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.t1 TSS g11288.t1 15424362 15424362
chr_1 g11288 g11288.t1 isoform g11288.t1 15424962 15427852
chr_1 g11288 g11288.t1 exon g11288.t1.exon1 15424962 15425104
chr_1 g11288 g11288.t1 cds g11288.t1.CDS1 15424962 15425104
chr_1 g11288 g11288.t1 exon g11288.t1.exon2 15425197 15425611
chr_1 g11288 g11288.t1 cds g11288.t1.CDS2 15425197 15425611
chr_1 g11288 g11288.t1 exon g11288.t1.exon3 15425811 15425885
chr_1 g11288 g11288.t1 cds g11288.t1.CDS3 15425811 15425885
chr_1 g11288 g11288.t1 exon g11288.t1.exon4 15425954 15427156
chr_1 g11288 g11288.t1 cds g11288.t1.CDS4 15425954 15427156
chr_1 g11288 g11288.t1 exon g11288.t1.exon5 15427219 15427300
chr_1 g11288 g11288.t1 cds g11288.t1.CDS5 15427219 15427300
chr_1 g11288 g11288.t1 exon g11288.t1.exon6 15427360 15427486
chr_1 g11288 g11288.t1 cds g11288.t1.CDS6 15427360 15427486
chr_1 g11288 g11288.t1 exon g11288.t1.exon7 15427552 15427852
chr_1 g11288 g11288.t1 cds g11288.t1.CDS7 15427552 15427852
chr_1 g11288 g11288.t1 TTS g11288.t1 15428187 15428187

Sequences

>g11288.t1 Gene=g11288 Length=2346
ATGGCGAGACCAAATTTTAGTAGTAATACAGGCCTTAGAAATATAAATCTGGAAGAAGTA
TGGGCAGATTTAGAAGAAGGAATCAAACAGATTTATAAACGTGAACAAAAAATGGCTGTA
CCACGTTATATGCAACTCTATACACATGTTTACAATTATTGCACGAGTGTTCATCAGCAG
CCACAACTTCGAGGAGCAACAACAAATAATAGAGCTGTTCGTCGCTCTGGTGCTGGTGCT
CAACAGCAACCTGTCTCAGGTGGTGCTCAATTGGTTGGTCTAGAGTTGTACAAACGTCTC
AAAGATTTTCTCCAAAGTTATCTTGTTCAACTTGAAGGCAAAGGTGTAGATTTGATGGGC
GAAGATGTACTGACATTCTATACAAAAGAATGGGAAGAATATCAATTCTCCAGTAAAGTA
TTGAATGGTGTATGCGCTTATCTCAATCGTCATTGGGTACGTCGAGAATGTGAGGAGGGA
CGAAAAGATATTTACGAAATCTATCAACTTGCTCTTGTCACATGGCGCGACAATCTGTTC
AAGAAACTCAACAAACAGGTGACCAATGCCGTTCTTAAATTGATTGAGAGTGAACGAAAT
GGCGATACTATAAATTCCAGTTTAGTATCTGGTGTCATAAATTGTTATGTTGAATTGGGT
CTCAATGAAGAGGATCCTCAAGCAAAAGGACAAAACTTGAAAGTTTATAAAGAGAGTTTT
GAAAATCAATTCCTTCAAGATACCGAACAGTTCTACACACGTGAATCTGATGAATTTTTG
GCCATTAATCCTGTAACAGAATATATGAAAAGAGTTGAGCAACGCTTGAATGAAGAAAAG
AAAAGAGTACAAGTATATTTGCACGAGTCAACTAATAGTCCTCTTGCAAATAGATGTGAA
ACAGTCCTCATTCATAAACACTTAGACGCTTTTCGTGTTGAATTTCAAAATTTGTTAAAT
GCTGACAAGAATGAAGATTTAGCGAGAATGTATATGCTTGTGTCTCGTACAGCTGATGGG
CTTGCAGATCTGAAAATTGCTCTTGAGAATCACATAAATAATCAAGGCCAACAAGCAATT
GATAAATGCGGAGAAGCAGCTGCTAATGATCCTAAAATATACGTTCAGACTATTCTTGAA
GTACACATGAAATTCAATAGTCTTGTAATGACTGCTTTCAACAATGATAGTGGTTTTGTT
GCCGCATTAGATAAAGCATGCAACAAATTCATCAATTCAAATTGCGTTACGCAAGCCAGT
AAGAACGAAAGTCGTTCACCTGAGTTGCTGGCCAAATATTGTGATATTTTATTGAAAAAG
AGCAGCAAAAATCCAGAAGAAGCAGAGCTTGAAGATACTCTAAATCATGTTATGATTGTT
TTCAAATATATAACCGATAAAGATGTATTTCAGAAATTTTACAGTAAAATGCTTGCAAAG
CGTCTTGTTTTTTACATGTCTGCGAGTGATGATGCTGAAGCTTCAATGATCTCGAAATTA
AAACAAGCCTGTGGCTTTGAATATACAAGTAAACTTCAAAGGATGTTCCAGGATATTGGA
TTAAGCAAAGATTTGAATGAAAAATATAAAGCATTCTTGAAAGAAAATTCGCAACTGAGT
AATCAAATTGATTTCAGTATTCAAGTGCTCTCATCAGGATCCTGGCCATTCGTTCAAAGC
ACACCATTTGTGTTGCCAAGTGAACTTGAACAGTCAGTTCAACGCTTTAATAGCTTTTAT
GCAAAACTTCACAGTGGACGAAAATTAAATTGGTTGTATAATATGTGTAAAGGAGAAATA
ACTACAAATTGCTTCCGAAATCGGTACATGTTTCAAGCCAACACTTTTCAAATGGCTATA
TTGCTGCAATATAATGATCAAACCAAATGGACCGTGCAACAGTTAATGGACAATACAGGT
ATAAGCTATGATAATATGCAACAAATACTTGGAATTTTGCTTAAAACACGTTTGCTCGAG
GCAGACGTTGATGAAAGCCAATTGCAACCAGATACTGAAATTTCATTATTCTTGGGATAT
AAAAATAAAAAGTTGCGAATCAACATAAATTTCCCATTGAAATCGGAACAGAAAGCTGAG
CAAGAAGTAACACATAAGCACATCGAGGAAGACCGTAAAATGCTCATTCAAGCAGCAATC
GTTCGCATCATGAAAATGCGAAAAGTGTTGAATCACACTCAATTAGTAACTGAAGTTTTG
AATCAACTCTCAACACGCTTTAAGCCCAAGGTTCAAATCATCAAAAAATGTATTGACATT
CTTATTGAAAAAGAATACCTCGAACGAATGGATGGTCAAAAGGACACTTACAGTTATGTA
GCATAA

