General information for g10962.t4
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.t4 | TSS | g10962.t4 | 13040144 | 13040144 |
| chr_1 | g10962 | g10962.t4 | isoform | g10962.t4 | 13040191 | 13042467 |
| chr_1 | g10962 | g10962.t4 | exon | g10962.t4.exon1 | 13040191 | 13040309 |
| chr_1 | g10962 | g10962.t4 | cds | g10962.t4.CDS1 | 13040191 | 13040309 |
| chr_1 | g10962 | g10962.t4 | exon | g10962.t4.exon2 | 13040425 | 13040649 |
| chr_1 | g10962 | g10962.t4 | cds | g10962.t4.CDS2 | 13040425 | 13040649 |
| chr_1 | g10962 | g10962.t4 | exon | g10962.t4.exon3 | 13040724 | 13041423 |
| chr_1 | g10962 | g10962.t4 | cds | g10962.t4.CDS3 | 13040724 | 13041423 |
| chr_1 | g10962 | g10962.t4 | exon | g10962.t4.exon4 | 13041482 | 13041655 |
| chr_1 | g10962 | g10962.t4 | cds | g10962.t4.CDS4 | 13041482 | 13041655 |
| chr_1 | g10962 | g10962.t4 | exon | g10962.t4.exon5 | 13041714 | 13041862 |
| chr_1 | g10962 | g10962.t4 | cds | g10962.t4.CDS5 | 13041714 | 13041862 |
| chr_1 | g10962 | g10962.t4 | exon | g10962.t4.exon6 | 13041920 | 13042467 |
| chr_1 | g10962 | g10962.t4 | cds | g10962.t4.CDS6 | 13041920 | 13042466 |
| chr_1 | g10962 | g10962.t4 | TTS | g10962.t4 | 13043165 | 13043165 |
Sequences
>g10962.t4 Gene=g10962 Length=1915
ATGAGTTTAAGACCACAAAAAATAGAATTTGATGTAGTTTGGGGCTGTCTTCGTCAAACT
GTTGATAAAGTTCTCAAACTTAATCGTGTTGAACGTGATGATTGGAATTCAAGTTTTACT
GATGTTTATACAATATGCGTTGCTTTCCCTGAACCTCTCGCAGATCGCCTCTATGCAGAG
ACTAAATTATTTCTTGAGAATCATGTCAAGGTACAATTGGAAGAGTTTAATTGTTATAGG
ACAGAAAATAATGATGGAGAAAATGGTCAAATGATGTTACACAAATACTACAGTGCATGG
AAAAATTACAGTCAAGGACTTGAGTATCTCAATTACCTATATCAATACTTGAATCAACAA
CACATAAAGAAACAAAAGGTATCAGAGGCTGAAATTTTATACGGAAATGGCACTACGCCG
CTCGCAATTTCGCAAGAACAGATGGAAATAGGAGAGTTAGGGCTTGATATCTGGAGATTA
TTTATGATACAAAATTTAGGCGATATTTTAGTAAAACAAATTCTTCAAGGAATTGAAAGA
GATAGACTTGAAAACAACTTAACATCAAAAGACATTGAAACAATTCACGGCGTAATTAAT
AGTTTCGTTTCTGTACAAGATTACAAAAAGAAAGGAAGTCTTCATTTATACGAAACTCTT
TTTGAAGAGAAATTATTAGAGGCCAGCGGTTCATATTTCATGTCGCAAGCATCAAAATTG
TTACAATCCTGCTCAGTTAGTCAATACATGCAAGAGGTTATAAGAGTTTTGGATGAAGAA
AACGTTAGAGCTCATAAATTTGTCCACATGAACTCGGTTAAAAAACTCAAAAAAGAATGC
GAAGATCGAATGATAAGTGATCATAAAGCTTTTCTTTATTCTGAATGTAAAGAAATGGTT
AGTAATGATAAACGAGATGACCTTAGAAATTTATACATACTTCTAAAGCCATTGCAAGAC
GGTCTTAAAGAACTTATTCAAATATTACTTGAACAAATCAAGAATGAAGGTGCTGAATCA
ATTATGAACTTAAAAGGAGAGAATGTTCATATTCAATTTGTTGAGAATATGCTTCAAGTA
CATCAAAAGTATGAGAATCTTATATCAGAGACATTCAAAAATGATCCTCTATTCTTGAGT
GCTTTGGATAAGGCTTGTGCAAGTGTTATCAATTCTAAATTGAGTGATGGAAAGACGACA
