General information for g9899.t1
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.t1 | TSS | g9899.t1 | 5911101 | 5911101 |
| chr_1 | g9899 | g9899.t1 | isoform | g9899.t1 | 5911222 | 5914093 |
| chr_1 | g9899 | g9899.t1 | exon | g9899.t1.exon1 | 5911222 | 5911230 |
| chr_1 | g9899 | g9899.t1 | cds | g9899.t1.CDS1 | 5911222 | 5911230 |
| chr_1 | g9899 | g9899.t1 | exon | g9899.t1.exon2 | 5911394 | 5911482 |
| chr_1 | g9899 | g9899.t1 | cds | g9899.t1.CDS2 | 5911394 | 5911482 |
| chr_1 | g9899 | g9899.t1 | exon | g9899.t1.exon3 | 5911554 | 5911599 |
| chr_1 | g9899 | g9899.t1 | cds | g9899.t1.CDS3 | 5911554 | 5911599 |
| chr_1 | g9899 | g9899.t1 | exon | g9899.t1.exon4 | 5911657 | 5913097 |
| chr_1 | g9899 | g9899.t1 | cds | g9899.t1.CDS4 | 5911657 | 5913097 |
| chr_1 | g9899 | g9899.t1 | exon | g9899.t1.exon5 | 5913154 | 5913176 |
| chr_1 | g9899 | g9899.t1 | cds | g9899.t1.CDS5 | 5913154 | 5913176 |
| chr_1 | g9899 | g9899.t1 | exon | g9899.t1.exon6 | 5913235 | 5913397 |
| chr_1 | g9899 | g9899.t1 | cds | g9899.t1.CDS6 | 5913235 | 5913397 |
| chr_1 | g9899 | g9899.t1 | exon | g9899.t1.exon7 | 5913464 | 5913885 |
| chr_1 | g9899 | g9899.t1 | cds | g9899.t1.CDS7 | 5913464 | 5913885 |
| chr_1 | g9899 | g9899.t1 | exon | g9899.t1.exon8 | 5913956 | 5914093 |
| chr_1 | g9899 | g9899.t1 | cds | g9899.t1.CDS8 | 5913956 | 5914093 |
| chr_1 | g9899 | g9899.t1 | TTS | g9899.t1 | 5914301 | 5914301 |
Sequences
>g9899.t1 Gene=g9899 Length=2331
ATGTTAAAGAATAAAGGTCAACTTCAATTTGAAGAAAAATGGCCTCATATGGAGCCAGTT
GTATTGAAGCTCTTGGTGCAAGATCATATTGATAATTCCGAGTGGCAAGATTTGTTTTAT
GCTGTTCATTCTGTTTGTTTATGGGATGAGAAAGGCGCTCAGAAAATTCATGAGAATTTA
GCAGACTTGATAGTTAAATTTATAAAGCAAGCACAAAAACGGGTTTTAGTTGCGGGTGAG
GAGCAAGCATTGCTTCGCTCATATATAATTGAATGGAGAAAATTTTTCACTCAGAGCTCC
TATCTTCCATTGCCTTTTTGGCAATTAGAGGCATCTCTGCAAACAAAATCCTCATCGAGC
CATAGTTCAAATAATAGCACTAAAAAATCTTCCACTAATGATGAAAATAGCATAGTGCGA
AAACTTATGTTAGACAGTTGGAATCAGAGTATATTTATTAACGTCAAAGATCGACTTCAA
GACTCAGCTATGAAATTAATTCAAGCAGAACGTAATGGTGAAGCTTTCGATTCTCAACTT
GTTATTGGTGTACGCGAAAGTTATGTAAATTTATGTTCAAATACTGAAGATAAATTAGAA
