BtaINT0035038 @ bosTau6
Intron Retention
Gene
ENSBTAG00000022777 | CDC42BPA
Description
Bos taurus CDC42 binding protein kinase alpha (DMPK-like) (CDC42BPA), mRNA. [Source:RefSeq mRNA;Acc:NM_001192937]
Coordinates
chr16:30838078-30840426:-
Coord C1 exon
chr16:30840226-30840426
Coord A exon
chr16:30838327-30840225
Coord C2 exon
chr16:30838078-30838326
Length
1899 bp
Sequences
Splice sites
5' ss Seq
AAAGTTAGT
5' ss Score
4.24
3' ss Seq
TTCTATTATTCTCTATTTAGGAG
3' ss Score
9.09
Exon sequences
Seq C1 exon
GTCCAATCCTCAGTGGCTGTTGGAACTCCAGATTATATCTCTCCTGAAATCCTTCAAGCCATGGAAGATGGAAAAGGCAGATATGGACCTGAGTGTGACTGGTGGTCTTTGGGGGTCTGTATGTATGAAATGCTTTATGGAGAAACACCATTTTATGCAGAATCTCTGGTGGAAACATATGGAAAAATCATGAATCACAAA
Seq A exon
GTTAGTATATTTTACTATTTTTCACATTAGTGTGGCAAATAATACATATAATAAAATTAAAATGTGATATTTAAAAAGATAATAATTTTCCAAAAACAATAAATAATCTAATTTCTATGCTAGCAGGGAACATGACCAACATGAGTAATCAAAATCCATAAATTATTTTTAAAAAATCTATAAATTATGCATAAAATTGTTAGTCCTCATCTTGTAATTTTGCAGAGATGCTAATAAGTAGACAATTAAATGATCTCTCCAGTAGAGTAACAAAGATCATGAGCAGACAATGTATCATTACTACTATAGTATCAGTATAATCATGACTAGAATGCATTTAAAATGCTTAATCTTAATAATAATAGATAGATGAAATCCAAATTAAAATAAGAATGGTATACTTTTCTCCCTGTCAAATTGGTAAAGATGAAAAGAAAATAGTACTCTGTACTATAAATGATCCATTGAAAAGAACAGTGTTAGATTAGACATCATTGATAGGGATGTAAATTGATATAATCTTTCTGTCAAGAAGTCTGTAAGTATTCATCAACAACCTTAGAAAGACATGGTTAAAACTTTTGGTTGGGCACCTTCAATATTAAGAATCTACCATGAGGGAATATTCATAGAACAAAGCTATATGTGTGAGAATACTTATCCCAGTATTATTTATGATCATCAAACATTGGAAACAGTCCAGATGCACAGCAGGAAAGAATAAAATTTTAATCCATTTAATACCAAATGAAATAGATTGTATAAGAAGTGGGAGACTCTGATTATCAGTCTCAGAAGATTGTGAGTAATTGCAAAAACCTAGAATATGAATAGGAATAGCCCATAAAGAGAGTGCTAATCTGTTCTTTTTAATTTGTTGTGGTAATACAATTAAAATTAATTGCTATATATATATAGTTGTTGTTAGTTGCTAAGTCATATACAACTGTTTTGTAACCCCATGGACTGTAACCCTTCAGGCTCCTCTGTCCATGGGATTTCCCAGCCAAGACTACTGGAGTGGGTTGCCATTTCCTTCTCCAGGGGATCTACCTGACCCAGGAATTGAACCCAGGTCTCTTGCATTGCAAGCGGATTCTTTACTACTGAGCCACTAGGGAAGCCCCAAATATATATATTAGTTTTACGAAGTTGATGCTTTTCTGTCTGGCTGCAAAGATAATCTGCTAAGTAGTTATCAAGAGTTTGGAAACAAGAAATAGCTGCAAAGTTGTCAATAGCATGTAAAGCATTTCTGATAGAAGTCATTGTACTGTAGCATGGCTGTTGAGAGCACAGATTCTGGAATCAGTTTCAGTTCAAATCCTAGCTCTACCATTGATTATGTAACCTTGAGCAATTGTTTTAACTGTTTCTTTGTTTCCTTTTCTATAAAATTAGAGTAATACAGTGGCTCTGAGGATTAAATGAGCTAAACAAGTAACATACTTCTAGTAGTACATGTTACATTCTTTACAAATGTTTAGTATTAATCATTAGTGTGTGACTTATATGAATGTTATCATATAATCAATATCATAATATTGATTATGATTTCATAATATCATAATCGTTATCATAATCAGATATACTATTGATTATGTAAATTCTATTACATTTAGTGAATTCTTTTTATTTTGACAGCATTTAAGGTGTTTTTACATTTAACTTATTCTTTCTGTAGTACATATATGACTAAGTTACATATGAAAAGTTCTTTCAGGAAAATGATCCTTTTAAATTTATTCTTGAATCTCCTTTAGTGTCAGTACTTTGTACCAGTACATATTTATTAGATATTTTAAAATATATATATATATATTTAAGAAGGTCAGTGTTAGCATCAACCTACTTAGTAAATTAGTGATTTATATTTTGTTTCTATTATTCTCTATTTAG
Seq C2 exon
GAGAGGTTTCAGTTTCCTCCTCAAGTGAGTGATGTGTCTGAAAATGCTAAGGATCTTATTCGAAGACTCATCTGTAGCAGAGAACATCGACTTGGTCAAAATGGAATAGAAGACTTTAAGAAGCACCCATTTTTCAATGGAATTGATTGGGATAATATTCGAAACTGTGAAGCACCTTATATTCCAGAAGTTAGTAGCCCAACAGACACGTCGAATTTTGATGTGGATGATGATTGTTTAAAGAATTCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000022777:ENSBTAT00000029173:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.169
Domain overlap (PFAM):
C1:
PF0006920=Pkinase=FE(24.7=100)
A:
NA
C2:
PF0006920=Pkinase=PD(16.5=53.0),PF0043319=Pkinase_C=PU(42.6=24.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGGCAGATATGGACCTGAGTGT
R:
AATTCGACGTGTCTGTTGGGC
Band lengths:
344-2243
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development