General information for g9998.t7
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Splicing factor U2AF 50 kDa subunit.
Parent gene
- The parent gene g9998 is located on chr_1: 6492178..6492702 (+ 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_1 | g9998 | g9998.t7 | isoform | g9998.t7 | 6491677 | 6492702 |
| chr_1 | g9998 | g9998.t7 | exon | g9998.t7.exon1 | 6491677 | 6492103 |
| chr_1 | g9998 | g9998.t7 | cds | g9998.t7.CDS1 | 6491820 | 6492103 |
| chr_1 | g9998 | g9998.t7 | exon | g9998.t7.exon2 | 6492177 | 6492702 |
| chr_1 | g9998 | g9998.t7 | cds | g9998.t7.CDS2 | 6492177 | 6492201 |
| chr_1 | g9998 | g9998.t7 | TTS | g9998.t7 | 6493093 | 6493093 |
| chr_1 | g9998 | g9998.t7 | TSS | g9998.t7 | NA | NA |
Sequences
>g9998.t7 Gene=g9998 Length=953
TCAAAGAATTACTTTTATCTTTTGGACAATTGAAAGCATTCAATTTAGTAAAAGATGCAG
CAACTGGATTATCAAAGGGATATGCTTTTGCCGAATACGTTGAATATGCAATTACAGATC
AAGCAATTGCAGGATTGAATGGAATGCAGCTAGGTGATAAGAAATTGATTGTACAGAGAG
CAAGTGTTGGTGCAAAAAATGCAGCAACAGTCGGACAAGTTGCACCTGTACAAATTCAAG
TTCCTGGATTGTCAATCGTTGGAGCATCTGGTCCTGCTACTGAAGTTCTATGTCTTTTGA
ATATGGTCACACCGGACGAATTGAAGGATGAAGAAGAATATGAGGATATTCTTGAAGATA
TCAAAGAGGAATGTAACAAATATGGTGTTGTTCGCTCAATTGAGATTCCGAGACCCATTG
AAGGCAAGTGTCGACGTGCCAGGTTGTGGTAAAGTATTTGTTGAATTTAATTCAATTATG
GATTGTCAGCATGCTCAGCAAGCACTAACTGGACGTAAATTTAGCGATCGTGTTGTGGTG
ACATCTTATTTTGATCCAGATAAATACCATCGTCGTGAATTTTAAAATATATAGAGAAAT
AACATTTTTTTCTCTCTCATGTTTTGTATTTTTATCAACAACTTAAATTTCATCATTTTT
CTGCACGAAAGAGAAGAGCTTCTGCAATAATAATAATAATAATAAACATTTACCTATAAG
AATGAACGATAAAAGAGAGAAGGAGTATAAGTGAACATACGAATGTTTGGACACAAAAAC
TCACTCAATCGTGACATTTTTTTCCTTTCCTATATTATTCTTTTGCTGCCATCTCTTCAC
TTTCGTTCTATTTAATTAAAGATAAACAGAACAAAAAAATCTCTCTTTTTCGTTTCTCCA
TATTTACAAACCGAAAACGAAAAAAGAAATGTCCATTGAAATGGACATGAATC
>g9998.t7 Gene=g9998 Length=102
MQLGDKKLIVQRASVGAKNAATVGQVAPVQIQVPGLSIVGASGPATEVLCLLNMVTPDEL
KDEEEYEDILEDIKEECNKYGVVRSIEIPRPIEGKCRRARLW
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g9998.t7 | CDD | cd12232 | RRM3_U2AF65 | 46 | 94 | 0.0e+00 |
| 4 | g9998.t7 | Gene3D | G3DSA:3.30.70.330 | - | 43 | 100 | 0.0e+00 |
| 1 | g9998.t7 | PANTHER | PTHR23139:SF9 | SPLICING FACTOR U2AF 65 KDA SUBUNIT | 1 | 94 | 0.0e+00 |
| 2 | g9998.t7 | PANTHER | PTHR23139 | RNA-BINDING PROTEIN | 1 | 94 | 0.0e+00 |
| 3 | g9998.t7 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 45 | 91 | 2.2e-06 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0003676 | nucleic acid 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.
