General information for g11288.t5
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Cullin-1.
Parent gene
- The parent gene g11288 is located on chr_1: 15426794..15429885 (+ strand)
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.t5 | TSS | g11288.t5 | 15424362 | 15424362 |
| chr_1 | g11288 | g11288.t5 | isoform | g11288.t5 | 15425207 | 15427156 |
| chr_1 | g11288 | g11288.t5 | exon | g11288.t5.exon1 | 15425207 | 15425611 |
| chr_1 | g11288 | g11288.t5 | cds | g11288.t5.CDS1 | 15425408 | 15425611 |
| chr_1 | g11288 | g11288.t5 | exon | g11288.t5.exon2 | 15425811 | 15425885 |
| chr_1 | g11288 | g11288.t5 | cds | g11288.t5.CDS2 | 15425811 | 15425885 |
| chr_1 | g11288 | g11288.t5 | exon | g11288.t5.exon3 | 15425954 | 15427156 |
| chr_1 | g11288 | g11288.t5 | cds | g11288.t5.CDS3 | 15425954 | 15427156 |
| chr_1 | g11288 | g11288.t5 | TTS | g11288.t5 | NA | NA |
Sequences
>g11288.t5 Gene=g11288 Length=1683
AATTATTGCACGAGTGTTCATCAGCAGCCACAACTTCGAGGAGCAACAACAAATAATAGA
GCTGTTCGTCGCTCTGGTGCTGGTGCTCAACAGCAACCTGTCTCAGGTGGTGCTCAATTG
GTTGGTCTAGAGTTGTACAAACGTCTCAAAGATTTTCTCCAAAGTTATCTTGTTCAACTT
GAAGGCAAAGGTGTAGATTTGATGGGCGAAGATGTACTGACATTCTATACAAAAGAATGG
GAAGAATATCAATTCTCCAGTAAAGTATTGAATGGTGTATGCGCTTATCTCAATCGTCAT
TGGGTACGTCGAGAATGTGAGGAGGGACGAAAAGATATTTACGAAATCTATCAACTTGCT
CTTGTCACATGGCGCGACAATCTGTTCAAGAAACTCAACAAACAGGTGACCAATGCCGTT
CTTAAATTGATTGAGAGTGAACGAAATGGCGATACTATAAATTCCAGTTTAGTATCTGGT
GTCATAAATTGTTATGTTGAATTGGGTCTCAATGAAGAGGATCCTCAAGCAAAAGGACAA
AACTTGAAAGTTTATAAAGAGAGTTTTGAAAATCAATTCCTTCAAGATACCGAACAGTTC
TACACACGTGAATCTGATGAATTTTTGGCCATTAATCCTGTAACAGAATATATGAAAAGA
GTTGAGCAACGCTTGAATGAAGAAAAGAAAAGAGTACAAGTATATTTGCACGAGTCAACT
AATAGTCCTCTTGCAAATAGATGTGAAACAGTCCTCATTCATAAACACTTAGACGCTTTT
CGTGTTGAATTTCAAAATTTGTTAAATGCTGACAAGAATGAAGATTTAGCGAGAATGTAT
ATGCTTGTGTCTCGTACAGCTGATGGGCTTGCAGATCTGAAAATTGCTCTTGAGAATCAC
ATAAATAATCAAGGCCAACAAGCAATTGATAAATGCGGAGAAGCAGCTGCTAATGATCCT
AAAATATACGTTCAGACTATTCTTGAAGTACACATGAAATTCAATAGTCTTGTAATGACT
GCTTTCAACAATGATAGTGGTTTTGTTGCCGCATTAGATAAAGCATGCAACAAATTCATC
AATTCAAATTGCGTTACGCAAGCCAGTAAGAACGAAAGTCGTTCACCTGAGTTGCTGGCC
AAATATTGTGATATTTTATTGAAAAAGAGCAGCAAAAATCCAGAAGAAGCAGAGCTTGAA
GATACTCTAAATCATGTTATGATTGTTTTCAAATATATAACCGATAAAGATGTATTTCAG
