General information for g6497.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Cullin-3-B.
Parent gene
- The parent gene g6497 is located on chr_2: 17288283..17289872 (+ 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 | g6497 | g6497.t1 | TSS | g6497.t1 | 17286065 | 17286065 |
| chr_2 | g6497 | g6497.t1 | isoform | g6497.t1 | 17286589 | 17289872 |
| chr_2 | g6497 | g6497.t1 | exon | g6497.t1.exon1 | 17286589 | 17286645 |
| chr_2 | g6497 | g6497.t1 | cds | g6497.t1.CDS1 | 17286589 | 17286645 |
| chr_2 | g6497 | g6497.t1 | exon | g6497.t1.exon2 | 17287144 | 17288283 |
| chr_2 | g6497 | g6497.t1 | cds | g6497.t1.CDS2 | 17287144 | 17288283 |
| chr_2 | g6497 | g6497.t1 | exon | g6497.t1.exon3 | 17288480 | 17288650 |
| chr_2 | g6497 | g6497.t1 | cds | g6497.t1.CDS3 | 17288480 | 17288650 |
| chr_2 | g6497 | g6497.t1 | exon | g6497.t1.exon4 | 17288712 | 17288997 |
| chr_2 | g6497 | g6497.t1 | cds | g6497.t1.CDS4 | 17288712 | 17288997 |
| chr_2 | g6497 | g6497.t1 | exon | g6497.t1.exon5 | 17289050 | 17289180 |
| chr_2 | g6497 | g6497.t1 | cds | g6497.t1.CDS5 | 17289050 | 17289180 |
| chr_2 | g6497 | g6497.t1 | exon | g6497.t1.exon6 | 17289247 | 17289464 |
| chr_2 | g6497 | g6497.t1 | cds | g6497.t1.CDS6 | 17289247 | 17289464 |
| chr_2 | g6497 | g6497.t1 | exon | g6497.t1.exon7 | 17289522 | 17289660 |
| chr_2 | g6497 | g6497.t1 | cds | g6497.t1.CDS7 | 17289522 | 17289660 |
| chr_2 | g6497 | g6497.t1 | exon | g6497.t1.exon8 | 17289720 | 17289872 |
| chr_2 | g6497 | g6497.t1 | cds | g6497.t1.CDS8 | 17289720 | 17289872 |
| chr_2 | g6497 | g6497.t1 | TTS | g6497.t1 | 17290056 | 17290056 |
Sequences
>g6497.t1 Gene=g6497 Length=2295
ATGAATCGACAGCCTCCTCCAAAGAAAGAAGGAAAAATGCGGATTCGTGCATTTCCCATG
ACGATGGATGAAAAATTTGTAGAATCAATATGGTCTTTACTAAAAAATGCAATTCAAGAG
ATTCAAAAGAAAAACAATTCTGGGCTATCTTTTGAAGAGTTGTATCGTAATGCTTACACA
ATGGTTCTTCATAAACATGGTGAACGACTTTATAATGGATTAAAGGAAGTTGTCACACAA
CATTTGCAACAAAAAGTTCGTGAAGATGTTCTTCGATCATTAAACAACAACTTTCTGCAG
ACATTAAATCAAGCTTGGACAGATCATCAAACATCAATGGTCATGATTAGAGACATTCTT
ATGTACATGGATCGTGTTTACGTACAACAAAATGATGTTGATAATGTTTATAACTTAGGA
CTCATAATATTTCGTGATGAAATCATAAGTCACGAAAGGATCAGAAATCACTTACGCGAG
