General information for g9561.t22
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative RING-box protein 1A.
Parent gene
- The parent gene g9561 is located on chr_1: 4062093..4066462 (- 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 | g9561 | g9561.t22 | TTS | g9561.t22 | 4061277 | 4061277 |
| chr_1 | g9561 | g9561.t22 | isoform | g9561.t22 | 4061454 | 4062093 |
| chr_1 | g9561 | g9561.t22 | exon | g9561.t22.exon1 | 4061454 | 4061552 |
| chr_1 | g9561 | g9561.t22 | cds | g9561.t22.CDS1 | 4061454 | 4061552 |
| chr_1 | g9561 | g9561.t22 | exon | g9561.t22.exon2 | 4061616 | 4061737 |
| chr_1 | g9561 | g9561.t22 | cds | g9561.t22.CDS2 | 4061616 | 4061737 |
| chr_1 | g9561 | g9561.t22 | exon | g9561.t22.exon3 | 4061854 | 4061881 |
| chr_1 | g9561 | g9561.t22 | cds | g9561.t22.CDS3 | 4061854 | 4061881 |
| chr_1 | g9561 | g9561.t22 | exon | g9561.t22.exon4 | 4062016 | 4062093 |
| chr_1 | g9561 | g9561.t22 | cds | g9561.t22.CDS4 | 4062016 | 4062093 |
| chr_1 | g9561 | g9561.t22 | TSS | g9561.t22 | 4062168 | 4062168 |
Sequences
>g9561.t22 Gene=g9561 Length=327
ATGGAGATTGATGATGAAGAAATGGATCAACTTCCATCCAGCTCATCTGGACCAAAAGGA
GAAAGAAAGCGATTTGAATGGAATGCCGTTGCTTTATGGGCTTGGGACATTGTCGTTGAC
AACTGTGCTATTTGCCGTAATCACATTATGGATCTCTGCATTGAATGTCAAGCAAATCAA
GCGAGTGCTACTAGCGAGGAATGTACAGTTGCTTGGGGTGTTTGCAATCACGCTTTCCAT
TTTCATTGCATCTCACGTTGGCTCAAAACTCGTCAAGTCTGTCCTCTAGATAATCGCGAA
TGGGAATTCCAAAAATATGGTCATTAA
>g9561.t22 Gene=g9561 Length=108
MEIDDEEMDQLPSSSSGPKGERKRFEWNAVALWAWDIVVDNCAICRNHIMDLCIECQANQ
ASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWEFQKYGH
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g9561.t22 | CDD | cd16485 | mRING-H2-C3H2C2D_RBX1 | 40 | 101 | 4.63629E-44 |
| 6 | g9561.t22 | Gene3D | G3DSA:3.30.40.10 | Zinc/RING finger domain | 12 | 108 | 1.3E-32 |
| 5 | g9561.t22 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 22 | - |
| 2 | g9561.t22 | PANTHER | PTHR11210 | RING BOX | 13 | 108 | 1.0E-61 |
| 3 | g9561.t22 | PANTHER | PTHR11210:SF45 | OS01G0106800 PROTEIN | 13 | 108 | 1.0E-61 |
| 1 | g9561.t22 | Pfam | PF12678 | RING-H2 zinc finger domain | 40 | 98 | 1.5E-25 |
| 7 | g9561.t22 | ProSiteProfiles | PS50089 | Zinc finger RING-type profile. | 53 | 98 | 9.303 |
| 4 | g9561.t22 | SUPERFAMILY | SSF57850 | RING/U-box | 26 | 105 | 3.04E-37 |
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:0008270 | zinc ion binding | MF |
KEGG
Orthology
- This transcript has been annotated with K03868 (E3 ubiquitin-protein ligase RBX1)
Pathway
- This transcript belongs to the following pathways
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. There were no conditions that were differentially expressed