HsaINT0031652 @ hg19
Intron Retention
Gene
ENSG00000143776 | CDC42BPA
Description
CDC42 binding protein kinase alpha (DMPK-like) [Source:HGNC Symbol;Acc:1737]
Coordinates
chr1:227221035-227222495:-
Coord C1 exon
chr1:227222356-227222495
Coord A exon
chr1:227221117-227222355
Coord C2 exon
chr1:227221035-227221116
Length
1239 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAGA
5' ss Score
10.06
3' ss Seq
ATGCTTTGCTTTTCGTTCAGGGA
3' ss Score
7.38
Exon sequences
Seq C1 exon
ATTCCTAAGCCAGCTGGAGTGAAGAAAGGGTGGCAGAGAGCACTGGCTATAGTGTGTGACTTCAAACTCTTTCTGTACGATATTGCTGAAGGAAAAGCATCTCAGCCCAGTGTTGTCATTAGTCAAGTGATTGACATGAG
Seq A exon
GTAAGAGTTTGAAGGTAAAATTATTTGTATCATTGCAACATAGGAATTTTAAAGTTTCTGATTTTCAAAAATTGTGTTGCCATGGTTTATTTAAATGAACTAATTTCGTATTTTCTAATTTGCTAATATTGCTATAGAAACAGAATTGAAAATAGGAAGTAAGGTGTATTTATAGGACAGGTTGGTATGTGTGTTGAGTGTGAGGGGCTAGGAGTTAAGGAAAAAGAAGTTGGTGTCCCAAAGACCTGTGTAAATGGGGTAATGGAGGCCTACCATGTGAAGTTTATATTATCACATCACCTAAAGGCTTAGAGTATAATTTCAATGTGAGGAAAGAAAATAAAAATCAGAAAGGCTTCTGGAAAACATAATCAGTAAACATTTAAGTAAGTACAGCCCTTGAACACTTCTGGTCTCATTTTTCAGATTCTTCCTGTGTTCCTTAGTTCTCTCTCCTTTACCTTTTCTCCTAACTCCAGGCACTATCCTTGAGTGATCATATTTACTCACAGCTTCAGCCATCTCCTCTGCATTGATGACTCCCAGACTTGTATCTCCAGTTCAGATATATCCATCCATTGCTCAAAACCGGAATTTCTAGCTGTGACTCAAATTGGCACTTCACATTGGCATCTCAAACGCATTATCTTCCCCTACAAATATGGAACATGACAGGATAGATGCAAGAAATATTGGCAAGAAAAATCTGATAGAACCTACTAAGGGACTGAATATAGATAGGGAAAAGAATCACAAATAGGACTAAGGTGTCAAGCCTGTAAGACTAAGGGAGTCATGGTACCAACAACAAAATTAAGGGAATCACAAGAAATTATTGTGGAGGAAATACGTTGTAGATGTTGAAGGAACAATAAAATATAACATGAGCTGGGTTGAGGGTACTTAAGATTTATTATGGGAGGCAAGAGGGTCCACTGGAGGCTCCAGAGACCTACCAGGGTTCAAATCCCAGTTCTACGTGTATACTTAACTGGCCTTGTGACTGTGGGTAAGCCAGCAATGATTTCTAGCTCTTGTATAATGTGCCACTAGGAAGTTATTCTTGATAAATTATTTGGGGCACTATTAATTACAATGGGGGAAAATTAATTTTTTTAAAAAATTAAATTTGGGTGTTTGGTGCAGTTAAGCTTTGGGTATGTGTTATTTGGATACACACCCCAAACCACACACACATAGCCACATATAGTAACTTTTAATGCTTTGCTTTTCGTTCAG
Seq C2 exon
GGATGAAGAATTTTCTGTGAGTTCAGTCTTGGCTTCTGATGTTATCCATGCAAGTCGGAAAGATATACCCTGTATATTTAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000143776-CDC42BPA:NM_003607:25
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.001 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
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:
TTCCTAAGCCAGCTGGAGTGA
R:
ATACAGGGTATATCTTTCCGACTTGC
Band lengths:
214-1453
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)