General information for g6499.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Cullin-3.
Parent gene
- The parent gene g6499 is located on chr_2: 17300888..17302866 (+ 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_2 | g6499 | g6499.t1 | isoform | g6499.t1 | 17300888 | 17302866 |
| chr_2 | g6499 | g6499.t1 | exon | g6499.t1.exon1 | 17300888 | 17300944 |
| chr_2 | g6499 | g6499.t1 | cds | g6499.t1.CDS1 | 17300888 | 17300944 |
| chr_2 | g6499 | g6499.t1 | exon | g6499.t1.exon2 | 17301443 | 17301973 |
| chr_2 | g6499 | g6499.t1 | cds | g6499.t1.CDS2 | 17301443 | 17301973 |
| chr_2 | g6499 | g6499.t1 | exon | g6499.t1.exon3 | 17302084 | 17302581 |
| chr_2 | g6499 | g6499.t1 | cds | g6499.t1.CDS3 | 17302084 | 17302581 |
| chr_2 | g6499 | g6499.t1 | exon | g6499.t1.exon4 | 17302777 | 17302866 |
| chr_2 | g6499 | g6499.t1 | cds | g6499.t1.CDS4 | 17302777 | 17302866 |
| chr_2 | g6499 | g6499.t1 | TSS | g6499.t1 | NA | NA |
| chr_2 | g6499 | g6499.t1 | TTS | g6499.t1 | NA | NA |
Sequences
>g6499.t1 Gene=g6499 Length=1176
ATGAATCGACAGCCTCCTCCAAAGAAAGAAGGAAAAATGCGGATTCGTGCATTTCCCATG
ACGATGGATGAAAAATTTGTAGAATCAATATGGTCTTTACTAAAAAAATGCAATTCAAGA
GATTCAAAAGAAAAACAATTCTGGGCTATCTTTGAAGAGTTGTATCGTAATGCTTACACA
ATGGTTCTTCATAAACATGGTGAACGACTTTATAATGGATTAAAGGAAGTTGTCACACAA
CATTTGCAACAAAAAGTTCGTGAAGATGTTCTTCGATCATTAAACAACAACTTTCTGCAG
ACATTAAATCAAGCTTGGACAGATCATCAAACATCAATGGTCATGATTAGAGACATTCTT
ATGTACATGGATCGTGTTTACGTACAACAAAATGATGTTGATAATGTTTATAACTTAGGA
CTCATAATATTTCGTGATGAAATCATAAGTCACGAAAGGATCAGAAATCACTTACGCGAG
ACACTATTAGCAATGATCATGAATGAACGAAAAGGAGAGGCAATAGATCATATCTTAATA
AAAAATGCATGTCAAATGCTAATGATTCTCGGTATCAATAATCGATGGGTTGAAGCAAGA
ATCACAGAAGAGGCAGAACGAGCGAAACTTTACCTGGATGAAAGCACTGAGCAGCGAATT
GTCGATGTAGTTCAAGATGAATTAATTAAGAAACATATGCGAACAATTGTTGAAATGGAG
AACTCTGGAGTAGTTTATATGCTTCGTAATACAAAGACCGATGATTTGGCATGCATGTAT
AAACTATTTTCACGTGTCAGTGAAGGTATCAAAACGATTTCTGAATGTGTTAGCAAATAT
CTTCGTGAACAAGGCACATCTTTAGTGAAAGAGGAAGAAGGTGGTACAAATCCAATTACA
TTTGTGCAAAATCTGCTTGATTTGAAAGATCGCTTTGATCATTTCTTGAAACATTCATTC
AGTACTGAGAAGACATTTAAACACATGATTTCATCAGATTTTGAATATTTCCTCAATTTG
AATAGTAAATCACCAGAATATCTTTCACTTTTTATTGATGATAAGCTCAAAAAAGGATGC
AAAGGGATGTCTGAACAAGAAATTGAAACGATTTTGGATAAAACAATGGTTCTGTTCCGC
TATTTACTTGAAAAAGATGTATTTGAACGCTATTAA
>g6499.t1 Gene=g6499 Length=391
MNRQPPPKKEGKMRIRAFPMTMDEKFVESIWSLLKKCNSRDSKEKQFWAIFEELYRNAYT
MVLHKHGERLYNGLKEVVTQHLQQKVREDVLRSLNNNFLQTLNQAWTDHQTSMVMIRDIL
MYMDRVYVQQNDVDNVYNLGLIIFRDEIISHERIRNHLRETLLAMIMNERKGEAIDHILI
KNACQMLMILGINNRWVEARITEEAERAKLYLDESTEQRIVDVVQDELIKKHMRTIVEME
NSGVVYMLRNTKTDDLACMYKLFSRVSEGIKTISECVSKYLREQGTSLVKEEEGGTNPIT
FVQNLLDLKDRFDHFLKHSFSTEKTFKHMISSDFEYFLNLNSKSPEYLSLFIDDKLKKGC
KGMSEQEIETILDKTMVLFRYLLEKDVFERY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 13 | g6499.t1 | Gene3D | G3DSA:1.20.1310.10 | Cullin Repeats | 16 | 147 | 0.000 |
| 12 | g6499.t1 | Gene3D | G3DSA:1.20.1310.10 | Cullin Repeats | 148 | 195 | 0.000 |
| 11 | g6499.t1 | Gene3D | G3DSA:1.20.1310.10 | Cullin Repeats | 196 | 233 | 0.000 |
| 9 | g6499.t1 | Gene3D | G3DSA:1.20.1310.10 | Cullin Repeats | 234 | 341 | 0.000 |
| 10 | g6499.t1 | Gene3D | G3DSA:1.20.1310.10 | Cullin Repeats | 342 | 391 | 0.000 |
| 4 | g6499.t1 | PANTHER | PTHR11932 | CULLIN | 8 | 191 | 0.000 |
| 6 | g6499.t1 | PANTHER | PTHR11932:SF95 | CULLIN-3A-RELATED | 8 | 191 | 0.000 |
| 3 | g6499.t1 | PANTHER | PTHR11932 | CULLIN | 197 | 391 | 0.000 |
| 5 | g6499.t1 | PANTHER | PTHR11932:SF95 | CULLIN-3A-RELATED | 197 | 391 | 0.000 |
| 2 | g6499.t1 | Pfam | PF00888 | Cullin family | 51 | 194 | 0.000 |
| 1 | g6499.t1 | Pfam | PF00888 | Cullin family | 196 | 391 | 0.000 |
| 14 | g6499.t1 | ProSiteProfiles | PS50069 | Cullin family profile. | 343 | 391 | 14.449 |
| 7 | g6499.t1 | SUPERFAMILY | SSF74788 | Cullin repeat-like | 27 | 341 | 0.000 |
| 8 | g6499.t1 | SUPERFAMILY | SSF75632 | Cullin homology domain | 337 | 391 | 0.000 |
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.
