General information for g5483.t9
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g5483 is located on chr_2: 9835346..9836011 (+ 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 | g5483 | g5483.t9 | isoform | g5483.t9 | 9833786 | 9834353 |
| chr_2 | g5483 | g5483.t9 | exon | g5483.t9.exon1 | 9833786 | 9834353 |
| chr_2 | g5483 | g5483.t9 | cds | g5483.t9.CDS1 | 9833929 | 9834351 |
| chr_2 | g5483 | g5483.t9 | TSS | g5483.t9 | NA | NA |
| chr_2 | g5483 | g5483.t9 | TTS | g5483.t9 | NA | NA |
Sequences
>g5483.t9 Gene=g5483 Length=568
AGCCTAAACCTGTGACTCAAAGAAAACGAAAATGGGGTGCACGTAAAGATGATGAAAAAG
TTATTGCTATAACTACAGATTCATTGGCAAATATTATCGCTGAAGAAGTTAAACCAGTTC
CTTTAAGTGATGTAAAATTAGCAATGAGTCCATCACCTGAACCAGAAGAAAAAAGACCAA
GAGTTAGACTTTCATCGGAAGATCGTGATGCAAAAAAGAAACTTTTAAAGGAACGTTTGA
GAAAACAAGAAGAAGAAGAGGAACGTCGAAATGAGCAAATTGCTAAAGCTAGTGAACGCA
GTCAAGTATCTCCGACAATTGTTGTCACAAATGGAGGTGCTGGAAAAGATCGTAAAGTGT
CACTTGTTAGCAATGAAGAAGCGATTGCAAAAACTTCATCCTCGCCAATATCGAAAAATC
AATGCTCAAAAGTTATATGTATCACAAATTTGGTACGTCCTCTAACATTTTTAGCTGTCA
AATCTTTGGTCTCACGAACTGGTGAACTTGATGATTTTTGGATAGATTCTATCAAATCAA
AATGCTTTGTAAAGTACAAAACAGAAGA
>g5483.t9 Gene=g5483 Length=141
MSPSPEPEEKRPRVRLSSEDRDAKKKLLKERLRKQEEEEERRNEQIAKASERSQVSPTIV
VTNGGAGKDRKVSLVSNEEAIAKTSSSPISKNQCSKVICITNLVRPLTFLAVKSLVSRTG
ELDDFWIDSIKSKCFVKYKTE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 4 | g5483.t9 | Coils | Coil | Coil | 18 | 54 | - |
| 2 | g5483.t9 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 48 | - |
| 3 | g5483.t9 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 63 | - |
| 1 | g5483.t9 | PANTHER | PTHR46589 | APOPTOTIC CHROMATIN CONDENSATION INDUCER IN THE NUCLEUS | 28 | 141 | 3.2E-15 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5483/g5483.t9; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5483.t9.fa.iupred3.txt does not exist
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.
