General information for g5885.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g5885 is located on chr_2: 12592133..12592869 (- 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 | g5885 | g5885.t2 | isoform | g5885.t2 | 12585866 | 12587137 |
| chr_2 | g5885 | g5885.t2 | exon | g5885.t2.exon1 | 12585866 | 12586886 |
| chr_2 | g5885 | g5885.t2 | cds | g5885.t2.CDS1 | 12586568 | 12586886 |
| chr_2 | g5885 | g5885.t2 | exon | g5885.t2.exon2 | 12587016 | 12587067 |
| chr_2 | g5885 | g5885.t2 | cds | g5885.t2.CDS2 | 12587016 | 12587032 |
| chr_2 | g5885 | g5885.t2 | exon | g5885.t2.exon3 | 12587120 | 12587137 |
| chr_2 | g5885 | g5885.t2 | TSS | g5885.t2 | NA | NA |
| chr_2 | g5885 | g5885.t2 | TTS | g5885.t2 | NA | NA |
Sequences
>g5885.t2 Gene=g5885 Length=1091
ACTAAGTCGTGCATTGAGATATTATTATGATAAATCAATCATGACGAAAGTACATGGAAA
AAGGTGAGAAGTTTGACTTTCATGGATTAATGGCAGCTTGTCATGCACAAGCACAAGGAT
GTGATTCAACAAGTATGCTTCCAAAATACCCTCCACATCTCCTTATGCCAAATGATTTTT
CAAGTTATGCAAGCACATCGACTGCCATTCCTACAAGTACAAATCAAGTATCAGCAGCAT
TGTCATCATCTTTCAAACCAGTACAACCAATCATTACTCCTCATGCAACTCCTTCTACTT
CTTCATCATCGTCATCACCATCGACAGTGGCACAAACACCAAACACTGAAAGAATACCTG
GATGGCCATATTTACCCTCAAACTTTTAAACAATTGAAATCTCAAATAATTTGTAAATGA
CATCGTTTTAATTGTCAGCATATAAAAGGCTATTCTGATCTCAAATTGTGAATTTATTAT
TATTTTTCCTTTAATTTCAGTCCCTTTTCCTTTTCTATTGTTTCAATTTTCTGTTCTTTC
CTCCAGTGAATTACATTTTTTTATACAAACATCACATGAATAATTTTTATACGTAAGTCT
GTGTAGCAATAATTAAAACTTTTTTTAATTTTAAAAATACATTCTTAATGAAGATATTGA
TACCTCAGCTGTTAGATAATAAGAAGAACAATTTAAATTTAAATCAAATGCTCAAAACTA
TAAAAAAAGTTCATGTGACAAATCTCTTTATGTCTCTTCTTTTAGTGTTGAGAATATGAA
AGAATGTTGTAATTAGATAATAAGTAGATGTTTTTTGTAATTATTCAAATCCTAATCAAA
TTATCTTAATATAATGATTAGAAATAAATCAGTGAATTAATAAAAGAACATGTTTAAAAG
AAATATGCATTTTTATGCGAAACGTTTTCAGAATCGGTAAAATGAGAAACGCTACTCAAA
TAAAACATGTTGTGCAACATTTTCTTCCCTCTTTTTTGTTACGTCTCATAGAGTCTCATA
AACATACTTTGTGCATGACACATTTAACTGAAATTTTACAACGGTAAAGAAGAAAACTAT
TGAATATTATT
>g5885.t2 Gene=g5885 Length=111
MEKGEKFDFHGLMAACHAQAQGCDSTSMLPKYPPHLLMPNDFSSYASTSTAIPTSTNQVS
AALSSSFKPVQPIITPHATPSTSSSSSSPSTVAQTPNTERIPGWPYLPSNF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value |
|---|---|---|---|---|---|---|
| g5885.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 72 | 111 | - |
| g5885.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 72 | 98 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5885/g5885.t2; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5885.t2.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. There were no conditions that were differentially expressed