ATTTATCGTGACAATTTTGAAGCAGCATATCTTCAAGCAACAACTGAGTTCTATCGTCTC
AAAGGGAATGAACAACTTCAAGCTAATGGAGTGCAGAGTTTTATGCGTTATGCTGATGCA
AAATTACGTGAAGAAGAAGCACGAGCACAAAGATATTTAGAACCAGTGAGTGCAAATGCT
TTGAGTGAATGTTGTGTGCGGGTGCTGATTGGTGATCATTTGTCTACTCTTCTCGCTGAA
TGCAAACCTCTCATTGAAGCTGGAGAAACTGAACGATTAAATCTCATGTTTCGATTATTG
GATCGAGTAAATGGTGGAGTTAATCCTATGCTTGAAGATCTTGAAAATCACATTGTGAAT
GCCGGACTATCTGATATGGTCGCTTCTGCTGATGTAATCACTCAAGATAGTGAAAAATAT
GTTGAACGTTTATTAGATTTGTTTCGACAATTTAGTAAGCTTGTTCAAGAAGCATTTAAT
GATGATCCGAGATTTTTGACAGCACGCGATAAAGCTTTCAAGACAGTGGTTAATGATACA
ACTGTATTTAAACTTGAGCTACCAACAAATACAACAGCACGAGGAACAAAAACAACAACA
CCTGAGAGTAAATGTCCTGAACTATTAGCAAATTATTGTGACATGCTACTAAGGAAAACT
CCACTGAGCAAAAAACTAACTAGTGATCAAATTGAAGCACGATTGAGAGATGTGCTTTTA
GTACTCAAATATGTTTGCAATAAGGATGTTTTTATGCGATATCATAAAGCACATTTAACA
AGAAGATTGATTTTAGATTCGAGTGCAGACAGTGAAAAAGAGGAAGATATGGTTGAATGG
TTGAGGGAAATTGGTATGCCAGCAGATTATGTAAATAAACTTGCAAGAATGTTTCAAGAT
ATTAAAGTCAGTGAGGATCTGAATGCTCAATTTAGATCACAAACCACACGACATGATGCT
ATAAATATCAAAATTCTTAATGCTGGTGCATGGGCTGCTCGTTCATCTGAACGTGTATCA
GTAAGCTTGCCACTCGAATTAGAAGATTATATACCGGAGGTAGAAGAATTTTATAAGAAA
AAGCATTCGGGAAGAAAACTACAATGGTATCATCACATGAGTAATGGAACAATCACATTT
GCCAACAATGTTGGACGTTTTGATTTGGATGTGACAACATTTCAAATGGCAGTACTATTT
GCGTGGAATCAACGTCCTAATGATAAAGTTTCATATGAGAATTTAAGGCTCGCAACTGAA
TTACCTGACCCTGAGCTAAGAAGAACTCTTTGGTCGCTTGTGGCGTTTCCTAAACTGAAA
AGACAGCTTTTAAATTATGATCCAATCGTTCAAGTGCCAAAAGATTTTGACGAGAACACG
GTTTTTTGGATAAATCAAGAATTCTCAATTATTAAAAATGGAAAGCCTCAAAAAAGAGGT
AAAATTAATTTAATTGGGAGACTTCAACTCAGTACAGAGCGCTCTCAGCAAGAAGACAAT
CAATCGATTGTGCAATTGAGAATTCTCAGAACACAAGAAGCAATCATTAAAATTATGAAA
ATGAGAAAGAGAATGTCGAATGCTGCTTTACAGTCTGAACTTATTGAGATATTGAAAAAT
ATGTTTTTACCCTCGAAAAAAATGATTAAAGAGCAATTGGAGTGGTTAATTGAACAAAAA
TATCTTGCTCGTGACGACAGTGATATAAACGTATTTAATTATATGGCTTGA
>g9899.t1 Gene=g9899 Length=776
MLKNKGQLQFEEKWPHMEPVVLKLLVQDHIDNSEWQDLFYAVHSVCLWDEKGAQKIHENL
ADLIVKFIKQAQKRVLVAGEEQALLRSYIIEWRKFFTQSSYLPLPFWQLEASLQTKSSSS
HSSNNSTKKSSTNDENSIVRKLMLDSWNQSIFINVKDRLQDSAMKLIQAERNGEAFDSQL
VIGVRESYVNLCSNTEDKLEIYRDNFEAAYLQATTEFYRLKGNEQLQANGVQSFMRYADA
KLREEEARAQRYLEPVSANALSECCVRVLIGDHLSTLLAECKPLIEAGETERLNLMFRLL
