Gene loci information

Transcript annotation

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

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.t2 TSS g7469.t2 23898116 23898116
chr_2 g7469 g7469.t2 isoform g7469.t2 23898364 23899357
chr_2 g7469 g7469.t2 exon g7469.t2.exon1 23898364 23898508
chr_2 g7469 g7469.t2 cds g7469.t2.CDS1 23898364 23898508
chr_2 g7469 g7469.t2 exon g7469.t2.exon2 23898625 23898863
chr_2 g7469 g7469.t2 cds g7469.t2.CDS2 23898625 23898863
chr_2 g7469 g7469.t2 exon g7469.t2.exon3 23898923 23899047
chr_2 g7469 g7469.t2 cds g7469.t2.CDS3 23898923 23899047
chr_2 g7469 g7469.t2 exon g7469.t2.exon4 23899112 23899357
chr_2 g7469 g7469.t2 cds g7469.t2.CDS4 23899112 23899355
chr_2 g7469 g7469.t2 TTS g7469.t2 NA NA

Sequences

>g7469.t2 Gene=g7469 Length=755
ATGGAAATTGATACACCGGATCGCAAGAAATCTAACTTTTCCTCATTGGCAACTTCATCA
AACAGCCCAAATGGATCGATTTCTCGTGGCGGCAGCAGTAACTCAAAGGGTGATATAAAG
AAACTCGTGATTAAGAATTTTAAAGCTAAACCAACGTTACCTGAAAATTATCAGGAAAAT
ACATGGCAAAAACTTAAGGAAGCAGTAATTGCAATTCAAACTTCAACACCTATCACTTAT
TGTTTAGAAGAACTTTATCAAGCAGTTGAAAATATGTGTAGTCATAAAATGGACTCTCAG
TTGTATGTAAATTTAACAGGATTAGCAGAAAGTCATGTCAAATCGAATATTCGTCCGTTC
CTTGCAGAACGTGTAGACAAATTGCTGTATCTAAAGAAGGTCAATGAATGTTGGCAATCA
CACTGTCAACAGATGATTATGATCCGTAGTATATTTCTATATTTAGATCGCACATATGTA
TTGCAAAATCCGACTGTTCATTCAATCTGGGATCTCGGTTTAGAGCTGTTTCGTGATCAT
ATTGCTACAAATGCAACAGTTCAATCAAGAACTGTTGAAGGAATTTTAATGCTCATAGAG
AAAGAACGTAATGGTGAGACTGTAGATCGGACTTTGCTGAAGAGTCTTTTACGAATGTTC
TCTGACCTTCAAATTTATAAAGAAGCTTTTGAGAATAAATTTTTGGTCGCCACTAAACAA
TTATATCAAGCTGAAGGTCAACGAAAAATGCAAGA

>g7469.t2 Gene=g7469 Length=251
MEIDTPDRKKSNFSSLATSSNSPNGSISRGGSSNSKGDIKKLVIKNFKAKPTLPENYQEN
TWQKLKEAVIAIQTSTPITYCLEELYQAVENMCSHKMDSQLYVNLTGLAESHVKSNIRPF
LAERVDKLLYLKKVNECWQSHCQQMIMIRSIFLYLDRTYVLQNPTVHSIWDLGLELFRDH
IATNATVQSRTVEGILMLIEKERNGETVDRTLLKSLLRMFSDLQIYKEAFENKFLVATKQ
LYQAEGQRKMQ

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g7469.t2 Gene3D G3DSA:1.20.1310.10 Cullin Repeats 49 180 1.6E-45
7 g7469.t2 Gene3D G3DSA:1.20.1310.10 Cullin Repeats 181 251 7.0E-21
6 g7469.t2 MobiDBLite mobidb-lite consensus disorder prediction 1 35 -
5 g7469.t2 MobiDBLite mobidb-lite consensus disorder prediction 10 35 -
2 g7469.t2 PANTHER PTHR11932:SF66 CULLIN-4B 25 251 7.2E-100
3 g7469.t2 PANTHER PTHR11932 CULLIN 25 251 7.2E-100
1 g7469.t2 Pfam PF00888 Cullin family 62 251 1.2E-46
4 g7469.t2 SUPERFAMILY SSF74788 Cullin repeat-like 55 251 7.32E-64

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