General information for g7469.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Cullin-4A.
Parent gene
- The parent gene g7469 is located on chr_2: 23900026..23901071 (+ 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 | g7469 | g7469.t1 | TSS | g7469.t1 | 23898116 | 23898116 |
| chr_2 | g7469 | g7469.t1 | isoform | g7469.t1 | 23898364 | 23901071 |
| chr_2 | g7469 | g7469.t1 | exon | g7469.t1.exon1 | 23898364 | 23898508 |
| chr_2 | g7469 | g7469.t1 | cds | g7469.t1.CDS1 | 23898364 | 23898508 |
| chr_2 | g7469 | g7469.t1 | exon | g7469.t1.exon2 | 23898625 | 23898863 |
| chr_2 | g7469 | g7469.t1 | cds | g7469.t1.CDS2 | 23898625 | 23898863 |
| chr_2 | g7469 | g7469.t1 | exon | g7469.t1.exon3 | 23898923 | 23899047 |
| chr_2 | g7469 | g7469.t1 | cds | g7469.t1.CDS3 | 23898923 | 23899047 |
| chr_2 | g7469 | g7469.t1 | exon | g7469.t1.exon4 | 23899112 | 23900483 |
| chr_2 | g7469 | g7469.t1 | cds | g7469.t1.CDS4 | 23899112 | 23900483 |
| chr_2 | g7469 | g7469.t1 | exon | g7469.t1.exon5 | 23900539 | 23900709 |
| chr_2 | g7469 | g7469.t1 | cds | g7469.t1.CDS5 | 23900539 | 23900709 |
| chr_2 | g7469 | g7469.t1 | exon | g7469.t1.exon6 | 23900768 | 23900920 |
| chr_2 | g7469 | g7469.t1 | cds | g7469.t1.CDS6 | 23900768 | 23900920 |
| chr_2 | g7469 | g7469.t1 | exon | g7469.t1.exon7 | 23900976 | 23901071 |
| chr_2 | g7469 | g7469.t1 | cds | g7469.t1.CDS7 | 23900976 | 23901071 |
| chr_2 | g7469 | g7469.t1 | TTS | g7469.t1 | 23901231 | 23901231 |
Sequences
>g7469.t1 Gene=g7469 Length=2301
ATGGAAATTGATACACCGGATCGCAAGAAATCTAACTTTTCCTCATTGGCAACTTCATCA
AACAGCCCAAATGGATCGATTTCTCGTGGCGGCAGCAGTAACTCAAAGGGTGATATAAAG
AAACTCGTGATTAAGAATTTTAAAGCTAAACCAACGTTACCTGAAAATTATCAGGAAAAT
ACATGGCAAAAACTTAAGGAAGCAGTAATTGCAATTCAAACTTCAACACCTATCACTTAT
TGTTTAGAAGAACTTTATCAAGCAGTTGAAAATATGTGTAGTCATAAAATGGACTCTCAG
TTGTATGTAAATTTAACAGGATTAGCAGAAAGTCATGTCAAATCGAATATTCGTCCGTTC
CTTGCAGAACGTGTAGACAAATTGCTGTATCTAAAGAAGGTCAATGAATGTTGGCAATCA
CACTGTCAACAGATGATTATGATCCGTAGTATATTTCTATATTTAGATCGCACATATGTA
TTGCAAAATCCGACTGTTCATTCAATCTGGGATCTCGGTTTAGAGCTGTTTCGTGATCAT
ATTGCTACAAATGCAACAGTTCAATCAAGAACTGTTGAAGGAATTTTAATGCTCATAGAG
