General information for g5019.t8
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g5019 is located on chr_2: 6478452..6478848 (+ 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 | g5019 | g5019.t8 | TSS | g5019.t8 | 6477811 | 6477811 |
| chr_2 | g5019 | g5019.t8 | isoform | g5019.t8 | 6478452 | 6478848 |
| chr_2 | g5019 | g5019.t8 | exon | g5019.t8.exon1 | 6478452 | 6478666 |
| chr_2 | g5019 | g5019.t8 | cds | g5019.t8.CDS1 | 6478581 | 6478666 |
| chr_2 | g5019 | g5019.t8 | exon | g5019.t8.exon2 | 6478728 | 6478848 |
| chr_2 | g5019 | g5019.t8 | cds | g5019.t8.CDS2 | 6478728 | 6478848 |
| chr_2 | g5019 | g5019.t8 | TTS | g5019.t8 | 6479061 | 6479061 |
Sequences
>g5019.t8 Gene=g5019 Length=336
TTTCGACGTGAAGAAGATGCTGAAAGAGCAGCAAAAGAACTGAATAATCGTTGGTTTGGT
GGACGACCAGTGTATGCAGAATTATCTCCCGTTACTGACTTTCGAGAAGCATGTTGTCGT
CAATATGAAATGGGTGAATGCACTCGCTCTGGTTTTTGTAATTTCATGCATTTGAAACCA
ATATCTCGTGAGCTTCGTCGTTATTTGTATTCTAGACGAAGAGGTCGTTCACGCTCAAGA
TCAAAATCACCAAGGCGTCGATCAAGATCAAGAAATCGTGATCGTCATTCAAGAGACAGA
GACCGTGGAGATAGAGATCGTCGGGGACGTTATTAA
>g5019.t8 Gene=g5019 Length=68
MGECTRSGFCNFMHLKPISRELRRYLYSRRRGRSRSRSKSPRRRSRSRNRDRHSRDRDRG
DRDRRGRY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 3 | g5019.t8 | MobiDBLite | mobidb-lite | consensus disorder prediction | 26 | 50 | - |
| 5 | g5019.t8 | MobiDBLite | mobidb-lite | consensus disorder prediction | 26 | 68 | - |
| 4 | g5019.t8 | MobiDBLite | mobidb-lite | consensus disorder prediction | 51 | 68 | - |
| 1 | g5019.t8 | PANTHER | PTHR12620:SF11 | SPLICING FACTOR U2AF 35 KDA SUBUNIT-RELATED | 1 | 66 | 8.0E-15 |
| 2 | g5019.t8 | PANTHER | PTHR12620 | U2 SNRNP AUXILIARY FACTOR, SMALL SUBUNIT | 1 | 66 | 8.0E-15 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5019/g5019.t8; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5019.t8.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0003723 | RNA binding | MF |
| GO:0089701 | U2AF complex | CC |
| GO:0000398 | mRNA splicing, via spliceosome | BP |
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.