ACACTATTAGCAATGATCATGAATGAACGAAAAGGAGAGGCAATAGATCATATCTTAATA
AAAAATGCATGTCAAATGCTAATGATTCTCGGTATCAATAATCGATGGGTATATGAGAAA
GATTTTGAACGTCCGTTTTTGACACAATCTGCTGCTTTCTATGCTATGGAATCACAAAAG
TTTTTATCCGAGAACAGTGCAAGTGTATATATTAAAAAGGTTGAAGCAAGAATCACAGAA
GAGGCAGAACGAGCGAAACTTTACCTGGATGAAAGCACTGAGCAGCGAATTGTCGATGTA
GTTCAAGATGAATTAATTAAGAAACATATGCGAACAATTGTTGAAATGGAGAACTCTGGA
GTAGTTTATATGCTTCGTAATACAAAGACCGATGATTTGGCATGCATGTATAAACTATTT
TCACGTGTCAGTGAAGGTATCAAAACGATTTCTGAATGTGTTAGCAAATATCTTCGTGAA
CAAGGCACATCTTTAGTGAAAGAGGAAGAAGGTGGTACAAATCCAATTACATTTGTGCAA
AATCTGCTTGATTTGAAAGATCGCTTTGATCATTTCTTGAAACATTCATTCAGTACTGAG
AAGACATTTAAACACATGATTTCATCAGATTTTGAATATTTCCTCAATTTGAATAGTAAA
TCACCAGAATATCTTTCACTTTTTATTGATGATAAGCTCAAAAAAGGATGCAAAGGGATG
TCTGAACAAGAAATTGAAACGATTTTGGATAAAACAATGGTTCTGTTCCGCTATTTACTT
GAAAAGGATGTATTTGAACGCTATTATAAAGCACACTTGGCGAAAAGATTGCTCCTTAAC
AAATCAGTCAGTGATGATTCAGAAAAGAATATGATATCAAAGTTAAAGACTGAATGTGGA
TGTCAATTTACATCAAAACTTGAGGGAATGTTCAAAGATATGCAAGTTTCAAACACAATT
ATGGAAGAATTTAAGAATCACGTGCATTCTCAGGGAATGAATTTGAGCGGTGTAGATTTA
AGTGTTCGTATATTGACAACTGGATTTTGGCCCACACAATCATCAACACCGAATTGTAAT
ATTCCAATTGCTCCGAGAGAGGCCTTTGATGCATTCAAAAAATTCTATCTAGCAAAACAC
TCAGGCCGACAGCTCACTCTTCAACCACAACTTGGCACTGCATTCATCAATGCTGTATTT
TATGGAAGTAAACAAGAAGCAGAAAGTGAGTCAGGAACCGTTTGCTCAACTTCGTCAGCA
CAGTTACATACTCGGAAACATGTGCTTCAAGTTTCAACCTATCAGATGTGTGTTTTGATG
CTGTTCAATAATCGTGAACGTTTGACATATGAGGAAATTCAACAAGAAACTGATATTCCT
GAGAAAGATTTGATTCGTGCTTTGCAATCATTATCGATGGGTAAATTGCAACAGCGTTTA
CTTATGCGAACACCGAAAACAAAAGAAATTGAGCCTTCAAATGAATTTTACGTTAATGAT
GGATTTGTCTCTAAATTTCACAAAGTTAAAATTCAAACTGTTGCTGCAAAGGGAGAAACA
GAACCAGAACGTCGCGAAACTCGAAACAAAGTTGATGAGGACCGTAAACATGAAATTGAA
GCTGCAATTGTTAGAATTATGAAATCACGCAAAAAGATGGCGCACAATTTATTGGTGTCT
GATGTCACAACTCAATTGCGTAGTCGCTTCCTGCCTTCACCAGTTATAATTAAAAAACGT
ATCGAAGGATTGATTGAGCGTGAATATCTTGCTCGTACACCAGAAGACCGTAAAGTTTAC
ATCTATCTAGCTTAA
>g6497.t1 Gene=g6497 Length=764
MNRQPPPKKEGKMRIRAFPMTMDEKFVESIWSLLKNAIQEIQKKNNSGLSFEELYRNAYT
MVLHKHGERLYNGLKEVVTQHLQQKVREDVLRSLNNNFLQTLNQAWTDHQTSMVMIRDIL
MYMDRVYVQQNDVDNVYNLGLIIFRDEIISHERIRNHLRETLLAMIMNERKGEAIDHILI
KNACQMLMILGINNRWVYEKDFERPFLTQSAAFYAMESQKFLSENSASVYIKKVEARITE
EAERAKLYLDESTEQRIVDVVQDELIKKHMRTIVEMENSGVVYMLRNTKTDDLACMYKLF