AAAGAACGTAATGGTGAGACTGTAGATCGGACTTTGCTGAAGAGTCTTTTACGAATGTTC
TCTGACCTTCAAATTTATAAAGAAGCTTTTGAGAATAAATTTTTGGTCGCCACTAAACAA
TTATATCAAGCTGAAGGTCAACGAAAAATGCAAGAACTTGATGTACCCGAATACTTGAAG
CATGTCGATAAACGTTTAACCGAAGAAAATGAACGACTATTACACTATTTAGATCAGTGT
ACAAAACTTCAACTTATTTTTACCGTTGAACGACAATTGCTTGCAGAACACATTACTGGT
ATATTACAAAAAGGATTGGATCAATTATTGGAAGAAAATCGCATATCGGATTTAACATTA
CTCTATTCGCTCTTCAGTCGTGTCAAAAATGGAACTCTTGAGCTTGTCACATCATATAAC
GCTTATATCAAGACAAAAGGCAAAACACTCGTTATTGATCCAGAGAAAGATAAGACAATG
GTACAAGATTTACTAGATTTCAAAGACAAAATGGACAATATCGTAGTTACATGCTTTGAA
CGTAATGAAAAGTTCTCACATAGTCTGCGTGAAGCATTTGAATTCTTTATCAATCAGCGT
ACGAATAAACCAGCTGAATTAATTGCCAAATACGTCGATATGAAATTACGCGCAGGTAAT
AAGGAAGCTACTGAAGAGGAATTGGAACAAATTCTTGATAAAATCATGGTACTCTTTCGT
TTCATTCATGGCAAAGATGTTTTCGAAGCATTTTACAAAAAAGACTTGGCTAAACGTTTA
TTAGTTGGGAAATCGGCTAGTGTTGATGCTGAAAAGAGTATGTTATCAAAGTTAAAACAA
GAGTGTGGCGGAGGTTTTACCTCAAAATTGGAGGGAATGTTTAAAGATATGGAATTGAGC
AAAGATATTAACATTGCGTTTAGACAACACATTGAAGGAAATGCTAATTCAAAAGATCTT
ATATTGTTTCATTCAATTGGAATTGATATGACTGTAAATATATTGACAATGGGCTACTGG
CCGACATATCCCGTTATGGAAGTTACAATGCCACCTCAATTAGTTGAGTATCAAAATGTT
TTCACAAAATTCTATCTGGCAAAGCATAGCGGAAGAAAATTGCAGTGGCAAGCAACTTTG
GGTCATTGTGTTTTGAAAGCACGTTTCGATCAGGGACCGAAAGATCTTCAAGTGTCCTTA
TTTCAATCATTAGTTTTATTGCTTTTTAACGATTGTGATGAGATGACATTAGAAGAGATT
TTACAAGCAACAAACATTGAAGATGGTGAATTAAGAAGAACACTTCAATCACTCGCATGC
GGAAAAGCAAGAGTGCTTACAAAAATTCCAAAAAGTCGTGAGGTTGAAGATCATGATAAA
TTTAAATTTAATAATGAATTCACAGCAAAATTATTCAGGATTAAAATTAATTCCATCCAA
ATGAAAGAAACTAATGAAGAGCAAAAAGCAACAGAGGAGAGAGTTTATCAAGATCGTCAA
TATCAAATTGATGCTGCAGTTGTGAGAATTATGAAAATGAGAAAAACATTAAGTCATAAT
TTGCTCATTAGTGAGCTTTATAAGCAACTTTCGTTCCCAGTCAAGCCTGCTGATTTGAAA
AAGAGAATTGAATCACTGATCGACCGTGACTACATGGAACGAGATAAAGATAATCAAAAT
CAATATAATTATGTTGCATAA
>g7469.t1 Gene=g7469 Length=766
MEIDTPDRKKSNFSSLATSSNSPNGSISRGGSSNSKGDIKKLVIKNFKAKPTLPENYQEN
TWQKLKEAVIAIQTSTPITYCLEELYQAVENMCSHKMDSQLYVNLTGLAESHVKSNIRPF
LAERVDKLLYLKKVNECWQSHCQQMIMIRSIFLYLDRTYVLQNPTVHSIWDLGLELFRDH
IATNATVQSRTVEGILMLIEKERNGETVDRTLLKSLLRMFSDLQIYKEAFENKFLVATKQ
LYQAEGQRKMQELDVPEYLKHVDKRLTEENERLLHYLDQCTKLQLIFTVERQLLAEHITG
ILQKGLDQLLEENRISDLTLLYSLFSRVKNGTLELVTSYNAYIKTKGKTLVIDPEKDKTM
VQDLLDFKDKMDNIVVTCFERNEKFSHSLREAFEFFINQRTNKPAELIAKYVDMKLRAGN
