General information for g9561.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 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.t1 | TTS | g9561.t1 | 4061277 | 4061277 |
| chr_1 | g9561 | g9561.t1 | isoform | g9561.t1 | 4061454 | 4062093 |
| chr_1 | g9561 | g9561.t1 | exon | g9561.t1.exon1 | 4061454 | 4061552 |
| chr_1 | g9561 | g9561.t1 | cds | g9561.t1.CDS1 | 4061454 | 4061552 |
| chr_1 | g9561 | g9561.t1 | exon | g9561.t1.exon2 | 4061616 | 4061737 |
| chr_1 | g9561 | g9561.t1 | cds | g9561.t1.CDS2 | 4061616 | 4061737 |
| chr_1 | g9561 | g9561.t1 | exon | g9561.t1.exon3 | 4061854 | 4061881 |
| chr_1 | g9561 | g9561.t1 | cds | g9561.t1.CDS3 | 4061854 | 4061881 |
| chr_1 | g9561 | g9561.t1 | exon | g9561.t1.exon4 | 4062007 | 4062093 |
| chr_1 | g9561 | g9561.t1 | cds | g9561.t1.CDS4 | 4062007 | 4062093 |
| chr_1 | g9561 | g9561.t1 | TSS | g9561.t1 | 4062168 | 4062168 |
Sequences
>g9561.t1 Gene=g9561 Length=336
ATGGAGATTGATGATGAAGAAATGGATCAACTTCCATCCAGCTCATCTGGACCAAAAGGA
GAAAGAAAGCGATTTGAAGTAAAAAAGTGGAATGCCGTTGCTTTATGGGCTTGGGACATT
GTCGTTGACAACTGTGCTATTTGCCGTAATCACATTATGGATCTCTGCATTGAATGTCAA
GCAAATCAAGCGAGTGCTACTAGCGAGGAATGTACAGTTGCTTGGGGTGTTTGCAATCAC
GCTTTCCATTTTCATTGCATCTCACGTTGGCTCAAAACTCGTCAAGTCTGTCCTCTAGAT
AATCGCGAATGGGAATTCCAAAAATATGGTCATTAA
>g9561.t1 Gene=g9561 Length=111
MEIDDEEMDQLPSSSSGPKGERKRFEVKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQ
ANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWEFQKYGH
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g9561.t1 | CDD | cd16485 | mRING-H2-C3H2C2D_RBX1 | 43 | 104 | 1.74213E-44 |
| 6 | g9561.t1 | Gene3D | G3DSA:3.30.40.10 | Zinc/RING finger domain | 13 | 111 | 5.1E-35 |
| 5 | g9561.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 23 | - |
| 2 | g9561.t1 | PANTHER | PTHR11210 | RING BOX | 13 | 111 | 1.9E-66 |
| 3 | g9561.t1 | PANTHER | PTHR11210:SF45 | OS01G0106800 PROTEIN | 13 | 111 | 1.9E-66 |
| 1 | g9561.t1 | Pfam | PF12678 | RING-H2 zinc finger domain | 43 | 101 | 1.6E-25 |
| 7 | g9561.t1 | ProSiteProfiles | PS50089 | Zinc finger RING-type profile. | 56 | 101 | 9.303 |
| 4 | g9561.t1 | SUPERFAMILY | SSF57850 | RING/U-box | 23 | 108 | 6.01E-40 |
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.
