Gene loci information

Transcript annotation

  • This transcript has been annotated as Cullin-1.

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 g11288 g11288.t7 isoform g11288.t7 15426794 15428192
chr_1 g11288 g11288.t7 exon g11288.t7.exon1 15426794 15427156
chr_1 g11288 g11288.t7 cds g11288.t7.CDS1 15426806 15427156
chr_1 g11288 g11288.t7 exon g11288.t7.exon2 15427219 15427300
chr_1 g11288 g11288.t7 cds g11288.t7.CDS2 15427219 15427300
chr_1 g11288 g11288.t7 exon g11288.t7.exon3 15427360 15427486
chr_1 g11288 g11288.t7 cds g11288.t7.CDS3 15427360 15427486
chr_1 g11288 g11288.t7 exon g11288.t7.exon4 15427552 15428192
chr_1 g11288 g11288.t7 cds g11288.t7.CDS4 15427552 15427852
chr_1 g11288 g11288.t7 TTS g11288.t7 15428187 15428187
chr_1 g11288 g11288.t7 TSS g11288.t7 NA NA

Sequences

>g11288.t7 Gene=g11288 Length=1213
GCTGAAGCTTCAATGATCTCGAAATTAAAACAAGCCTGTGGCTTTGAATATACAAGTAAA
CTTCAAAGGATGTTCCAGGATATTGGATTAAGCAAAGATTTGAATGAAAAATATAAAGCA
TTCTTGAAAGAAAATTCGCAACTGAGTAATCAAATTGATTTCAGTATTCAAGTGCTCTCA
TCAGGATCCTGGCCATTCGTTCAAAGCACACCATTTGTGTTGCCAAGTGAACTTGAACAG
TCAGTTCAACGCTTTAATAGCTTTTATGCAAAACTTCACAGTGGACGAAAATTAAATTGG
TTGTATAATATGTGTAAAGGAGAAATAACTACAAATTGCTTCCGAAATCGGTACATGTTT
CAAGCCAACACTTTTCAAATGGCTATATTGCTGCAATATAATGATCAAACCAAATGGACC
GTGCAACAGTTAATGGACAATACAGGTATAAGCTATGATAATATGCAACAAATACTTGGA
ATTTTGCTTAAAACACGTTTGCTCGAGGCAGACGTTGATGAAAGCCAATTGCAACCAGAT
ACTGAAATTTCATTATTCTTGGGATATAAAAATAAAAAGTTGCGAATCAACATAAATTTC
CCATTGAAATCGGAACAGAAAGCTGAGCAAGAAGTAACACATAAGCACATCGAGGAAGAC
CGTAAAATGCTCATTCAAGCAGCAATCGTTCGCATCATGAAAATGCGAAAAGTGTTGAAT
CACACTCAATTAGTAACTGAAGTTTTGAATCAACTCTCAACACGCTTTAAGCCCAAGGTT
CAAATCATCAAAAAATGTATTGACATTCTTATTGAAAAAGAATACCTCGAACGAATGGAT
GGTCAAAAGGACACTTACAGTTATGTAGCATAAAAAATTCGACGAAAATATTTGTTATTA
ATTTTCTTTAGCTCATTTCAATTTTACCATCTTCTAATTATTATTTTGTGAAGTTAATCA
TCTGCTGTTTTGTTTTATGCACACGTTTTGTATCTTTGTTCAACTACTTAGATCTTTCAA
TTAAATCATTCTTTTATTATAGATTTATTTCTTCGTACATGCTATATATACTATTTCTTC
AGACTTTAATGAGAAAATATACATACACATATGAGTATGTCTTGTAATATTCAAAACTAT
TTTGGAAAGAAAAATGTTAGTTTTAATGTGGAAAGCACTGAAAAGAATAAAAAATAATTA
AAAACTCCAAATT

>g11288.t7 Gene=g11288 Length=286
MISKLKQACGFEYTSKLQRMFQDIGLSKDLNEKYKAFLKENSQLSNQIDFSIQVLSSGSW
PFVQSTPFVLPSELEQSVQRFNSFYAKLHSGRKLNWLYNMCKGEITTNCFRNRYMFQANT
FQMAILLQYNDQTKWTVQQLMDNTGISYDNMQQILGILLKTRLLEADVDESQLQPDTEIS
LFLGYKNKKLRININFPLKSEQKAEQEVTHKHIEEDRKMLIQAAIVRIMKMRKVLNHTQL
VTEVLNQLSTRFKPKVQIIKKCIDILIEKEYLERMDGQKDTYSYVA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g11288.t7 Coils Coil Coil 27 47 -
7 g11288.t7 Gene3D G3DSA:1.20.1310.10 Cullin Repeats 1 42 2.6E-12
8 g11288.t7 Gene3D G3DSA:4.10.1030.10 Ring Box Chain A; domain 5 46 118 5.5E-30
9 g11288.t7 Gene3D G3DSA:1.10.10.10 winged helix repressor DNA binding domain 119 181 7.4E-21
10 g11288.t7 Gene3D G3DSA:1.10.10.10 winged helix repressor DNA binding domain 182 286 7.1E-42
3 g11288.t7 PANTHER PTHR11932 CULLIN 1 285 2.7E-125
4 g11288.t7 PANTHER PTHR11932:SF81 CULLIN-1 1 285 2.7E-125
1 g11288.t7 Pfam PF00888 Cullin family 1 180 1.4E-57
2 g11288.t7 Pfam PF10557 Cullin protein neddylation domain 216 277 8.9E-27
12 g11288.t7 ProSitePatterns PS01256 Cullin family signature. 259 286 -
15 g11288.t7 ProSiteProfiles PS50069 Cullin family profile. 1 159 38.511
13 g11288.t7 SMART SM00182 cul_2 1 109 1.8E-33
14 g11288.t7 SMART SM00884 Cullin_Nedd8_2 213 280 8.3E-37
6 g11288.t7 SUPERFAMILY SSF75632 Cullin homology domain 1 195 1.29E-61
5 g11288.t7 SUPERFAMILY SSF46785 Winged helix DNA-binding domain 197 286 4.99E-31

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