General information for g5836.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Longitudinals lacking protein-like.
Parent gene
- The parent gene g5836 is located on chr_2: 12214641..12215869 (+ 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 | g5836 | g5836.t2 | TSS | g5836.t2 | 12213210 | 12213210 |
| chr_2 | g5836 | g5836.t2 | isoform | g5836.t2 | 12213234 | 12214758 |
| chr_2 | g5836 | g5836.t2 | exon | g5836.t2.exon1 | 12213234 | 12213343 |
| chr_2 | g5836 | g5836.t2 | exon | g5836.t2.exon2 | 12214073 | 12214244 |
| chr_2 | g5836 | g5836.t2 | cds | g5836.t2.CDS1 | 12214149 | 12214244 |
| chr_2 | g5836 | g5836.t2 | exon | g5836.t2.exon3 | 12214335 | 12214409 |
| chr_2 | g5836 | g5836.t2 | cds | g5836.t2.CDS2 | 12214335 | 12214409 |
| chr_2 | g5836 | g5836.t2 | exon | g5836.t2.exon4 | 12214478 | 12214566 |
| chr_2 | g5836 | g5836.t2 | cds | g5836.t2.CDS3 | 12214478 | 12214566 |
| chr_2 | g5836 | g5836.t2 | exon | g5836.t2.exon5 | 12214635 | 12214758 |
| chr_2 | g5836 | g5836.t2 | cds | g5836.t2.CDS4 | 12214635 | 12214758 |
| chr_2 | g5836 | g5836.t2 | TTS | g5836.t2 | 12215662 | 12215662 |
Sequences
>g5836.t2 Gene=g5836 Length=570
GCTAAGTAAGCTATATCACATAAATTCAAGACTTTTTCGGTAATTTGACAACAGAAACTA
TAAATAAACGCGATATTTATCAAGATAAAGGTACATTAATTGAATTTAAGTAAACGGGCA
TCATCAAACCATAATAAAAACAACAAATAACAAAACTACCAACAGAGTGAAAATCGTCAT
ATAAAGATGGGCGAGCAGCAATTTTTCTTGAAATGGAATGACTTTCAAAACAACATGGTC
TCATCATTCAAACACTTGCGTGATGAAAAAAGCTTTACCGATGTGACTCTAGCATGTGAT
GGCCAAACTTGCAAAGCACACAAAATGGTTCTATCTGCCTGCAGTCCATATTTCAAGACT
TTGCTTGAAGAAAATCCATCAAAACATCCGATTATCATTTTGAAGGATGTTTCATTCAAT
CATTTGCAAGCTATCTTAGAATTCATGTATGCAGGAGAAGTTAATGTTTCGCAGGAACAA
TTGCCCTCATTCTTGAAAACAGCTGATAGATTAAAAGTAAAAGGCCTTGCAGAGACTCAA
TCACCGTTCTCAAACAAGAGAGAGGGTTGA
>g5836.t2 Gene=g5836 Length=127
MGEQQFFLKWNDFQNNMVSSFKHLRDEKSFTDVTLACDGQTCKAHKMVLSACSPYFKTLL
EENPSKHPIIILKDVSFNHLQAILEFMYAGEVNVSQEQLPSFLKTADRLKVKGLAETQSP
FSNKREG
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g5836.t2 | CDD | cd18315 | BTB_POZ_BAB-like | 30 | 113 | 0.00 |
| 6 | g5836.t2 | Gene3D | G3DSA:3.30.710.10 | Potassium Channel Kv1.1; Chain A | 4 | 119 | 0.00 |
| 2 | g5836.t2 | PANTHER | PTHR23110:SF95 | LONGITUDINALS LACKING PROTEIN-LIKE-RELATED | 2 | 118 | 0.00 |
| 3 | g5836.t2 | PANTHER | PTHR23110 | BTB DOMAIN TRANSCRIPTION FACTOR | 2 | 118 | 0.00 |
| 1 | g5836.t2 | Pfam | PF00651 | BTB/POZ domain | 21 | 117 | 0.00 |
| 7 | g5836.t2 | ProSiteProfiles | PS50097 | BTB domain profile. | 31 | 96 | 22.65 |
| 5 | g5836.t2 | SMART | SM00225 | BTB_4 | 31 | 126 | 0.00 |
| 4 | g5836.t2 | SUPERFAMILY | SSF54695 | POZ domain | 7 | 116 | 0.00 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5836/g5836.t2; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5836.t2.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0005515 | protein 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.
