General information for g5330.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g5330 is located on chr_2: 8870818..8871753 (- 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 | g5330 | g5330.t1 | isoform | g5330.t1 | 8870818 | 8871753 |
| chr_2 | g5330 | g5330.t1 | exon | g5330.t1.exon1 | 8870818 | 8871753 |
| chr_2 | g5330 | g5330.t1 | cds | g5330.t1.CDS1 | 8870818 | 8871753 |
| chr_2 | g5330 | g5330.t1 | TSS | g5330.t1 | NA | NA |
| chr_2 | g5330 | g5330.t1 | TTS | g5330.t1 | NA | NA |
Sequences
>g5330.t1 Gene=g5330 Length=936
ATGAAAATTGAAATAAGTGGAAAAGTGGATTTTAAACAAAACATTCAAGATGCATTTGAA
AATAATTGGTTAATTTGTATCGATGGAAAGAAATCAGAATTTTCTTTTGAATCAGACGAA
ATCGATCCTTATGAAGTTGTTACGTATTCAGGCAGCATCATTTTAAAGCCTAAAAAAGAA
GGCATTCTTCGTAAAGCAGAACAAATAAAAATGTTTATTGAAATGAAAAACCATGAAAAT
TTTTCATTTGTAACGACTGATTTAATTCATCATGATGGTGGCGTTTTCCATTTTTTAACA
CCACCAAAACGTTGCTTTGCATCAACGTTTATTCTTCACATTGAAATTCCCAAATTGAAA
GATGTTGAATTATCTAATTCGAAAGATCATTTGAAGAAATTGCTACAAACCGGTGAACAT
GCAGATGTTATAATTAAAACCACTGGAAATGACATTCCAGTACATAAATTCATGCTGACA
CGTTATGAACATTTTGATCAAATGTTTAAGAGCGACATCCAAGAAGCTAGAATTGGAATA
GTCAAAACACGTCATGATTATGAATTAATGTTTGAGCTCATGAAGTACATCTACTATGAA
GAATGCAATTTAGATAAATTTGCTATCGATTTGCTAACTGTATCTGATGAATACAACATT
GTTGATCTTTTTAACTTGTGTGAGAATTTCTTAATTAAAAGTATCACAATGGATAACTTT
TTTGATGTTGCGTTAATCGTGATTGCAAATGAAAGACTCAAGAAGCTCAAAAAAGAAATA
ATCAAGTTCTTCAGTGAAAATCAAATTGAGATAATTACCACTGAAAAATGGTGTGAATTT
GCAGAGAAATATCCGAGACATGCGATGGATTATATGGAAATTCAAGCTCATAATGCTTAC
AAGAAGATGCGTTTATCACATATGGATGATGTTTAA
>g5330.t1 Gene=g5330 Length=311
MKIEISGKVDFKQNIQDAFENNWLICIDGKKSEFSFESDEIDPYEVVTYSGSIILKPKKE
GILRKAEQIKMFIEMKNHENFSFVTTDLIHHDGGVFHFLTPPKRCFASTFILHIEIPKLK
DVELSNSKDHLKKLLQTGEHADVIIKTTGNDIPVHKFMLTRYEHFDQMFKSDIQEARIGI
VKTRHDYELMFELMKYIYYEECNLDKFAIDLLTVSDEYNIVDLFNLCENFLIKSITMDNF
FDVALIVIANERLKKLKKEIIKFFSENQIEIITTEKWCEFAEKYPRHAMDYMEIQAHNAY
KKMRLSHMDDV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g5330.t1 | Gene3D | G3DSA:3.30.710.10 | Potassium Channel Kv1.1; Chain A | 113 | 267 | 0.000 |
| 2 | g5330.t1 | PANTHER | PTHR24413:SF213 | FI01029P-RELATED | 118 | 292 | 0.000 |
| 3 | g5330.t1 | PANTHER | PTHR24413 | SPECKLE-TYPE POZ PROTEIN | 118 | 292 | 0.000 |
| 1 | g5330.t1 | Pfam | PF00651 | BTB/POZ domain | 131 | 234 | 0.000 |
| 7 | g5330.t1 | ProSiteProfiles | PS50097 | BTB domain profile. | 141 | 206 | 11.626 |
| 5 | g5330.t1 | SMART | SM00225 | BTB_4 | 141 | 235 | 0.000 |
| 4 | g5330.t1 | SUPERFAMILY | SSF54695 | POZ domain | 124 | 235 | 0.000 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5330/g5330.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5330.t1.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.
