HsaINT0031667 @ hg19
Intron Retention
Gene
ENSG00000143776 | CDC42BPA
Description
CDC42 binding protein kinase alpha (DMPK-like) [Source:HGNC Symbol;Acc:1737]
Coordinates
chr1:227333190-227335260:-
Coord C1 exon
chr1:227335060-227335260
Coord A exon
chr1:227333439-227335059
Coord C2 exon
chr1:227333190-227333438
Length
1621 bp
Sequences
Splice sites
5' ss Seq
AAAGTTAGT
5' ss Score
4.24
3' ss Seq
TTCTGTTTTTCTCTGTTTAGGAG
3' ss Score
10.28
Exon sequences
Seq C1 exon
GTTCAGTCCTCAGTGGCTGTAGGAACTCCAGATTATATCTCTCCTGAAATCCTTCAAGCCATGGAAGATGGAAAAGGGAGATATGGACCTGAATGTGACTGGTGGTCTTTGGGGGTCTGTATGTATGAAATGCTTTACGGAGAAACACCATTTTATGCAGAATCGCTGGTGGAGACATACGGAAAAATCATGAACCACAAA
Seq A exon
GTTAGTATGTTTTACTTTTGTTCAAATTAATGTGGTAAATAACACATATAATAAAACCATTTTTAAAGAGAAAATATTTTTCTAAAAACAGTGAACAATCACATTTCTATCCTAGTATGGGACAGGACAACATAAATAGTCAAAATCCATAAATTATTCATAAGTTATTAGTTCTAATTTTCTTGTATTTTATTAGAGATGCCGCTAAGTAGGAAATTAAGTGGTCTCCCCAGTAGAATAACAAAGGTCGTAAGTAGAGAATTTAGATCATTGCTTACTATAGTATATGTATAATCATGACTAGAATATGTGTAAAAAAATTTTCAACTTTAGTGGTAATAAGTGCAATACAAATTTAAAATAAGGATGAGATACTTTTTTTTCTTGTCAAATTAGCAAAGATCAAAAGAAAAATAGTACTCTGTACCATAAATAATGCAGTGAGATGGGCATTCTAAGACATTAATAGGAATATAAATTGGTGTAACCTTTCTGTTCAGGAAGTTTACAGGTGTGCACCTAGAGCCTTAAAAAATGGTTAGAGGTTTTGATTGAGCAACTTCAGTCTAGGAATCTACCCTATGACATTCTCAGTAGAACAAAGATATATGTACAAGGATACCTATTCTAACGTTATTTATGATCACAGAACACTAGAAGCAACACAGACACACAACAAGAACAAATTAATGAAACGTTAATATATTTAGTACTAAGTGAAATAGACTGTTCATAATAATAAGAAGAAAGGTTTTATTAGCAGTCTTAGAAGATTGTGAGCAGTTGCAAATACTTAGAATATGAATATCCGATAGAAGGGAATGATAATCTATTCTTTTTAATTTGTTCTAGTGAAGCAATTATGATTAGTTGCTTTACATGTATAAAAATCAGTTTTATAGGGTTTATATTCTTCTTCCTGTTTGCAAAGATAATGTTTCATATAGTTATAAAGAGTTGAAAGACTGGAAATAGCAGCAGGGTTGTAAATAGCATGTACATCATTTGAATTAGAAAAAAATATTGTAGTATATATTTAACAGCACAGATTACAGCTTCAGTTCAAATTCTGGTTCTGCCACTTCCTAGATGTGTAATGTTGAGAAAGTTACTTGAATTCTGTGTGTCTTTATTTCTTCTATAATATTAGCATAGTAGGAGTACCCACCTAAAATGACTGTTTTGAGGGTTAAATGAGTAACGTACTTTAAATAGTGTCAGATACATATTATGTCCTTTAAAAATATTTATTATTAGTTAATCATTAGTATGTAACTTATATGACCATTATCAATCATCTATCTTGATTTAAATAGAGTCAAATTCCACTACTTTGAAGTAATTTCTCTTCATTCTGATAGCAGTTTAAGATATCTAAGGTACAATGTATTCTTCTTTCTATAGCGCATGCATGATTGAGTCATATATGAAATTAAAAGTCCTAGGAAAATGATCTTCTGTCATTCATCCCTGTATTCCTTTAGTATTAGTACTTTGCACCAACATGCAGTTATTAGATATATTTAAAATAAAATGTATTTTTAAGAAAATAAATAAGTCAACCAACTACTTAGTATGTTAAACACTGATTTATATTTTGTTTCTGTTTTTCTCTGTTTAG
Seq C2 exon
GAGAGGTTTCAGTTTCCAGCCCAAGTGACTGATGTGTCTGAAAATGCTAAGGATCTTATTCGAAGGCTCATTTGTAGCAGAGAACATCGACTTGGTCAAAATGGAATAGAAGACTTTAAGAAACACCCATTTTTCAGTGGAATTGATTGGGATAATATTCGGAACTGTGAAGCACCTTATATTCCAGAAGTTAGTAGCCCAACAGATACATCGAATTTTGATGTAGATGATGATTGTTTAAAAAATTCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000143776-CDC42BPA:NM_003607:7
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.145
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:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCTCTCCTGAAATCCTTCAAGCC
R:
AAGGTGCTTCACAGTTCCGAA
Band lengths:
342-1963
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
- Pre-implantation embryo development
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)