HsaINT0035706 @ hg19
Intron Retention
Gene
ENSG00000074054 | CLASP1
Description
cytoplasmic linker associated protein 1 [Source:HGNC Symbol;Acc:17088]
Coordinates
chr2:122216416-122217701:-
Coord C1 exon
chr2:122217556-122217701
Coord A exon
chr2:122216552-122217555
Coord C2 exon
chr2:122216416-122216551
Length
1004 bp
Sequences
Splice sites
5' ss Seq
GGGGTAAGG
5' ss Score
8.05
3' ss Seq
GTATCCTTTTCTTGTTTTAGGCA
3' ss Score
10.44
Exon sequences
Seq C1 exon
CTAAAAAAGATTAGATCTTTACTTTTGGCTGGTGCTGCTGAGTATGATAACTTCTTTCAACATTTGCGTCTTTTGGATGGAGCCTTTAAACTCTCTGCTAAGGACCTGCGGTCTCAGGTAGTGCGGGAGGCTTGTATCACGTTGGG
Seq A exon
GTAAGGACTGCGATGCTCCATATTCTCACCATAAAATAGTGTCACCACAGAGCTTCAGAGATGTCTCCTTGAACATGTGAGCTGGGTCTCTTTAATGTAACTTCTGACTAGTCTCCAAGACCCATTCCAGTTAACACTTCTTTCAGTAGTTTTACAATACTTTTTGCTCAATTATGTGAAGTGTGACAGATTTTAAATTTTATTCAGTGACATAGCTCTGAAGTCTTTATTTCAAACTTTGAAGCAGTTATTAATATGGAAAAGTGAAATTCTATAAAATCCTGTTTCTCTGATTTTTCATTGATTTTTGCTGGCAGGCAATAGCGTGTTTATCAGAATGTTTGTTCCTAGAAGAGTACTGTAGTTATAAAGTTAAAGGCATTTACTGCAGTAAGATTTTATTCTAGCTGTACGTGTACTAGTGATCAAAGCTATTAAAACTTTGTGTTAGAATGTATGTCGGAATATCAAAGCAGCAGCAGCAGCAGGAGGAGGCATTGCAGCTGTTTTAAGTTTTGGCTGAAGTCAGATTTTGAAGCCTGAATATTTTATGTTAAGATAAAAGAAAAAAGAAAAAGGAGCCAAGGGTGCTTTTTCATATTTGTGTTTTATTAATATATAATCAGTTTGTTTGCTATTTTAAGACTAGCTGGGGCAGGTGGGCTGGTATGTGCCTGGAGTCCCAGCTACTTGGAAAGCCAAAGTGGGAGGATTGATTGAGCCCAGGAGTTCAAGTTCAACGTGGGCAAGGTAGTGAGATCCTGCCTCTAGAAAACAAACAAAAAGCTCCACAGACTAGTTGGAAATGTTTTTTTTTAAAAAAAAAAACAACAAAACTTTTGGGCTAAGAACTATTTGCCAAGTTCTTAACATGCACATCGGAAATCTCAGACCCTTGTCCTTTCTAGATAACTTTAAATGAAGGCTCTAGATGTTAAGTGGTTTATATGCTTCACTGTCTCTAAGAAAAATAACTATAGTCCAGTATCCTTTTCTTGTTTTAG
Seq C2 exon
GCATCTGTCATCAGTTCTGGGGAATAAGTTTGACCATGGAGCTGAAGCCATTATGCCAACTATCTTTAATTTAATTCCAAACAGTGCCAAAATTATGGCCACATCTGGTGTTGTAGCTGTTAGGTTAATTATTCGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000074054-CLASP1:NM_001142273:12
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (disopred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF123483=CLASP_N=FE(22.0=100)
A:
NA
C2:
PF123483=CLASP_N=FE(20.6=100),PF123333=Ipi1_N=PU(0.6=2.2)
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:
AGATCTTTACTTTTGGCTGGTGCT
R:
CCGAATAATTAACCTAACAGCTACAA
Band lengths:
270-1274
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- 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)