General information for g5288.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g5288 is located on chr_2: 8396548..8397851 (- 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 | g5288 | g5288.t4 | isoform | g5288.t4 | 8395370 | 8396319 |
| chr_2 | g5288 | g5288.t4 | exon | g5288.t4.exon1 | 8395370 | 8395960 |
| chr_2 | g5288 | g5288.t4 | exon | g5288.t4.exon2 | 8396016 | 8396319 |
| chr_2 | g5288 | g5288.t4 | cds | g5288.t4.CDS1 | 8396016 | 8396129 |
| chr_2 | g5288 | g5288.t4 | TSS | g5288.t4 | NA | NA |
| chr_2 | g5288 | g5288.t4 | TTS | g5288.t4 | NA | NA |
Sequences
>g5288.t4 Gene=g5288 Length=895
CGATTCAGTTGACGTTTCAGTCGCTGTATCAACTGATAACGGATTGATCACGCCAATTGT
ATTTAGTGCTGATCGTAAAGGAGTCGAAGCTATCTCAACAGATGTAAAGACACTTGCAGG
AAAAGCTAGAGAAGGAAAATTGCAACCACAAGAATTCCAGGGTGGCACTTTCACTGTTTC
AAATCTCGGAATGTTTGATGTTACTCATTTCTGTGCTATCATTAATCCACCACAATCGTG
CATCTTGGCAGTTGGTGGTAGTCAAAAACGTCTTGTTATTGACGAAAATTCTGAAAAGGG
GTAACTTCAAAGAAGCAACCTTTATCTCGGTGACTTTAAGTGCCGATCATAGAACAGTTG
ATGGAGCTGTTGGAGCCCGTTGGTTGCAATATTTCAGAAAATATATGGAAGATCCTGCCA
CAATGTTACTGTAAATTTAAATTAGGTTCTACTTCGATCCAAGTCATCTGAGCTGCTTAT
GCTTTGCAAAGTTTTATAATTTTATCATTTTCACACATAGGAGAAAAATTCATATTTTCA
ACAAAAAATTCTTTTTTCGTTATAAAAATTTAATCATAATTGGTTTATCTATATTGTATG
TAGAAAATGTTCTGCGCTGGAGTGCAACTATAAAAAAAAGATTGATCTAAATTTAAGCAC
TGAACTGTACTCAATGAATCTGAAATAACAAAACAAGGAAAAAGCATCCTAACAAGTTGA
AAGAACTTGATAAAAAATGTTTAAAAAAACATGAAAACGTTAGTTTAAAAATAAAATATA
AATTATTCGAATGAAAATTTTTGCTATTACATAAACTTATATTTGCAGCTTACTGAAAAA
AAAAATGCATTCCACTTTAATATGAAAAGGAAAAAGAAAAAAAATCGAGGCCAAT
>g5288.t4 Gene=g5288 Length=37
MFDVTHFCAIINPPQSCILAVGGSQKRLVIDENSEKG
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 3 | g5288.t4 | Gene3D | G3DSA:3.30.559.10 | Chloramphenicol Acetyltransferase | 1 | 36 | 0e+00 |
| 1 | g5288.t4 | Pfam | PF00198 | 2-oxoacid dehydrogenases acyltransferase (catalytic domain) | 1 | 33 | 5e-07 |
| 2 | g5288.t4 | SUPERFAMILY | SSF52777 | CoA-dependent acyltransferases | 1 | 33 | 1e-07 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5288/g5288.t4; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5288.t4.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0016746 | acyltransferase activity | 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.
