General information for g5009.t12
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g5009 is located on chr_2: 6422853..6423614 (- 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 | g5009 | g5009.t12 | TTS | g5009.t12 | 6407996 | 6407996 |
| chr_2 | g5009 | g5009.t12 | isoform | g5009.t12 | 6408876 | 6411618 |
| chr_2 | g5009 | g5009.t12 | exon | g5009.t12.exon1 | 6408876 | 6409757 |
| chr_2 | g5009 | g5009.t12 | cds | g5009.t12.CDS1 | 6409605 | 6409757 |
| chr_2 | g5009 | g5009.t12 | exon | g5009.t12.exon2 | 6409854 | 6409964 |
| chr_2 | g5009 | g5009.t12 | cds | g5009.t12.CDS2 | 6409854 | 6409964 |
| chr_2 | g5009 | g5009.t12 | exon | g5009.t12.exon3 | 6411092 | 6411157 |
| chr_2 | g5009 | g5009.t12 | cds | g5009.t12.CDS3 | 6411092 | 6411157 |
| chr_2 | g5009 | g5009.t12 | exon | g5009.t12.exon4 | 6411368 | 6411551 |
| chr_2 | g5009 | g5009.t12 | cds | g5009.t12.CDS4 | 6411368 | 6411475 |
| chr_2 | g5009 | g5009.t12 | exon | g5009.t12.exon5 | 6411616 | 6411618 |
| chr_2 | g5009 | g5009.t12 | TSS | g5009.t12 | NA | NA |
Sequences
>g5009.t12 Gene=g5009 Length=1246
AAGATATTTCAAATGCGCACCCAATCATGGAATTTTTGTGCCTGAAGGAAAGGTTGTTTT
ATCACCATTAGCACGAAAAATGCGCCTTTCAAGACAAAATTCACAAGAATCGTTAACATC
AAACATTACACTTAACAGCTTGGCTTCGACAAATACTTCAAAATTGCGGTTAAATGCAAC
ACAAAAGCGCCTATCGACACTTAATAAGTCACCATCGGCAACGTCAACACCAAAACCCTC
GTTCTCGTTGCAGGACATTTTACGAGAGAAATCGAATCATATTGAACAAATCATGAAAGA
ACGAGATATTGAACGTGAAGAAATGGCAGCTCAAACAGTTCTTTATCAAAAGAATCTTAA
TCAGAGTCCAAGTCCTGACGTTGAAGAACATATTGGAAGATGGGCTACATATATTCGACA
GAGAAGTGAACACATTGATGACTTGAGACGACAATTCACAGGTTGGACTGGCAATCACGA
GAGACATTGCATTCTTCATGATGTCTTTTTGACATAAAATAACAACTGATCTAATGAAAA
GTGAAAATTATTTTCTAACATTTAAGAAGTTTTTTTTACATACGTATGATTTAATAAAAT
GTTATTGCAAGGGTTAGTCATATTTTCTTGTCAGCCCTTGGCTTAATTTCTTCTTTCAGC
TTGCATTTCTTATTTTCATAAAATATTTAGCATCGCTACTAACCATTAATTTTCAATATA
AGAATGAATTTTTTGTTCTTGGAAATTTTGGTTCTCAAAATTTGTTTTTTTACGAAACAC
TCCTTTGAAAGAGAAATTCTGTAATGTAATTCTTTCTTAATCTTTAAAGTAATGAAAAAA
AGATTATGAAAGAAACTGTTGTTTGATTAAAAAATTTGTTTTATGTCCATAGTCAATAGA
AATAAATTCGTTTTGTATTTGCTTAGCTAACTCTTTACTAATTCTTTTATTAACTTTTTG
ATTACAAAAATAAAGAAATGTCACAAAATCAGCTATTCTTTTAATTTGATTTAAATTTTT
ATCTTTTGAGTTCATGTGGGTTTGTTTAAAATAAAGAATAAAACATCCATATTTGTAGAT
GTTTAAAATATTTATGTAATTGTTTCCAAAACACTTTCTCTCCATAATCACTCCATATTT
TTCTCTTTTTCAGTCAGACAGACACAGATTAAAGAAATTATTATCATACTATATTTCAAT
AAATACCATTTTTATCAACTCAGTTGAGCATTTATTATGACATTCA
>g5009.t12 Gene=g5009 Length=145
MRLSRQNSQESLTSNITLNSLASTNTSKLRLNATQKRLSTLNKSPSATSTPKPSFSLQDI
LREKSNHIEQIMKERDIEREEMAAQTVLYQKNLNQSPSPDVEEHIGRWATYIRQRSEHID
DLRRQFTGWTGNHERHCILHDVFLT
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value |
|---|---|---|---|---|---|---|
| g5009.t12 | Coils | Coil | Coil | 61 | 81 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5009/g5009.t12; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5009.t12.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