Gene loci information

Transcript annotation

  • This transcript has been annotated as Cullin-2.

Parent gene

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.t5 TSS g10962.t5 13040144 13040144
chr_1 g10962 g10962.t5 isoform g10962.t5 13040728 13041922
chr_1 g10962 g10962.t5 exon g10962.t5.exon1 13040728 13041423
chr_1 g10962 g10962.t5 cds g10962.t5.CDS1 13040821 13041423
chr_1 g10962 g10962.t5 exon g10962.t5.exon2 13041482 13041655
chr_1 g10962 g10962.t5 cds g10962.t5.CDS2 13041482 13041655
chr_1 g10962 g10962.t5 exon g10962.t5.exon3 13041714 13041862
chr_1 g10962 g10962.t5 cds g10962.t5.CDS3 13041714 13041862
chr_1 g10962 g10962.t5 exon g10962.t5.exon4 13041920 13041922
chr_1 g10962 g10962.t5 cds g10962.t5.CDS4 13041920 13041920
chr_1 g10962 g10962.t5 TTS g10962.t5 NA NA

Sequences

>g10962.t5 Gene=g10962 Length=1022
TTGAATCAACAACACATAAAGAAACAAAAGGTATCAGAGGCTGAAATTTTATACGGAAAT
GGCACTACGCCGCTCGCAATTTCGCAAGAACAGATGGAAATAGGAGAGTTAGGGCTTGAT
ATCTGGAGATTATTTATGATACAAAATTTAGGCGATATTTTAGTAAAACAAATTCTTCAA
GGAATTGAAAGAGATAGACTTGAAAACAACTTAACATCAAAAGACATTGAAACAATTCAC
GGCGTAATTAATAGTTTCGTTTCTGTACAAGATTACAAAAAGAAAGGAAGTCTTCATTTA
TACGAAACTCTTTTTGAAGAGAAATTATTAGAGGCCAGCGGTTCATATTTCATGTCGCAA
GCATCAAAATTGTTACAATCCTGCTCAGTTAGTCAATACATGCAAGAGGTTATAAGAGTT
TTGGATGAAGAAAACGTTAGAGCTCATAAATTTGTCCACATGAACTCGGTTAAAAAACTC
AAAAAAGAATGCGAAGATCGAATGATAAGTGATCATAAAGCTTTTCTTTATTCTGAATGT
AAAGAAATGGTTAGTAATGATAAACGAGATGACCTTAGAAATTTATACATACTTCTAAAG
CCATTGCAAGACGGTCTTAAAGAACTTATTCAAATATTACTTGAACAAATCAAGAATGAA
GGTGCTGAATCAATTATGAACTTAAAAGGAGAGAATGTTCATATTCAATTTGTTGAGAAT
ATGCTTCAAGTACATCAAAAGTATGAGAATCTTATATCAGAGACATTCAAAAATGATCCT
CTATTCTTGAGTGCTTTGGATAAGGCTTGTGCAAGTGTTATCAATTCTAAATTGAGTGAT
GGAAAGACGACATGCAGAAGTGCTGAACTCGTTGCAAAATATTGTGACAATTTGTTAAAG
AAATCTAAATCCACCGAAAGTGAAATTGAATCGAAATTATCTAAGAGTATCACAATTTTT
AAATATATCGAGGATAAGGATGTTTACCAAAAATTCTATAGTAGGATGCTTGCTAAACGA
CT

>g10962.t5 Gene=g10962 Length=309
MEIGELGLDIWRLFMIQNLGDILVKQILQGIERDRLENNLTSKDIETIHGVINSFVSVQD
YKKKGSLHLYETLFEEKLLEASGSYFMSQASKLLQSCSVSQYMQEVIRVLDEENVRAHKF
VHMNSVKKLKKECEDRMISDHKAFLYSECKEMVSNDKRDDLRNLYILLKPLQDGLKELIQ
ILLEQIKNEGAESIMNLKGENVHIQFVENMLQVHQKYENLISETFKNDPLFLSALDKACA
SVINSKLSDGKTTCRSAELVAKYCDNLLKKSKSTESEIESKLSKSITIFKYIEDKDVYQK
FYSRMLAKR

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g10962.t5 Gene3D G3DSA:1.20.1310.10 Cullin Repeats 22 141 0.0
7 g10962.t5 Gene3D G3DSA:1.20.1310.10 Cullin Repeats 142 251 0.0
6 g10962.t5 Gene3D G3DSA:1.20.1310.10 Cullin Repeats 254 309 0.0
2 g10962.t5 PANTHER PTHR11932:SF131 CULLIN-2 1 309 0.0
3 g10962.t5 PANTHER PTHR11932 CULLIN 1 309 0.0
1 g10962.t5 Pfam PF00888 Cullin family 2 309 0.0
9 g10962.t5 ProSiteProfiles PS50069 Cullin family profile. 255 309 18.1
4 g10962.t5 SUPERFAMILY SSF74788 Cullin repeat-like 2 245 0.0
5 g10962.t5 SUPERFAMILY SSF75632 Cullin homology domain 252 309 0.0

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.

Raw TPM values