General information for g9899.t5
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.t5 | TSS | g9899.t5 | 5911553 | 5911553 |
| chr_1 | g9899 | g9899.t5 | isoform | g9899.t5 | 5912186 | 5914093 |
| chr_1 | g9899 | g9899.t5 | exon | g9899.t5.exon1 | 5912186 | 5913097 |
| chr_1 | g9899 | g9899.t5 | cds | g9899.t5.CDS1 | 5912215 | 5913097 |
| chr_1 | g9899 | g9899.t5 | exon | g9899.t5.exon2 | 5913154 | 5913176 |
| chr_1 | g9899 | g9899.t5 | cds | g9899.t5.CDS2 | 5913154 | 5913176 |
| chr_1 | g9899 | g9899.t5 | exon | g9899.t5.exon3 | 5913235 | 5913397 |
| chr_1 | g9899 | g9899.t5 | cds | g9899.t5.CDS3 | 5913235 | 5913397 |
| chr_1 | g9899 | g9899.t5 | exon | g9899.t5.exon4 | 5913464 | 5913885 |
| chr_1 | g9899 | g9899.t5 | cds | g9899.t5.CDS4 | 5913464 | 5913885 |
| chr_1 | g9899 | g9899.t5 | exon | g9899.t5.exon5 | 5913956 | 5914093 |
| chr_1 | g9899 | g9899.t5 | cds | g9899.t5.CDS5 | 5913956 | 5914093 |
| chr_1 | g9899 | g9899.t5 | TTS | g9899.t5 | 5914301 | 5914301 |
Sequences
>g9899.t5 Gene=g9899 Length=1658
AACTTCAAGCTAATGGAGTGCAGAGTTTTATGCGTTATGCTGATGCAAAATTACGTGAAG
AAGAAGCACGAGCACAAAGATATTTAGAACCAGTGAGTGCAAATGCTTTGAGTGAATGTT
GTGTGCGGGTGCTGATTGGTGATCATTTGTCTACTCTTCTCGCTGAATGCAAACCTCTCA
TTGAAGCTGGAGAAACTGAACGATTAAATCTCATGTTTCGATTATTGGATCGAGTAAATG
GTGGAGTTAATCCTATGCTTGAAGATCTTGAAAATCACATTGTGAATGCCGGACTATCTG
ATATGGTCGCTTCTGCTGATGTAATCACTCAAGATAGTGAAAAATATGTTGAACGTTTAT
TAGATTTGTTTCGACAATTTAGTAAGCTTGTTCAAGAAGCATTTAATGATGATCCGAGAT
TTTTGACAGCACGCGATAAAGCTTTCAAGACAGTGGTTAATGATACAACTGTATTTAAAC
TTGAGCTACCAACAAATACAACAGCACGAGGAACAAAAACAACAACACCTGAGAGTAAAT
GTCCTGAACTATTAGCAAATTATTGTGACATGCTACTAAGGAAAACTCCACTGAGCAAAA
AACTAACTAGTGATCAAATTGAAGCACGATTGAGAGATGTGCTTTTAGTACTCAAATATG
TTTGCAATAAGGATGTTTTTATGCGATATCATAAAGCACATTTAACAAGAAGATTGATTT
TAGATTCGAGTGCAGACAGTGAAAAAGAGGAAGATATGGTTGAATGGTTGAGGGAAATTG
GTATGCCAGCAGATTATGTAAATAAACTTGCAAGAATGTTTCAAGATATTAAAGTCAGTG
AGGATCTGAATGCTCAATTTAGATCACAAACCACACGACATGATGCTATAAATATCAAAA
TTCTTAATGCTGGTGCATGGGCTGCTCGTTCATCTGAACGTGTATCAGTAAGCTTGCCAC
TCGAATTAGAAGATTATATACCGGAGGTAGAAGAATTTTATAAGAAAAAGCATTCGGGAA
GAAAACTACAATGGTATCATCACATGAGTAATGGAACAATCACATTTGCCAACAATGTTG
GACGTTTTGATTTGGATGTGACAACATTTCAAATGGCAGTACTATTTGCGTGGAATCAAC
GTCCTAATGATAAAGTTTCATATGAGAATTTAAGGCTCGCAACTGAATTACCTGACCCTG
AGCTAAGAAGAACTCTTTGGTCGCTTGTGGCGTTTCCTAAACTGAAAAGACAGCTTTTAA
ATTATGATCCAATCGTTCAAGTGCCAAAAGATTTTGACGAGAACACGGTTTTTTGGATAA
