General information for g5936.t9
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g5936 is located on chr_2: 12908497..12909940 (+ 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 | g5936 | g5936.t9 | TSS | g5936.t9 | 12907679 | 12907679 |
| chr_2 | g5936 | g5936.t9 | isoform | g5936.t9 | 12907797 | 12909285 |
| chr_2 | g5936 | g5936.t9 | exon | g5936.t9.exon1 | 12907797 | 12908069 |
| chr_2 | g5936 | g5936.t9 | exon | g5936.t9.exon2 | 12908135 | 12908194 |
| chr_2 | g5936 | g5936.t9 | exon | g5936.t9.exon3 | 12908255 | 12908324 |
| chr_2 | g5936 | g5936.t9 | cds | g5936.t9.CDS1 | 12908270 | 12908324 |
| chr_2 | g5936 | g5936.t9 | exon | g5936.t9.exon4 | 12908389 | 12908436 |
| chr_2 | g5936 | g5936.t9 | cds | g5936.t9.CDS2 | 12908389 | 12908436 |
| chr_2 | g5936 | g5936.t9 | exon | g5936.t9.exon5 | 12908492 | 12908645 |
| chr_2 | g5936 | g5936.t9 | cds | g5936.t9.CDS3 | 12908492 | 12908645 |
| chr_2 | g5936 | g5936.t9 | exon | g5936.t9.exon6 | 12908788 | 12909285 |
| chr_2 | g5936 | g5936.t9 | cds | g5936.t9.CDS4 | 12908788 | 12908839 |
| chr_2 | g5936 | g5936.t9 | TTS | g5936.t9 | 12909252 | 12909252 |
Sequences
>g5936.t9 Gene=g5936 Length=1103
ATGTCATATTCAGCTAGACCACCGCCCAAAATTGAGGGCATGATTTCTTTAAAAGTAAGA
AGCACATTATTATTCCTTCATCCACCATTTTTTAAAAGACGTATTATCGCAAAAAAAAAA
AAAATAGGTTGACAATTTGACTTATCGAACTACTCCCGAAGACTTGAGACGAGTTTTTGA
GCGATGCGGTGATGTTGGTGACATTTATATTCCAAGAGATAGACATACTCGTGAGTCGAG
AGGATTTGCTTTTGTTCGATTTTATGACAAACGTGATGCTGAGGAAGCTCTTCAAGAAAT
GGATGGAAGAATGCTTGATGGACGTGAATTGAGTGCAAATGGCCAGATATGGGAGACCTA
CATCTCCACAAAGACGTTCTAACAGACACGATCGTCGCCGAAGATCCCGTTCGAGAGACC
GTAGAGGAGGTGGAGGTGGAAGACGCTCAAGATCACGTTCAAGAGACCGAAGAGGACGCC
GTCGTTCATACTCACGTTCCAAATCTCGTTCAAGATCAGCAAATAGTCGCAGCAACAGCA
AATCTTCACGCGATCGTTCACGCTCTCCAGTTCGTAAGAATCGCAGCTCAAGCAATTAAG
CAGAGTAAAAAAATCGTAACAAAATTTGATAAAGAAATGAAATATCTAATACTATAACTA
CTACTCTTTTGTTTGATAGAAAAATAAGCAAATTTCTTGATAGATTTTAAGCATTTTCAA
GTTTTCCTATTTTAAAATAGACATTAAAACATACTTTATGAAATTATACGTGTGCTAAGG
CAATTTATTTGTATTATTCTGTCATCTTTTAAAAACGAACAATCAGTTCTTTTTTTAACA
AATATAATCATTTTGTAATTTTAGCAATTATAAATGTCGCTATAATGAACACATGTCCTA
TCTTACACTTCCTTTAGAATACATTTTTTTTCTGTAAGGTTCAATATATATTTTGAGTTT
ATAAGACAAGAGAATTAACTTTTCTTGTCATAATAACATTTAATGAAGAAATTAATTGAT
ATATACCAATCAATAATAATATGCATAAAAATATCAACATTTTAAAAAATAAAAAATAAT
ATTTTATCCTACTTTTACCTACA
>g5936.t9 Gene=g5936 Length=102
MGDLHLHKDVLTDTIVAEDPVRETVEEVEVEDAQDHVQETEEDAVVHTHVPNLVQDQQIV
AATANLHAIVHALQFVRIAAQAIKQSKKIVTKFDKEMKYLIL
Protein features from InterProScan
No InterPro annotations for this transcript.
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5936/g5936.t9; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5936.t9.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.