KEATEEELEQILDKIMVLFRFIHGKDVFEAFYKKDLAKRLLVGKSASVDAEKSMLSKLKQ
ECGGGFTSKLEGMFKDMELSKDINIAFRQHIEGNANSKDLILFHSIGIDMTVNILTMGYW
PTYPVMEVTMPPQLVEYQNVFTKFYLAKHSGRKLQWQATLGHCVLKARFDQGPKDLQVSL
FQSLVLLLFNDCDEMTLEEILQATNIEDGELRRTLQSLACGKARVLTKIPKSREVEDHDK
FKFNNEFTAKLFRIKINSIQMKETNEEQKATEERVYQDRQYQIDAAVVRIMKMRKTLSHN
LLISELYKQLSFPVKPADLKKRIESLIDRDYMERDKDNQNQYNYVA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g7469.t1 | Gene3D | G3DSA:1.20.1310.10 | Cullin Repeats | 49 | 180 | 1.5E-44 |
| 9 | g7469.t1 | Gene3D | G3DSA:1.20.1310.10 | Cullin Repeats | 181 | 297 | 2.6E-38 |
| 8 | g7469.t1 | Gene3D | G3DSA:1.20.1310.10 | Cullin Repeats | 298 | 401 | 2.7E-38 |
| 10 | g7469.t1 | Gene3D | G3DSA:1.20.1310.10 | Cullin Repeats | 402 | 514 | 1.5E-45 |
| 12 | g7469.t1 | Gene3D | G3DSA:1.10.10.2620 | - | 527 | 682 | 1.9E-54 |
| 13 | g7469.t1 | Gene3D | G3DSA:1.10.10.10 | winged helix repressor DNA binding domain | 693 | 766 | 2.5E-33 |
| 18 | g7469.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 35 | - |
| 17 | g7469.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 10 | 35 | - |
| 3 | g7469.t1 | PANTHER | PTHR11932:SF66 | CULLIN-4B | 25 | 766 | 0.0 |
| 4 | g7469.t1 | PANTHER | PTHR11932 | CULLIN | 25 | 766 | 0.0 |
| 1 | g7469.t1 | Pfam | PF00888 | Cullin family | 62 | 667 | 5.1E-205 |
| 2 | g7469.t1 | Pfam | PF10557 | Cullin protein neddylation domain | 698 | 758 | 1.2E-22 |
| 14 | g7469.t1 | ProSitePatterns | PS01256 | Cullin family signature. | 739 | 766 | - |
| 19 | g7469.t1 | ProSiteProfiles | PS50069 | Cullin family profile. | 403 | 639 | 60.119 |
| 15 | g7469.t1 | SMART | SM00182 | cul_2 | 433 | 589 | 2.0E-72 |
| 16 | g7469.t1 | SMART | SM00884 | Cullin_Nedd8_2 | 695 | 760 | 2.3E-34 |
| 5 | g7469.t1 | SUPERFAMILY | SSF74788 | Cullin repeat-like | 55 | 399 | 1.33E-114 |
| 7 | g7469.t1 | SUPERFAMILY | SSF75632 | Cullin homology domain | 399 | 677 | 6.15E-102 |
| 6 | g7469.t1 | SUPERFAMILY | SSF46785 | Winged helix DNA-binding domain | 678 | 766 | 1.61E-27 |
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 K10609 (cullin 4)
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.