SRVSEGIKTISECVSKYLREQGTSLVKEEEGGTNPITFVQNLLDLKDRFDHFLKHSFSTE
KTFKHMISSDFEYFLNLNSKSPEYLSLFIDDKLKKGCKGMSEQEIETILDKTMVLFRYLL
EKDVFERYYKAHLAKRLLLNKSVSDDSEKNMISKLKTECGCQFTSKLEGMFKDMQVSNTI
MEEFKNHVHSQGMNLSGVDLSVRILTTGFWPTQSSTPNCNIPIAPREAFDAFKKFYLAKH
SGRQLTLQPQLGTAFINAVFYGSKQEAESESGTVCSTSSAQLHTRKHVLQVSTYQMCVLM
LFNNRERLTYEEIQQETDIPEKDLIRALQSLSMGKLQQRLLMRTPKTKEIEPSNEFYVND
GFVSKFHKVKIQTVAAKGETEPERRETRNKVDEDRKHEIEAAIVRIMKSRKKMAHNLLVS
DVTTQLRSRFLPSPVIIKKRIEGLIEREYLARTPEDRKVYIYLA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 14 | g6497.t1 | Coils | Coil | Coil | 231 | 251 | - |
| 11 | g6497.t1 | Gene3D | G3DSA:1.20.1310.10 | Cullin Repeats | 16 | 147 | 2.7E-48 |
| 9 | g6497.t1 | Gene3D | G3DSA:1.20.1310.10 | Cullin Repeats | 148 | 270 | 1.4E-43 |
| 10 | g6497.t1 | Gene3D | G3DSA:1.20.1310.10 | Cullin Repeats | 271 | 378 | 1.2E-34 |
| 8 | g6497.t1 | Gene3D | G3DSA:1.20.1310.10 | Cullin Repeats | 379 | 493 | 2.6E-45 |
| 12 | g6497.t1 | Gene3D | G3DSA:1.10.10.2620 | - | 496 | 675 | 1.2E-44 |
| 13 | g6497.t1 | Gene3D | G3DSA:1.10.10.10 | winged helix repressor DNA binding domain | 676 | 764 | 5.6E-36 |
| 3 | g6497.t1 | PANTHER | PTHR11932 | CULLIN | 20 | 760 | 3.4E-270 |
| 4 | g6497.t1 | PANTHER | PTHR11932:SF126 | CULLIN-3 | 20 | 760 | 3.4E-270 |
| 1 | g6497.t1 | Pfam | PF00888 | Cullin family | 31 | 662 | 1.6E-223 |
| 2 | g6497.t1 | Pfam | PF10557 | Cullin protein neddylation domain | 694 | 756 | 1.1E-25 |
| 15 | g6497.t1 | ProSitePatterns | PS01256 | Cullin family signature. | 737 | 764 | - |
| 18 | g6497.t1 | ProSiteProfiles | PS50069 | Cullin family profile. | 380 | 632 | 57.466 |
| 16 | g6497.t1 | SMART | SM00182 | cul_2 | 410 | 560 | 1.9E-78 |
| 17 | g6497.t1 | SMART | SM00884 | Cullin_Nedd8_2 | 691 | 758 | 2.1E-37 |
| 5 | g6497.t1 | SUPERFAMILY | SSF74788 | Cullin repeat-like | 24 | 378 | 6.02E-109 |
| 7 | g6497.t1 | SUPERFAMILY | SSF75632 | Cullin homology domain | 374 | 672 | 9.29E-93 |
| 6 | g6497.t1 | SUPERFAMILY | SSF46785 | Winged helix DNA-binding domain | 677 | 764 | 6.35E-28 |
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 K03869 (cullin 3)
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.
