General information for g16383.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative DNA repair protein RAD50.
Parent gene
- The parent gene g16383 is located on chr_4: 9294914..9298248 (+ 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 | g16383 | g16383.t2 | TSS | g16383.t2 | 9291967 | 9291967 |
| chr_4 | g16383 | g16383.t2 | isoform | g16383.t2 | 9292585 | 9293584 |
| chr_4 | g16383 | g16383.t2 | exon | g16383.t2.exon1 | 9292585 | 9292655 |
| chr_4 | g16383 | g16383.t2 | cds | g16383.t2.CDS1 | 9292587 | 9292655 |
| chr_4 | g16383 | g16383.t2 | exon | g16383.t2.exon2 | 9292710 | 9292765 |
| chr_4 | g16383 | g16383.t2 | cds | g16383.t2.CDS2 | 9292710 | 9292765 |
| chr_4 | g16383 | g16383.t2 | exon | g16383.t2.exon3 | 9292824 | 9292959 |
| chr_4 | g16383 | g16383.t2 | cds | g16383.t2.CDS3 | 9292824 | 9292959 |
| chr_4 | g16383 | g16383.t2 | exon | g16383.t2.exon4 | 9293338 | 9293584 |
| chr_4 | g16383 | g16383.t2 | cds | g16383.t2.CDS4 | 9293338 | 9293583 |
| chr_4 | g16383 | g16383.t2 | TTS | g16383.t2 | 9293851 | 9293851 |
Sequences
>g16383.t2 Gene=g16383 Length=510
CAATGTCATTGCTCAATAAACTTTATATACAAGGTATTCGATCTTTTGGACTCGATCGGG
AAGATGAACAAAAAATTGAATTTACACCTCCTGTTACATTTATTGTTGGTGAAAATGGAA
GTGGAAAAACTGCAATAATTGAATGTTTAAAATATGCAATAACTGGTGATCTTCCTTCTG
GATCTGATCGAGGAAAAAGCTTTGTGCATGAATCATCTCTTTATAACAACCGTGCAACTG
TTGCTGGAAATGTCAAATTAACTGTGTCAAATTCACAAAATGTAAACCATACAGTAACAC
GGTCATTAAAATTCAATGTTTCAGACAACAATAAACGTGATAAAAGAAAAATTCAAGTTT
CAATTACCAAACAAGAAGAAGATATAACATATTCAATTGATAATGCTGATACTTACATGT
GCAATGTTATGGGTGTTTCAAAATCAATTCTGAATAATGTAATTTTCTGTCATCAAGAGG
ATTCAAATTGGCCATTGGATGAAGGCAAAA
>g16383.t2 Gene=g16383 Length=169
MSLLNKLYIQGIRSFGLDREDEQKIEFTPPVTFIVGENGSGKTAIIECLKYAITGDLPSG
SDRGKSFVHESSLYNNRATVAGNVKLTVSNSQNVNHTVTRSLKFNVSDNNKRDKRKIQVS
ITKQEEDITYSIDNADTYMCNVMGVSKSILNNVIFCHQEDSNWPLDEGK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g16383.t2 | CDD | cd03240 | ABC_Rad50 | 4 | 165 | 0 |
| 4 | g16383.t2 | Gene3D | G3DSA:3.40.50.300 | - | 3 | 169 | 0 |
| 2 | g16383.t2 | PANTHER | PTHR18867 | RAD50 | 1 | 169 | 0 |
| 1 | g16383.t2 | Pfam | PF13476 | AAA domain | 6 | 167 | 0 |
| 3 | g16383.t2 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 4 | 164 | 0 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
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.
