General information for g9899.t6
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Cullin-5.
Parent gene
- The parent gene g9899 is located on chr_1: 5914093..5918686 (+ 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 | g9899 | g9899.t6 | isoform | g9899.t6 | 5913094 | 5914093 |
| chr_1 | g9899 | g9899.t6 | exon | g9899.t6.exon1 | 5913094 | 5913125 |
| chr_1 | g9899 | g9899.t6 | exon | g9899.t6.exon2 | 5913235 | 5913397 |
| chr_1 | g9899 | g9899.t6 | cds | g9899.t6.CDS1 | 5913343 | 5913397 |
| chr_1 | g9899 | g9899.t6 | exon | g9899.t6.exon3 | 5913464 | 5913885 |
| chr_1 | g9899 | g9899.t6 | cds | g9899.t6.CDS2 | 5913464 | 5913885 |
| chr_1 | g9899 | g9899.t6 | exon | g9899.t6.exon4 | 5913956 | 5914093 |
| chr_1 | g9899 | g9899.t6 | cds | g9899.t6.CDS3 | 5913956 | 5914093 |
| chr_1 | g9899 | g9899.t6 | TTS | g9899.t6 | 5914301 | 5914301 |
| chr_1 | g9899 | g9899.t6 | TSS | g9899.t6 | NA | NA |
Sequences
>g9899.t6 Gene=g9899 Length=755
GCTGGTAAGTGACTAAATTTAAAAATTTTAATGAACGTGTATCAGTAAGCTTGCCACTCG
AATTAGAAGATTATATACCGGAGGTAGAAGAATTTTATAAGAAAAAGCATTCGGGAAGAA
AACTACAATGGTATCATCACATGAGTAATGGAACAATCACATTTGCCAACAATGTTGGAC
GTTTTGATTTGGATGTGACAACATTTCAAATGGCAGTACTATTTGCGTGGAATCAACGTC
CTAATGATAAAGTTTCATATGAGAATTTAAGGCTCGCAACTGAATTACCTGACCCTGAGC
TAAGAAGAACTCTTTGGTCGCTTGTGGCGTTTCCTAAACTGAAAAGACAGCTTTTAAATT
ATGATCCAATCGTTCAAGTGCCAAAAGATTTTGACGAGAACACGGTTTTTTGGATAAATC
AAGAATTCTCAATTATTAAAAATGGAAAGCCTCAAAAAAGAGGTAAAATTAATTTAATTG
GGAGACTTCAACTCAGTACAGAGCGCTCTCAGCAAGAAGACAATCAATCGATTGTGCAAT
TGAGAATTCTCAGAACACAAGAAGCAATCATTAAAATTATGAAAATGAGAAAGAGAATGT
CGAATGCTGCTTTACAGTCTGAACTTATTGAGATATTGAAAAATATGTTTTTACCCTCGA
AAAAAATGATTAAAGAGCAATTGGAGTGGTTAATTGAACAAAAATATCTTGCTCGTGACG
ACAGTGATATAAACGTATTTAATTATATGGCTTGA
>g9899.t6 Gene=g9899 Length=204
MSNGTITFANNVGRFDLDVTTFQMAVLFAWNQRPNDKVSYENLRLATELPDPELRRTLWS
LVAFPKLKRQLLNYDPIVQVPKDFDENTVFWINQEFSIIKNGKPQKRGKINLIGRLQLST
ERSQQEDNQSIVQLRILRTQEAIIKIMKMRKRMSNAALQSELIEILKNMFLPSKKMIKEQ
LEWLIEQKYLARDDSDINVFNYMA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g9899.t6 | Gene3D | G3DSA:1.10.10.2620 | - | 1 | 116 | 1.2E-39 |
| 10 | g9899.t6 | Gene3D | G3DSA:1.10.10.10 | winged helix repressor DNA binding domain | 117 | 204 | 2.8E-32 |
| 3 | g9899.t6 | PANTHER | PTHR11932 | CULLIN | 1 | 204 | 4.1E-113 |
| 4 | g9899.t6 | PANTHER | PTHR11932:SF76 | CULLIN-5 | 1 | 204 | 4.1E-113 |
| 1 | g9899.t6 | Pfam | PF00888 | Cullin family | 1 | 96 | 3.2E-23 |
| 2 | g9899.t6 | Pfam | PF10557 | Cullin protein neddylation domain | 135 | 196 | 9.3E-18 |
| 8 | g9899.t6 | ProSitePatterns | PS01256 | Cullin family signature. | 177 | 204 | - |
| 11 | g9899.t6 | ProSiteProfiles | PS50069 | Cullin family profile. | 1 | 62 | 13.094 |
| 7 | g9899.t6 | SMART | SM00884 | Cullin_Nedd8_2 | 131 | 198 | 1.5E-23 |
| 6 | g9899.t6 | SUPERFAMILY | SSF75632 | Cullin homology domain | 1 | 97 | 2.88E-14 |
| 5 | g9899.t6 | SUPERFAMILY | SSF46785 | Winged helix DNA-binding domain | 117 | 204 | 5.44E-22 |
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.
