General information for g5009.t16
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.t16 | isoform | g5009.t16 | 6409200 | 6411780 |
| chr_2 | g5009 | g5009.t16 | exon | g5009.t16.exon1 | 6409200 | 6409964 |
| chr_2 | g5009 | g5009.t16 | TTS | g5009.t16 | 6409506 | 6409506 |
| chr_2 | g5009 | g5009.t16 | cds | g5009.t16.CDS1 | 6409818 | 6409964 |
| chr_2 | g5009 | g5009.t16 | exon | g5009.t16.exon2 | 6411092 | 6411157 |
| chr_2 | g5009 | g5009.t16 | cds | g5009.t16.CDS2 | 6411092 | 6411157 |
| chr_2 | g5009 | g5009.t16 | exon | g5009.t16.exon3 | 6411368 | 6411551 |
| chr_2 | g5009 | g5009.t16 | cds | g5009.t16.CDS3 | 6411368 | 6411475 |
| chr_2 | g5009 | g5009.t16 | exon | g5009.t16.exon4 | 6411616 | 6411780 |
| chr_2 | g5009 | g5009.t16 | TSS | g5009.t16 | NA | NA |
Sequences
>g5009.t16 Gene=g5009 Length=1180
AATTATTCCCGAAATAAATGATCGTGTTATTGTCAAGAGTGCAACTGGAAGTCGTGCTGG
AATTCTTCGTTATCGTGGAGAGCCAGCATTTGCTAGTGGTATTTGGTGTGGTGTTGAATA
TGAAGAGCCTGTTGGCAAAAATGACGGATCAGTTAGTGGACAAAGATATTTCAAATGCGC
ACCCAATCATGGAATTTTTGTGCCTGAAGGAAAGGTTGTTTTATCACCATTAGCACGAAA
AATGCGCCTTTCAAGACAAAATTCACAAGAATCGTTAACATCAAACATTACACTTAACAG
CTTGGCTTCGACAAATACTTCAAAATTGCGGTTAAATGCAACACAAAAGCGCCTATCGAC
ACTTAATAAGTCACCATCGGCAACGTCAACACCAAAACCCTCGTTCTCGTTGCAGGACAT
TTTACGAGAGAAATCGAATCATATTGAACAAATCATGAAAGAACGAGATATTGAACGTGA
AGAAATGGCAGCTCAAACAGTTCTTTATCAAAAGAATCTTAATCAGGTAAAATTTCTTGT
ACAATTAATTTGTTTTTTTTAGCTTGAACATTTTTTTATCTGTGTCTGCGTCTGAACAAA
GACATTGTCTTATTTACAAAAGAGTCCAAGTCCTGACGTTGAAGAACATATTGGAAGATG
GGCTACATATATTCGACAGAGAAGTGAACACATTGATGACTTGAGACGACAATTCACAGG
TTGGACTGGCAATCACGAGAGACATTGCATTCTTCATGATGTCTTTTTGACATAAAATAA
CAACTGATCTAATGAAAAGTGAAAATTATTTTCTAACATTTAAGAAGTTTTTTTTACATA
CGTATGATTTAATAAAATGTTATTGCAAGGGTTAGTCATATTTTCTTGTCAGCCCTTGGC
TTAATTTCTTCTTTCAGCTTGCATTTCTTATTTTCATAAAATATTTAGCATCGCTACTAA
CCATTAATTTTCAATATAAGAATGAATTTTTTGTTCTTGGAAATTTTGGTTCTCAAAATT
TGTTTTTTTACGAAACACTCCTTTGAAAGAGAAATTCTGTAATGTAATTCTTTCTTAATC
TTTAAAGTAATGAAAAAAAGATTATGAAAGAAACTGTTGTTTGATTAAAAAATTTGTTTT
ATGTCCATAGTCAATAGAAATAAATTCGTTTTGTATTTGC
>g5009.t16 Gene=g5009 Length=106
MRLSRQNSQESLTSNITLNSLASTNTSKLRLNATQKRLSTLNKSPSATSTPKPSFSLQDI
LREKSNHIEQIMKERDIEREEMAAQTVLYQKNLNQVKFLVQLICFF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value |
|---|---|---|---|---|---|---|
| g5009.t16 | 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.t16; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5009.t16.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.