AAATTTTACAGTAAAATGCTTGCAAAGCGTCTTGTTTTTTACATGTCTGCGAGTGATGAT
GCTGAAGCTTCAATGATCTCGAAATTAAAACAAGCCTGTGGCTTTGAATATACAAGTAAA
CTTCAAAGGATGTTCCAGGATATTGGATTAAGCAAAGATTTGAATGAAAAATATAAAGCA
TTCTTGAAAGAAAATTCGCAACTGAGTAATCAAATTGATTTCAGTATTCAAGTGCTCTCA
TCAGGATCCTGGCCATTCGTTCAAAGCACACCATTTGTGTTGCCAAGTGAACTTGAACAG
TCAGTTCAACGCTTTAATAGCTTTTATGCAAAACTTCACAGTGGACGAAAATTAAATTGG
TTGTATAATATGTGTAAAGGAGAAATAACTACAAATTGCTTCCGAAATCGGTACATGTTT
CAA
>g11288.t5 Gene=g11288 Length=494
MGEDVLTFYTKEWEEYQFSSKVLNGVCAYLNRHWVRRECEEGRKDIYEIYQLALVTWRDN
LFKKLNKQVTNAVLKLIESERNGDTINSSLVSGVINCYVELGLNEEDPQAKGQNLKVYKE
SFENQFLQDTEQFYTRESDEFLAINPVTEYMKRVEQRLNEEKKRVQVYLHESTNSPLANR
CETVLIHKHLDAFRVEFQNLLNADKNEDLARMYMLVSRTADGLADLKIALENHINNQGQQ
AIDKCGEAAANDPKIYVQTILEVHMKFNSLVMTAFNNDSGFVAALDKACNKFINSNCVTQ
ASKNESRSPELLAKYCDILLKKSSKNPEEAELEDTLNHVMIVFKYITDKDVFQKFYSKML
AKRLVFYMSASDDAEASMISKLKQACGFEYTSKLQRMFQDIGLSKDLNEKYKAFLKENSQ
LSNQIDFSIQVLSSGSWPFVQSTPFVLPSELEQSVQRFNSFYAKLHSGRKLNWLYNMCKG
EITTNCFRNRYMFQ
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g11288.t5 | Coils | Coil | Coil | 151 | 171 | - |
| 13 | g11288.t5 | Coils | Coil | Coil | 404 | 424 | - |
| 8 | g11288.t5 | Gene3D | G3DSA:1.20.1310.10 | Cullin Repeats | 1 | 66 | 3.4E-27 |
| 7 | g11288.t5 | Gene3D | G3DSA:1.20.1310.10 | Cullin Repeats | 67 | 189 | 2.1E-48 |
| 9 | g11288.t5 | Gene3D | G3DSA:1.20.1310.10 | Cullin Repeats | 190 | 304 | 1.6E-40 |
| 10 | g11288.t5 | Gene3D | G3DSA:1.20.1310.10 | Cullin Repeats | 305 | 419 | 8.5E-47 |
| 11 | g11288.t5 | Gene3D | G3DSA:4.10.1030.10 | Ring Box Chain A; domain 5 | 423 | 494 | 2.5E-29 |
| 2 | g11288.t5 | PANTHER | PTHR11932 | CULLIN | 1 | 494 | 1.0E-230 |
| 3 | g11288.t5 | PANTHER | PTHR11932:SF81 | CULLIN-1 | 1 | 494 | 1.0E-230 |
| 1 | g11288.t5 | Pfam | PF00888 | Cullin family | 2 | 492 | 2.7E-164 |
| 14 | g11288.t5 | ProSiteProfiles | PS50069 | Cullin family profile. | 307 | 494 | 51.019 |
| 6 | g11288.t5 | SMART | SM00182 | cul_2 | 337 | 486 | 1.6E-79 |
| 4 | g11288.t5 | SUPERFAMILY | SSF74788 | Cullin repeat-like | 2 | 298 | 4.45E-103 |
| 5 | g11288.t5 | SUPERFAMILY | SSF75632 | Cullin homology domain | 304 | 493 | 1.44E-75 |
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.