ATCAAGAATTCTCAATTATTAAAAATGGAAAGCCTCAAAAAAGAGGTAAAATTAATTTAA
TTGGGAGACTTCAACTCAGTACAGAGCGCTCTCAGCAAGAAGACAATCAATCGATTGTGC
AATTGAGAATTCTCAGAACACAAGAAGCAATCATTAAAATTATGAAAATGAGAAAGAGAA
TGTCGAATGCTGCTTTACAGTCTGAACTTATTGAGATATTGAAAAATATGTTTTTACCCT
CGAAAAAAATGATTAAAGAGCAATTGGAGTGGTTAATTGAACAAAAATATCTTGCTCGTG
ACGACAGTGATATAAACGTATTTAATTATATGGCTTGA
>g9899.t5 Gene=g9899 Length=542
MRYADAKLREEEARAQRYLEPVSANALSECCVRVLIGDHLSTLLAECKPLIEAGETERLN
LMFRLLDRVNGGVNPMLEDLENHIVNAGLSDMVASADVITQDSEKYVERLLDLFRQFSKL
VQEAFNDDPRFLTARDKAFKTVVNDTTVFKLELPTNTTARGTKTTTPESKCPELLANYCD
MLLRKTPLSKKLTSDQIEARLRDVLLVLKYVCNKDVFMRYHKAHLTRRLILDSSADSEKE
EDMVEWLREIGMPADYVNKLARMFQDIKVSEDLNAQFRSQTTRHDAINIKILNAGAWAAR
SSERVSVSLPLELEDYIPEVEEFYKKKHSGRKLQWYHHMSNGTITFANNVGRFDLDVTTF
QMAVLFAWNQRPNDKVSYENLRLATELPDPELRRTLWSLVAFPKLKRQLLNYDPIVQVPK
DFDENTVFWINQEFSIIKNGKPQKRGKINLIGRLQLSTERSQQEDNQSIVQLRILRTQEA
IIKIMKMRKRMSNAALQSELIEILKNMFLPSKKMIKEQLEWLIEQKYLARDDSDINVFNY
MA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g9899.t5 | Gene3D | G3DSA:1.20.1310.10 | Cullin Repeats | 1 | 39 | 4.5E-5 |
| 11 | g9899.t5 | Gene3D | G3DSA:1.20.1310.10 | Cullin Repeats | 41 | 149 | 1.2E-41 |
| 13 | g9899.t5 | Gene3D | G3DSA:1.20.1310.10 | Cullin Repeats | 169 | 284 | 1.6E-40 |
| 14 | g9899.t5 | Gene3D | G3DSA:1.10.10.2620 | - | 285 | 454 | 4.6E-64 |
| 15 | g9899.t5 | Gene3D | G3DSA:1.10.10.10 | winged helix repressor DNA binding domain | 455 | 542 | 1.7E-31 |
| 3 | g9899.t5 | PANTHER | PTHR11932 | CULLIN | 1 | 542 | 4.6E-297 |
| 4 | g9899.t5 | PANTHER | PTHR11932:SF76 | CULLIN-5 | 1 | 542 | 4.6E-297 |
| 1 | g9899.t5 | Pfam | PF00888 | Cullin family | 1 | 434 | 1.2E-145 |
| 2 | g9899.t5 | Pfam | PF10557 | Cullin protein neddylation domain | 473 | 534 | 4.5E-17 |
| 10 | g9899.t5 | ProSitePatterns | PS01256 | Cullin family signature. | 515 | 542 | - |
| 16 | g9899.t5 | ProSiteProfiles | PS50069 | Cullin family profile. | 170 | 400 | 54.813 |
| 8 | g9899.t5 | SMART | SM00182 | cul_2 | 202 | 348 | 4.9E-61 |
| 9 | g9899.t5 | SMART | SM00884 | Cullin_Nedd8_2 | 469 | 536 | 1.5E-23 |
| 5 | g9899.t5 | SUPERFAMILY | SSF74788 | Cullin repeat-like | 1 | 149 | 2.22E-40 |
| 7 | g9899.t5 | SUPERFAMILY | SSF75632 | Cullin homology domain | 168 | 435 | 2.75E-67 |
| 6 | g9899.t5 | SUPERFAMILY | SSF46785 | Winged helix DNA-binding domain | 455 | 542 | 6.08E-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 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.
