General information for g5485.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g5485 is located on chr_2: 9838755..9839954 (+ 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_2 | g5485 | g5485.t1 | TSS | g5485.t1 | 9837707 | 9837707 |
| chr_2 | g5485 | g5485.t1 | isoform | g5485.t1 | 9837772 | 9838755 |
| chr_2 | g5485 | g5485.t1 | exon | g5485.t1.exon1 | 9837772 | 9838755 |
| chr_2 | g5485 | g5485.t1 | cds | g5485.t1.CDS1 | 9837772 | 9838755 |
| chr_2 | g5485 | g5485.t1 | TTS | g5485.t1 | 9838865 | 9838865 |
Sequences
>g5485.t1 Gene=g5485 Length=984
ATGGGTGAAAAAGAAGATGATAGAAATGATAAAAAGCTTCAAAAAGAGCGTAAACGAATA
GAAATACAGAAAAGAAAGTTTCAATTGGAACAAGAACGTATGATTAAGCCAGGAGAATGC
AACAAATTTTTAACTGCAAATATCGATAGCGAACTTTTAAAACAAACTGCTTTGAGTAAA
ATCAAAGAAAAGTTTGAAGAGCTCAATATTAATATTCATGCATCTAGAAGTTCAACGCCA
AATACAATCACATGGAAACGTCGAATAAGTCAAAGAATTATAAATGATAATGGAGACATA
ATAAATTTTGACGATGTAGAAAAGGATGAACCGTATTTGATGGTAATTCTAATGGCAGAT
TCATTTGTAAAAGCAGTAAAAGAAAATAAATTGCTTGAGATTATACAGGCTGCGCAAGAA
ATGTGTTCGAATTTGGTAATTTCAACTAGTCTAATAATTTACGGTTTAAAGGCTTATTGC
CGAAAGCATAAAAATACGATAACAGTTAGAGAGACTGAAATAAAGCTCGTTCAAATTCAA
ATGCTAGCAAACTGCAGTCATCGAATGCATGAAAATCCTGAGGATCTTGCGCTCACATGT
GCACAAATGAGTAAATCTATTGCAGAAGAACCTTTCAAAAACAAACAAAATCAAAAATTA
GACCAAGAGCAATTCTTTCTCACAAGCGATACAAAAATTAATGCATGTGAAAATGATCGC
GATTCTCTTTCTCGATTGTGGCATGCACAATTGAATTGTTTGCCGAAAGTAACATTTGAT
GTTGCTCAATCAATTACAAAAGAATATTCTACACCAACAAGATTAATAGAAGCTTATCGC
AAATATAATAATAAAAATCAAATGTTAACAGATATTCCAATAATTAGAACAGGACCACTT
TCGAAAACACGTCGTATTGGACCAGAGCTGAGCAGAAAAATTGCAACTTTAATGACATCA
AAAAATCCAAACGATCTTCTTTAA
>g5485.t1 Gene=g5485 Length=327
MGEKEDDRNDKKLQKERKRIEIQKRKFQLEQERMIKPGECNKFLTANIDSELLKQTALSK
IKEKFEELNINIHASRSSTPNTITWKRRISQRIINDNGDIINFDDVEKDEPYLMVILMAD
SFVKAVKENKLLEIIQAAQEMCSNLVISTSLIIYGLKAYCRKHKNTITVRETEIKLVQIQ
MLANCSHRMHENPEDLALTCAQMSKSIAEEPFKNKQNQKLDQEQFFLTSDTKINACENDR
DSLSRLWHAQLNCLPKVTFDVAQSITKEYSTPTRLIEAYRKYNNKNQMLTDIPIIRTGPL
SKTRRIGPELSRKIATLMTSKNPNDLL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g5485.t1 | Coils | Coil | Coil | 10 | 33 | - |
| 3 | g5485.t1 | Gene3D | G3DSA:3.40.50.10130 | - | 39 | 219 | 1.2E-23 |
| 4 | g5485.t1 | Gene3D | G3DSA:1.10.150.670 | - | 234 | 327 | 1.1E-24 |
| 2 | g5485.t1 | PANTHER | PTHR21077 | EME1 PROTEIN | 3 | 325 | 1.4E-43 |
| 1 | g5485.t1 | Pfam | PF02732 | ERCC4 domain | 49 | 197 | 1.0E-9 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5485/g5485.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5485.t1.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0005634 | nucleus | CC |
| GO:0003677 | DNA binding | MF |
| GO:0006281 | DNA repair | BP |
| GO:0048476 | Holliday junction resolvase complex | CC |
| GO:0004518 | nuclease activity | MF |
KEGG
Orthology
- This transcript has been annotated with K10882 (crossover junction endonuclease EME1 [EC:3.1.22.-])
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.