TGCAGAAGTGCTGAACTCGTTGCAAAATATTGTGACAATTTGTTAAAGAAATCTAAATCC
ACCGAAAGTGAAATTGAATCGAAATTATCTAAGAGTATCACAATTTTTAAATATATCGAG
GATAAGGATGTTTACCAAAAATTCTATAGTAGGATGCTTGCTAAACGACTCATACATGAT
CAATCAATTAACATGGAATTGGAAGAAGTAATGATTAATAAGCTCAAACAAGCTTGTGGA
TATGAATTTACTAACAAACTACATCGTATGTATACGGATATTGGAATAAGTGTTGATTTG
AATAACAAATTCAATCAACATCTCAAAAATCTCAATGACGAACTGAATATAAACTTATCA
ATCAAAGTACTACAAGCAGGTGCTTGGCCTTTAGGACCGCAAACAAATATATCTTTTGCA
GTTCCACAAGAATTTGAGCAACCAATCAGAAAATTTGAATCTTTCTACAACTCTAGTTTT
AGTGGCAGAAAATTAACATGGCTCCATCATTTATGCGCTGGCGAGCTAAAAGTGTCTCTT
GCTAAAAAATCCTATCTTATTACAATGCAAACCTATCAAATGGCTATGCTTTTGCTTTTT
GAGAATTGTGATTCAATGAGCTGTAAAGAAGTGAGAGAGATGTTACAGCTTAGTCACGAC
AATTTTCAAAAACATTTACAATCACTTATTGATTCTAAAATTCTTAACCTTGACA
>g10962.t4 Gene=g10962 Length=638
MSLRPQKIEFDVVWGCLRQTVDKVLKLNRVERDDWNSSFTDVYTICVAFPEPLADRLYAE
TKLFLENHVKVQLEEFNCYRTENNDGENGQMMLHKYYSAWKNYSQGLEYLNYLYQYLNQQ
HIKKQKVSEAEILYGNGTTPLAISQEQMEIGELGLDIWRLFMIQNLGDILVKQILQGIER
DRLENNLTSKDIETIHGVINSFVSVQDYKKKGSLHLYETLFEEKLLEASGSYFMSQASKL
LQSCSVSQYMQEVIRVLDEENVRAHKFVHMNSVKKLKKECEDRMISDHKAFLYSECKEMV
SNDKRDDLRNLYILLKPLQDGLKELIQILLEQIKNEGAESIMNLKGENVHIQFVENMLQV
HQKYENLISETFKNDPLFLSALDKACASVINSKLSDGKTTCRSAELVAKYCDNLLKKSKS
TESEIESKLSKSITIFKYIEDKDVYQKFYSRMLAKRLIHDQSINMELEEVMINKLKQACG
YEFTNKLHRMYTDIGISVDLNNKFNQHLKNLNDELNINLSIKVLQAGAWPLGPQTNISFA
VPQEFEQPIRKFESFYNSSFSGRKLTWLHHLCAGELKVSLAKKSYLITMQTYQMAMLLLF
ENCDSMSCKEVREMLQLSHDNFQKHLQSLIDSKILNLD
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g10962.t4 | Gene3D | G3DSA:1.20.1310.10 | Cullin Repeats | 1 | 171 | 0.000 |
| 7 | g10962.t4 | Gene3D | G3DSA:1.20.1310.10 | Cullin Repeats | 172 | 288 | 0.000 |
| 10 | g10962.t4 | Gene3D | G3DSA:1.20.1310.10 | Cullin Repeats | 290 | 398 | 0.000 |
| 9 | g10962.t4 | Gene3D | G3DSA:1.20.1310.10 | Cullin Repeats | 401 | 513 | 0.000 |
| 11 | g10962.t4 | Gene3D | G3DSA:1.10.10.2620 | - | 514 | 638 | 0.000 |
| 2 | g10962.t4 | PANTHER | PTHR11932:SF131 | CULLIN-2 | 5 | 638 | 0.000 |
| 3 | g10962.t4 | PANTHER | PTHR11932 | CULLIN | 5 | 638 | 0.000 |
| 1 | g10962.t4 | Pfam | PF00888 | Cullin family | 14 | 636 | 0.000 |
| 12 | g10962.t4 | ProSiteProfiles | PS50069 | Cullin family profile. | 402 | 630 | 55.641 |
| 6 | g10962.t4 | SMART | SM00182 | cul_2 | 430 | 580 | 0.000 |
| 4 | g10962.t4 | SUPERFAMILY | SSF74788 | Cullin repeat-like | 10 | 392 | 0.000 |
| 5 | g10962.t4 | SUPERFAMILY | SSF75632 | Cullin homology domain | 399 | 637 | 0.000 |
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. There were no conditions that were differentially expressed