DRVNGGVNPMLEDLENHIVNAGLSDMVASADVITQDSEKYVERLLDLFRQFSKLVQEAFN
DDPRFLTARDKAFKTVVNDTTVFKLELPTNTTARGTKTTTPESKCPELLANYCDMLLRKT
PLSKKLTSDQIEARLRDVLLVLKYVCNKDVFMRYHKAHLTRRLILDSSADSEKEEDMVEW
LREIGMPADYVNKLARMFQDIKVSEDLNAQFRSQTTRHDAINIKILNAGAWAARSSERVS
VSLPLELEDYIPEVEEFYKKKHSGRKLQWYHHMSNGTITFANNVGRFDLDVTTFQMAVLF
AWNQRPNDKVSYENLRLATELPDPELRRTLWSLVAFPKLKRQLLNYDPIVQVPKDFDENT
VFWINQEFSIIKNGKPQKRGKINLIGRLQLSTERSQQEDNQSIVQLRILRTQEAIIKIMK
MRKRMSNAALQSELIEILKNMFLPSKKMIKEQLEWLIEQKYLARDDSDINVFNYMA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g9899.t1 | Gene3D | G3DSA:1.20.1310.10 | Cullin Repeats | 1 | 150 | 1.1E-38 |
| 13 | g9899.t1 | Gene3D | G3DSA:1.20.1310.10 | Cullin Repeats | 151 | 273 | 2.3E-39 |
| 14 | g9899.t1 | Gene3D | G3DSA:1.20.1310.10 | Cullin Repeats | 275 | 383 | 2.1E-41 |
| 11 | g9899.t1 | Gene3D | G3DSA:1.20.1310.10 | Cullin Repeats | 403 | 518 | 2.8E-40 |
| 15 | g9899.t1 | Gene3D | G3DSA:1.10.10.2620 | - | 519 | 688 | 8.9E-64 |
| 16 | g9899.t1 | Gene3D | G3DSA:1.10.10.10 | winged helix repressor DNA binding domain | 689 | 776 | 2.9E-31 |
| 3 | g9899.t1 | PANTHER | PTHR11932 | CULLIN | 5 | 776 | 0.0 |
| 4 | g9899.t1 | PANTHER | PTHR11932:SF76 | CULLIN-5 | 5 | 776 | 0.0 |
| 1 | g9899.t1 | Pfam | PF00888 | Cullin family | 14 | 668 | 7.1E-195 |
| 2 | g9899.t1 | Pfam | PF10557 | Cullin protein neddylation domain | 707 | 768 | 7.3E-17 |
| 10 | g9899.t1 | ProSitePatterns | PS01256 | Cullin family signature. | 749 | 776 | - |
| 17 | g9899.t1 | ProSiteProfiles | PS50069 | Cullin family profile. | 404 | 634 | 54.813 |
| 8 | g9899.t1 | SMART | SM00182 | cul_2 | 436 | 582 | 4.9E-61 |
| 9 | g9899.t1 | SMART | SM00884 | Cullin_Nedd8_2 | 703 | 770 | 1.5E-23 |
| 5 | g9899.t1 | SUPERFAMILY | SSF74788 | Cullin repeat-like | 10 | 383 | 3.92E-93 |
| 7 | g9899.t1 | SUPERFAMILY | SSF75632 | Cullin homology domain | 402 | 669 | 6.41E-67 |
| 6 | g9899.t1 | SUPERFAMILY | SSF46785 | Winged helix DNA-binding domain | 689 | 776 | 9.98E-21 |
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 transcript has been annotated with K10612 (cullin 5)
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.
