General information for g10962.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Cullin-2.
Parent gene
- The parent gene g10962 is located on chr_1: 13040728..13042993 (+ 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 | g10962 | g10962.t3 | TSS | g10962.t3 | 13040144 | 13040144 |
| chr_1 | g10962 | g10962.t3 | isoform | g10962.t3 | 13040191 | 13041423 |
| chr_1 | g10962 | g10962.t3 | exon | g10962.t3.exon1 | 13040191 | 13040309 |
| chr_1 | g10962 | g10962.t3 | cds | g10962.t3.CDS1 | 13040191 | 13040309 |
| chr_1 | g10962 | g10962.t3 | exon | g10962.t3.exon2 | 13040425 | 13040649 |
| chr_1 | g10962 | g10962.t3 | cds | g10962.t3.CDS2 | 13040425 | 13040649 |
| chr_1 | g10962 | g10962.t3 | exon | g10962.t3.exon3 | 13040724 | 13041423 |
| chr_1 | g10962 | g10962.t3 | cds | g10962.t3.CDS3 | 13040724 | 13041423 |
| chr_1 | g10962 | g10962.t3 | TTS | g10962.t3 | NA | NA |
Sequences
>g10962.t3 Gene=g10962 Length=1044
ATGAGTTTAAGACCACAAAAAATAGAATTTGATGTAGTTTGGGGCTGTCTTCGTCAAACT
GTTGATAAAGTTCTCAAACTTAATCGTGTTGAACGTGATGATTGGAATTCAAGTTTTACT
GATGTTTATACAATATGCGTTGCTTTCCCTGAACCTCTCGCAGATCGCCTCTATGCAGAG
ACTAAATTATTTCTTGAGAATCATGTCAAGGTACAATTGGAAGAGTTTAATTGTTATAGG
ACAGAAAATAATGATGGAGAAAATGGTCAAATGATGTTACACAAATACTACAGTGCATGG
AAAAATTACAGTCAAGGACTTGAGTATCTCAATTACCTATATCAATACTTGAATCAACAA
CACATAAAGAAACAAAAGGTATCAGAGGCTGAAATTTTATACGGAAATGGCACTACGCCG
CTCGCAATTTCGCAAGAACAGATGGAAATAGGAGAGTTAGGGCTTGATATCTGGAGATTA
TTTATGATACAAAATTTAGGCGATATTTTAGTAAAACAAATTCTTCAAGGAATTGAAAGA
GATAGACTTGAAAACAACTTAACATCAAAAGACATTGAAACAATTCACGGCGTAATTAAT
AGTTTCGTTTCTGTACAAGATTACAAAAAGAAAGGAAGTCTTCATTTATACGAAACTCTT
TTTGAAGAGAAATTATTAGAGGCCAGCGGTTCATATTTCATGTCGCAAGCATCAAAATTG
TTACAATCCTGCTCAGTTAGTCAATACATGCAAGAGGTTATAAGAGTTTTGGATGAAGAA
AACGTTAGAGCTCATAAATTTGTCCACATGAACTCGGTTAAAAAACTCAAAAAAGAATGC
GAAGATCGAATGATAAGTGATCATAAAGCTTTTCTTTATTCTGAATGTAAAGAAATGGTT
AGTAATGATAAACGAGATGACCTTAGAAATTTATACATACTTCTAAAGCCATTGCAAGAC
GGTCTTAAAGAACTTATTCAAATATTACTTGAACAAATCAAGAATGAAGGTGCTGAATCA
ATTATGAACTTAAAAGGAGAGAAT
>g10962.t3 Gene=g10962 Length=348
MSLRPQKIEFDVVWGCLRQTVDKVLKLNRVERDDWNSSFTDVYTICVAFPEPLADRLYAE
TKLFLENHVKVQLEEFNCYRTENNDGENGQMMLHKYYSAWKNYSQGLEYLNYLYQYLNQQ
HIKKQKVSEAEILYGNGTTPLAISQEQMEIGELGLDIWRLFMIQNLGDILVKQILQGIER
DRLENNLTSKDIETIHGVINSFVSVQDYKKKGSLHLYETLFEEKLLEASGSYFMSQASKL
LQSCSVSQYMQEVIRVLDEENVRAHKFVHMNSVKKLKKECEDRMISDHKAFLYSECKEMV
SNDKRDDLRNLYILLKPLQDGLKELIQILLEQIKNEGAESIMNLKGEN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g10962.t3 | Gene3D | G3DSA:1.20.1310.10 | Cullin Repeats | 1 | 171 | 0 |
| 5 | g10962.t3 | Gene3D | G3DSA:1.20.1310.10 | Cullin Repeats | 172 | 288 | 0 |
| 7 | g10962.t3 | Gene3D | G3DSA:1.20.1310.10 | Cullin Repeats | 289 | 348 | 0 |
| 2 | g10962.t3 | PANTHER | PTHR11932:SF131 | CULLIN-2 | 5 | 348 | 0 |
| 3 | g10962.t3 | PANTHER | PTHR11932 | CULLIN | 5 | 348 | 0 |
| 1 | g10962.t3 | Pfam | PF00888 | Cullin family | 14 | 343 | 0 |
| 4 | g10962.t3 | SUPERFAMILY | SSF74788 | Cullin repeat-like | 10 | 348 | 0 |
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:0006511 | ubiquitin-dependent protein catabolic process | BP |
| GO:0031625 | ubiquitin protein ligase 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.
