DreINT0131733 @ danRer10
Intron Retention
Gene
ENSDARG00000063097 | scube1
Description
signal peptide, CUB domain, EGF-like 1 [Source:ZFIN;Acc:ZDB-GENE-050302-78]
Coordinates
chr4:9003999-9007935:-
Coord C1 exon
chr4:9007721-9007935
Coord A exon
chr4:9004122-9007720
Coord C2 exon
chr4:9003999-9004121
Length
3599 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGT
5' ss Score
10.86
3' ss Seq
CAGCCTCTTATCCTCCACAGATG
3' ss Score
9.24
Exon sequences
Seq C1 exon
GTGCGCAAACCAATCAGCGGCGTCCGGAGTCTCGAGCTGTGGTGCTCGCTCTGCCAGCAGCAGCAGAAAGGCTGCTTATCAAAGAAACGCACAACTGGAGAGACCCATTCACTCACAGCCTCTAACCATGGGTCCTGCCTGCTTCTCCTGGGAAGTCTGTTTGCTTTTCCTCCTCATAAATACTTTAGATGTCATGGGAAATGTTGGAGTCCCAG
Seq A exon
GTAAGTCTTCATCTGTCTTTTTAAAAATGTATTTTAACAAACCTTATATTATTTTTTGTTAAACTTTTATTACCTGAAATTTAAGTCTGTAAGGACTGTAAGTCAGTGCTTTCTTTTTTTGCATGTGATTTTAGCGAAACTGCAATGCACTCTGTCTGATTAAGCCAGCTGCGTTCATTTAGAAAAACAATTTAGTCCTACTTTGCCCTGTCATTAGTGCATTAAATGCGCATTTGAACGCGCCGGTTTGGTTTTATTTACGCGTGATATTCCTCAAGGAGAGCTTTTGCTGGTGTCTTTTCAGATTTCCTTGGGGTCTATAGGAACATGAGCCGCCCTGATGGGGTCGGTGCGGGGGGCTTATCGACCCCTCACTCCTCCACTACCGTCAATACGCATTGTGTCTCTCCATAATGAATGCCTGGAAAAGTCAATAATGAGACAAACAATAAAAACAGATTGTCAGCGACCCGACGGGAGATTTTGTGACATTTTAGCTTCTTAAAACATTTTGCAAATAATCCAAAATGATTAACTCATTCCCGAATGAGTTTGGCGATGCGCATTATGTACTTCTGGATTTTTCCTGATTGAATCTTTTAAAATAGACGTAATTTATTCTTGTTAAGCTATAAAATGCACTAACAGAAGTGTTGTGCCTCTGTTTATGCGGATTGAAACGGTTGGATGATGGGTAAAAAGCGCGCACCGCTGCGCTAAAGGTGTTCAGTTGCATTCAGCTTTGCGTAAAGTTGAAGAATCGCTCTATTTGATGGAAAGACACAATAAGTTTTAGGGGCCACTGCTGGTGCGGCAAAGGGTGAAACTGCACATTGATAGCCAAGCAAACCGCCTCACTGACCTCTTCAAAAAAGTCAATCTCTCCTAAATGAGCTCGCCAGCAGTCTGCTTGTTCGTTCATTCATTCACATCATGGAGAATGAATGAGCGAGTTCAGCTTTTGCATCAGTTCATCACCTCATTGGACAGTTTTTCCTTGCTTAATAGGCTGAACGCCTTCTTTCCGGAGACAACTTATTTTGTCTGAGTTGATTTTGGTCCTTTTTTTGCCCTGTTCTGCTCAGCTTCACCTGTCTAAGCCAGCAGTGAGATCCAAACTGCTCTCAGATCAGCGACAAAGAACATTTACCACACCCTGAATCAGTCAAACAGGCACGAAGTCACTGTTAATCATAAAAGTCTATTTTTATTTCATTCACTTTGTATTTTGGTACAGCTGAGATATGTTCTGTTGCTTGTGACGTTTACATTATTAATTTAGCAGACACTTTTATACAAAATATGTATGTAATTGATTTTAACATATGCATTTAACAGATATAACTGAGCTAAAATTATAAATAATGACTCTCTTTGTTTTTGTTTTTATTTTGTATCCTAAAAATTAAGGTTTCAGAAGATTGCAGTGATGTTTTAGAGAAACCATTTTTGTTTTTCTTTTCCGAAAAATCCTTTAGTGAATCCTTTTAGTGAAAGAGAGTTGTTTAAGGTTCTTCATGGAATCTTTGATGGCAATAAAAAGGTGTTTCTGCAGTCATACCAGCTAATTTGTGTCTTCAGCGAACATAACTTAAAACAACCACAGTGTGAAGAACATTTTAAAATCTAAAAACAAAAACAAAAAAACACTCTGTGCAATGTTGACAGTTCTAGTAATATAATGTATTTTTTTCTAATAAATGTAATATAATGCATTTTGCTCAATCCGTATTTTTCATTACACAATATGCACAAAACATTAACAAAACCAGTAATACAAGTAGTTCTATTATTATTTTTATTATTATTATCATTAGATTTTTTAATTAACCCAAGAAGAATATGTATTCAAAGATGCATTTTTGAAATTATTCAGCAGTCCAAACACACGGTTGTACAGTCTTTGCAGAAACTTTCCACAGAGGTCATTATTATTATCATACCATAAAGATATTCTGCCCTTACCTTACCCCTAAACCCCTTTTTACATGTTCTTCATTCATGTTATTTATGAGCCTTTTTTCCCAGGGGGTCCAACAGAACCCTTTAGAGAACAGATCTTTGAGAAGAACATATTAAAATCTAAAAACAACAACAACAACTACTACTACAACAAGAAAACACTTTGTGCAATGTTGAAGGTTCTAGTAATATCTAGTAATGTATTTTGTCCATACAATTTAATACATTGCATTTTGCTGAGTCAGTATATTTTCAATTACACAATATACACAAAACATTAACAAAACAAATCTTTTATAGTTGTCTTTGCTGGAACGTTCCACAAATGTAATTATTGTTTACACAGATAGTATATTCTACCCTAACCTTGCTACTAAATGCTTTTTACACGTTCTTTATTCATGTGATTTATGAGCCTTTATGGGATCCAAAAGAACCCTTAGAGAACAGATCTTTGAGAGGAACATTTTAAAGTTTAAAAACAACAACAACAACTATAACAAGAAAACACTGTGCAATGATGAAAGTTCTCCGCAGAACAGTTCTCTTTAGCATTCATTCATTCATTCATTCATTCATTCATTCATTCATTCATTCATTCAATAATTAATTTATTTAATTTCATGTAATTGCGTAACGGTGGCGCAGTGGGTAGCATGATTGCCTCACAGCAAGAACTTCGCTGGTTCGAGCCTCGGCTGGGTTAGTTGGCATTTCTGTGTGGAGCTTGTATGTTCTCCCTGTGTTGACGTGTGTTCCCTCCGGATGCTCCTGTTCCCCACACAGCTAAAAGACATGCGCTAGGTGAATTGGATAGGCTAGTGTATGTGTGTGAATGGGAGTGTATGGGTGTTTCCCAGTGATAGGTTGCAGCCGGAAGGGCATTCGTTGTGTAAAACATATGCTGAATAAGTTGGTGGTTCATTCCACTGTGTTGAGCCCAGATGAATAAAGGGACTAAGCCAAAAAGAAAAGGAATGAGTAAATTTCATGTTATTTATTTGTTTATTTGTTTTACCTTTTATTTTTATTTGCATTGTGGTTCACTAAGGATGAAGAACTTCTGTGATGGGGCACCATTCGGATGTGATACGTAACAACTGCTATCATCATACTATCATGTCAGTACAGGGTGATTCAAAAAGAATACCACAACCTTCGGGTTGATGTCACTCGGGTGTCTGGAGGGGGTCATTATAAACATTTATGAACTTTAAGTACTCTTCACATTGATAAATTACCCAAGGTTCCATCATGTTTCTTTGATTAAATACAGATTTTTAAAGTTGTGGTTTTCTTTTTAAATAACCCTGTAAGGTTTATTACACATTTTTAAAACATGCTCTATATAAGAGTTTGTGTAATTGTGTAAAATAAATGCATTTATTTTATTAATATTTATACATATGCAGTACATCACTAGAACTCAATGTGCAATGCTAAACGTTCTCCACAGACTCACCAATGTTTCGTTTCAATAAAGCACTAGATCTATTAATCCAAAAAAAGCATCACTTTTTTAAAGCGCCAACCTCTCAGCGCGTCCTCATCTTGAAGTGACACTGTTAAGTGACACTGTTAATCTTTTCAGCTCTGGCATGTGTAACAAGCATTTATCAGCCTCTTATCCTCCACAG
Seq C2 exon
ATGCTGACGAGTGCTCTGAAGCCACAGACGACTGTCACATCGACGCTCTCTGCCAGAACACTCCAAAGTCCTTCAAGTGCATCTGCAAGACCGGTTACAAAGGAGATGGCAAGCACTGCGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000063097:ENSDART00000091876:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.012 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF129472=EGF_3=WD(100=85.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]