVSHPVFAIHGCHDDVVNNLSAIDVLNSSGLVNYFG
KWKDFCEVNLEPFIICKDKIKIALYGLSHIPDRKLFDLFANDKVNVKFPDQVNDFYNILT
IHQNRIEKGKNNFIPVDMLPKFMNLIIWGHEHECKIDIEQCNDKMFITQPGSSIATSLNQ
SEAVRKHVGILEINSNSMKFLK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g17418.t3 | CDD | cd00840 | MPP_Mre11_N | 2 | 239 | 0.00000 |
| 4 | g17418.t3 | Gene3D | G3DSA:3.60.21.10 | - | 1 | 262 | 0.00000 |
| 2 | g17418.t3 | PANTHER | PTHR10139 | DOUBLE-STRAND BREAK REPAIR PROTEIN MRE11 | 2 | 262 | 0.00000 |
| 1 | g17418.t3 | Pfam | PF00149 | Calcineurin-like phosphoesterase | 4 | 214 | 0.00017 |
| 3 | g17418.t3 | SUPERFAMILY | SSF56300 | Metallo-dependent phosphatases | 2 | 259 | 0.00000 |
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. There were no conditions that were differentially expressed