General information for g9920.t13
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g9920 is located on chr_1: 6047787..6048622 (- 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_1 | g9920 | g9920.t13 | isoform | g9920.t13 | 6047683 | 6048622 |
| chr_1 | g9920 | g9920.t13 | exon | g9920.t13.exon1 | 6047683 | 6048622 |
| chr_1 | g9920 | g9920.t13 | cds | g9920.t13.CDS1 | 6048302 | 6048622 |
| chr_1 | g9920 | g9920.t13 | TSS | g9920.t13 | 6048700 | 6048700 |
| chr_1 | g9920 | g9920.t13 | TTS | g9920.t13 | NA | NA |
Sequences
>g9920.t13 Gene=g9920 Length=940
ATGGATTTACTTGATGATTCGTTTGATAAAGTAATATTTGATGTTGAAATTCCAGAAGAT
TCTAAGCAAAAAAGTGAAATTCAAGCCGGTCCATCAACATCGAGTGCATCAGTTTCTAAA
CAAAATGAAAAGTCACAAGAAAATCAACCAGAGAAAGAAGTTGTGATATATGTTGGCAAT
GCAATACAAGTTAATCCCTGTCAAAAGGGAAATCCATTACTTAAATCAATAAATTCAATT
CCTTGGGAATTTAATGAGAAATTAATTCCAGATTATGTTGTAGGCAAAAGAGGTAAAAAT
CGACTGAAATTTATAATATAAATTATTAATGCTAATGATTGTTACTAATTTCAGCATGTG
TATTATTTCTATCAGTTAAATATCATCAATTGAAACCTGATTACATACATGAGCGATTAA
GACAGTTAAGGAAAAATTACGAGTTGAGAATTCTACTTGTTCATGTCGATATTAAAGAAC
CACATAATGCACTTAAACATCTTACAAGAATTTGTCTTCTTGCTGATTTTACTTTAATGT
TGGCTTGGTCGTATGAAGAGGCAGGAAAAATTATTGAGACATACAAAATGTTTGAAAATG
CATCAGCTGAGAGAATTCAAGAAAAACAAGAAACAGATAGCTATCAGAATGTTGTCAATG
CATTAACGAGTATAAAATCTATAAACAAAACTGATGCAATGACACTTTTAAATAATTTTG
GTACTCTCGAAAATCTCATTCAAGCTAGTGAAAATCAATTGTATTCTTGCGTCGGACTTG
GACCAAAGAAAGCACAAAAGCTTCATAAACTTCTCAATCAGAATTTTTTGAAATAATTTT
GGTAATTCCTTTATTTAAATGAAATATTTATTTTAATCTAATAAAAAAACGGAAAAGTAT
AAAATTGTTAAATGGAGATATTAATGTGAGAATTTATTTT
>g9920.t13 Gene=g9920 Length=106
MDLLDDSFDKVIFDVEIPEDSKQKSEIQAGPSTSSASVSKQNEKSQENQPEKEVVIYVGN
AIQVNPCQKGNPLLKSINSIPWEFNEKLIPDYVVGKRGKNRLKFII
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g9920.t13 | Gene3D | G3DSA:3.40.50.10130 | - | 60 | 101 | 1.4E-8 |
| 3 | g9920.t13 | MobiDBLite | mobidb-lite | consensus disorder prediction | 20 | 51 | - |
| 4 | g9920.t13 | MobiDBLite | mobidb-lite | consensus disorder prediction | 25 | 44 | - |
| 1 | g9920.t13 | Pfam | PF03834 | Binding domain of DNA repair protein Ercc1 (rad10/Swi10) | 62 | 97 | 1.4E-8 |
| 2 | g9920.t13 | SUPERFAMILY | SSF52980 | Restriction endonuclease-like | 60 | 96 | 1.23E-7 |
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:0005634 | nucleus | CC |
| GO:0006281 | DNA repair | BP |
| GO:0003684 | damaged DNA binding | 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.