>g11288.t1 Gene=g11288 Length=781
MARPNFSSNTGLRNINLEEVWADLEEGIKQIYKREQKMAVPRYMQLYTHVYNYCTSVHQQ
PQLRGATTNNRAVRRSGAGAQQQPVSGGAQLVGLELYKRLKDFLQSYLVQLEGKGVDLMG
EDVLTFYTKEWEEYQFSSKVLNGVCAYLNRHWVRRECEEGRKDIYEIYQLALVTWRDNLF
KKLNKQVTNAVLKLIESERNGDTINSSLVSGVINCYVELGLNEEDPQAKGQNLKVYKESF
ENQFLQDTEQFYTRESDEFLAINPVTEYMKRVEQRLNEEKKRVQVYLHESTNSPLANRCE
TVLIHKHLDAFRVEFQNLLNADKNEDLARMYMLVSRTADGLADLKIALENHINNQGQQAI
DKCGEAAANDPKIYVQTILEVHMKFNSLVMTAFNNDSGFVAALDKACNKFINSNCVTQAS
KNESRSPELLAKYCDILLKKSSKNPEEAELEDTLNHVMIVFKYITDKDVFQKFYSKMLAK
RLVFYMSASDDAEASMISKLKQACGFEYTSKLQRMFQDIGLSKDLNEKYKAFLKENSQLS
NQIDFSIQVLSSGSWPFVQSTPFVLPSELEQSVQRFNSFYAKLHSGRKLNWLYNMCKGEI
TTNCFRNRYMFQANTFQMAILLQYNDQTKWTVQQLMDNTGISYDNMQQILGILLKTRLLE
ADVDESQLQPDTEISLFLGYKNKKLRININFPLKSEQKAEQEVTHKHIEEDRKMLIQAAI
VRIMKMRKVLNHTQLVTEVLNQLSTRFKPKVQIIKKCIDILIEKEYLERMDGQKDTYSYV
A

Protein features from InterProScan

Transcript Database ID Name Start End E.value
16 g11288.t1 Coils Coil Coil 269 289 -
15 g11288.t1 Coils Coil Coil 522 542 -
10 g11288.t1 Gene3D G3DSA:1.20.1310.10 Cullin Repeats 17 184 6.6E-57
11 g11288.t1 Gene3D G3DSA:1.20.1310.10 Cullin Repeats 185 307 4.5E-48
9 g11288.t1 Gene3D G3DSA:1.20.1310.10 Cullin Repeats 308 422 3.3E-40
8 g11288.t1 Gene3D G3DSA:1.20.1310.10 Cullin Repeats 423 537 1.8E-46
12 g11288.t1 Gene3D G3DSA:4.10.1030.10 Ring Box Chain A; domain 5 541 613 2.5E-29
14 g11288.t1 Gene3D G3DSA:1.10.10.10 winged helix repressor DNA binding domain 614 676 3.2E-20
13 g11288.t1 Gene3D G3DSA:1.10.10.10 winged helix repressor DNA binding domain 677 781 4.1E-41
20 g11288.t1 MobiDBLite mobidb-lite consensus disorder prediction 65 84 -
3 g11288.t1 PANTHER PTHR11932 CULLIN 12 780 0.0
4 g11288.t1 PANTHER PTHR11932:SF81 CULLIN-1 12 780 0.0
1 g11288.t1 Pfam PF00888 Cullin family 21 675 9.5E-194
2 g11288.t1 Pfam PF10557 Cullin protein neddylation domain 711 772 3.9E-26
17 g11288.t1 ProSitePatterns PS01256 Cullin family signature. 754 781 -
21 g11288.t1 ProSiteProfiles PS50069 Cullin family profile. 425 654 60.775
18 g11288.t1 SMART SM00182 cul_2 455 604 1.6E-79
19 g11288.t1 SMART SM00884 Cullin_Nedd8_2 708 775 8.3E-37
5 g11288.t1 SUPERFAMILY SSF74788 Cullin repeat-like 17 416 1.18E-125
7 g11288.t1 SUPERFAMILY SSF75632 Cullin homology domain 422 690 3.79E-96
6 g11288.t1 SUPERFAMILY SSF46785 Winged helix DNA-binding domain 692 781 3.3E-30

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

Pathway

  • This transcript belongs to the following pathways

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