General information for g5885.t17
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g5885 is located on chr_2: 12592133..12592869 (- 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 | g5885 | g5885.t17 | TTS | g5885.t17 | 12591884 | 12591884 |
| chr_2 | g5885 | g5885.t17 | isoform | g5885.t17 | 12592133 | 12592869 |
| chr_2 | g5885 | g5885.t17 | exon | g5885.t17.exon1 | 12592133 | 12592869 |
| chr_2 | g5885 | g5885.t17 | cds | g5885.t17.CDS1 | 12592134 | 12592556 |
| chr_2 | g5885 | g5885.t17 | TSS | g5885.t17 | 12592869 | 12592869 |
Sequences
>g5885.t17 Gene=g5885 Length=737
AGTTTTGTGCAAAAATTTTCATTAGCTGGTTCGTAGGCTCATCGCTGCGTAGTAAAAATT
AAATTTCATTTTGTTAAGTCTTGCCTGCGAATTTATTGGCGAAAAAATATTTATTGTTAT
AACAAAGAAAGCAAAATAAATTTATTAGAGCTTTTAATAAAAATGAATGTGATAATGAAT
ATCGATGATAATACGAAATATTGTGAAATTTTCTAGAAATAATTTTTCTGTTTGATATTT
TCTTTGTGAGAATGGAAAAAATAAAAAGGGTAACAAAATGTAGACAATTAAATTATAATC
AGATGCCTTCAAGATGCAAAGAAATGACAGTGAAATAGTGATAAACGATGATGATAGTGA
AAGTACAAGCATTGAATCTCTTTTAGTGCAAAAATATGAGTCACCATCAAATAGTGGTGG
CAGTGAGGTTGTTGAAAGTAGTGCGCAGGATGAGAATGATGAAGTCATTTTTGTGCCAAA
TAATCCGACAACATGGTCGGAAAAGCATATTGAAACATGGGTTAAATGGGCATCAGATCA
ATTTGAAATTAAACCGCCATTGGATGTTTCGCGCTTTCCAAAAAGTGGTGCAGAATTGGC
AAAATTTACTAAAGCAGATTTCTTTATCATCTGCGGATCATTCGAGGGCGGTAGAATGGT
TATGGATCATTTTAAATATATGATGGAAAATGTTGGTGAAAGTGTCGAAGAAACGCTCCT
TACTGATGGTGAACCAG
>g5885.t17 Gene=g5885 Length=141
MQRNDSEIVINDDDSESTSIESLLVQKYESPSNSGGSEVVESSAQDENDEVIFVPNNPTT
WSEKHIETWVKWASDQFEIKPPLDVSRFPKSGAELAKFTKADFFIICGSFEGGRMVMDHF
KYMMENVGESVEETLLTDGEP
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g5885.t17 | Gene3D | G3DSA:1.10.150.50 | Transcription Factor | 34 | 127 | 3.3E-16 |
| 4 | g5885.t17 | MobiDBLite | mobidb-lite | consensus disorder prediction | 29 | 48 | - |
| 1 | g5885.t17 | Pfam | PF02198 | Sterile alpha motif (SAM)/Pointed domain | 52 | 124 | 3.1E-11 |
| 6 | g5885.t17 | ProSiteProfiles | PS51433 | Pointed (PNT) domain profile. | 40 | 127 | 27.047 |
| 3 | g5885.t17 | SMART | SM00251 | SAM2_3 | 41 | 127 | 0.0089 |
| 2 | g5885.t17 | SUPERFAMILY | SSF47769 | SAM/Pointed domain | 41 | 123 | 1.97E-15 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5885/g5885.t17; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5885.t17.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0043565 | sequence-specific DNA 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.
