Gene loci information

Transcript annotation

  • This transcript has been annotated as Cullin-4B.

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_2 g7469 g7469.t4 isoform g7469.t4 23900026 23901071
chr_2 g7469 g7469.t4 exon g7469.t4.exon1 23900026 23900483
chr_2 g7469 g7469.t4 cds g7469.t4.CDS1 23900079 23900483
chr_2 g7469 g7469.t4 exon g7469.t4.exon2 23900539 23900709
chr_2 g7469 g7469.t4 cds g7469.t4.CDS2 23900539 23900709
chr_2 g7469 g7469.t4 exon g7469.t4.exon3 23900768 23900920
chr_2 g7469 g7469.t4 cds g7469.t4.CDS3 23900768 23900920
chr_2 g7469 g7469.t4 exon g7469.t4.exon4 23900976 23901071
chr_2 g7469 g7469.t4 cds g7469.t4.CDS4 23900976 23901071
chr_2 g7469 g7469.t4 TTS g7469.t4 23901231 23901231
chr_2 g7469 g7469.t4 TSS g7469.t4 NA NA

Sequences

>g7469.t4 Gene=g7469 Length=878
TATCAAAGTTAAAACAAGAGTGTGGCGGAGGTTTTACCTCAAAATTGGAGGGAATGTTTA
AAGATATGGAATTGAGCAAAGATATTAACATTGCGTTTAGACAACACATTGAAGGAAATG
CTAATTCAAAAGATCTTATATTGTTTCATTCAATTGGAATTGATATGACTGTAAATATAT
TGACAATGGGCTACTGGCCGACATATCCCGTTATGGAAGTTACAATGCCACCTCAATTAG
TTGAGTATCAAAATGTTTTCACAAAATTCTATCTGGCAAAGCATAGCGGAAGAAAATTGC
AGTGGCAAGCAACTTTGGGTCATTGTGTTTTGAAAGCACGTTTCGATCAGGGACCGAAAG
ATCTTCAAGTGTCCTTATTTCAATCATTAGTTTTATTGCTTTTTAACGATTGTGATGAGA
TGACATTAGAAGAGATTTTACAAGCAACAAACATTGAAGATGGTGAATTAAGAAGAACAC
TTCAATCACTCGCATGCGGAAAAGCAAGAGTGCTTACAAAAATTCCAAAAAGTCGTGAGG
TTGAAGATCATGATAAATTTAAATTTAATAATGAATTCACAGCAAAATTATTCAGGATTA
AAATTAATTCCATCCAAATGAAAGAAACTAATGAAGAGCAAAAAGCAACAGAGGAGAGAG
TTTATCAAGATCGTCAATATCAAATTGATGCTGCAGTTGTGAGAATTATGAAAATGAGAA
AAACATTAAGTCATAATTTGCTCATTAGTGAGCTTTATAAGCAACTTTCGTTCCCAGTCA
AGCCTGCTGATTTGAAAAAGAGAATTGAATCACTGATCGACCGTGACTACATGGAACGAG
ATAAAGATAATCAAAATCAATATAATTATGTTGCATAA

>g7469.t4 Gene=g7469 Length=274
MFKDMELSKDINIAFRQHIEGNANSKDLILFHSIGIDMTVNILTMGYWPTYPVMEVTMPP
QLVEYQNVFTKFYLAKHSGRKLQWQATLGHCVLKARFDQGPKDLQVSLFQSLVLLLFNDC
DEMTLEEILQATNIEDGELRRTLQSLACGKARVLTKIPKSREVEDHDKFKFNNEFTAKLF
RIKINSIQMKETNEEQKATEERVYQDRQYQIDAAVVRIMKMRKTLSHNLLISELYKQLSF
PVKPADLKKRIESLIDRDYMERDKDNQNQYNYVA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g7469.t4 Gene3D G3DSA:1.10.10.2620 - 35 191 2.2E-55
11 g7469.t4 Gene3D G3DSA:1.10.10.10 winged helix repressor DNA binding domain 201 274 5.1E-34
3 g7469.t4 PANTHER PTHR11932:SF66 CULLIN-4B 1 274 4.1E-142
4 g7469.t4 PANTHER PTHR11932 CULLIN 1 274 4.1E-142
1 g7469.t4 Pfam PF00888 Cullin family 1 175 6.2E-61
2 g7469.t4 Pfam PF10557 Cullin protein neddylation domain 206 266 2.6E-23
9 g7469.t4 ProSitePatterns PS01256 Cullin family signature. 247 274 -
12 g7469.t4 ProSiteProfiles PS50069 Cullin family profile. 1 147 34.517
7 g7469.t4 SMART SM00182 cul_2 1 97 9.3E-8
8 g7469.t4 SMART SM00884 Cullin_Nedd8_2 203 268 2.3E-34
6 g7469.t4 SUPERFAMILY SSF75632 Cullin homology domain 1 190 1.15E-60
5 g7469.t4 SUPERFAMILY SSF46785 Winged helix DNA-binding domain 186 274 2.55E-28

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
GO:0031461 cullin-RING ubiquitin ligase complex CC

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