HsaINT0027577 @ hg19
Intron Retention
Gene
ENSG00000126247 | CAPNS1
Description
calpain, small subunit 1 [Source:HGNC Symbol;Acc:1481]
Coordinates
chr19:36630918-36632122:+
Coord C1 exon
chr19:36630918-36631059
Coord A exon
chr19:36631060-36631898
Coord C2 exon
chr19:36631899-36632122
Length
839 bp
Sequences
Splice sites
5' ss Seq
GCGGTAAGC
5' ss Score
8.99
3' ss Seq
GTCCCCTTTTTTCCCCCCAGCAG
3' ss Score
9.64
Exon sequences
Seq C1 exon
CGGGCGACAGCAGGGCCGCGGTGCAGTGTCCGACCCGAGAGTTGCGGCCTGAGTCACCGGCCCCGCCCTCCGGAGCCGGACGCTGCGGGAGGCCCGGGAGCGGCAGTGGAACCGACTCCCAGAACTCCGGACGTGTGCGGCG
Seq A exon
GTAAGCGCCCGGCCCGTACCCCCTCCGCACCCCGCAACTCCGACTTTGGCGGCCCCCAGACCCGGCGAAACCGTGAAGTCTCGGCCTCAGGAGCCCCCCAGATCCATGGTCTCAGATTCGAACCCTCAGACCTGTTCGATCTCCTTTTATGCCGTCCCGGGGACCCTTCTCCACCCTCTGTCTCATGATCCAAAATACAGGCCCATAGGTTTCAGAGATACCCTGTGAATTCTTCCTTGGGGTGTCCTGAACCGCGATCGTAGATCTGTGCCCCCAGTTCCAGCGGGGAACCCCATTGTCCGGGAACCCAGAGCTCACAGCCACGATCTTAGACCCGAGCCCACAGAGCCAGAGGTGACACTGGAATCCTGCCGCTGGGAATACCTAAATTCTCAAGCCCACATTTGGGATTTCCTAAACCCCGCCCTGGGGCCCTTTAGGCCGTGGATGTTTGCTCCGCGCCCATGACCTGCCAAGGACCTCTACATTCAGGCTGGGCTCTGGATCTCACATTCTAGCGCCCAGACATGTCGGGAACGCCTTACGCCAACTTGGGGTCCCCACCAAGAGAACCCCCACCAGATCTGCACCCTCCCCTTCACGCGTGCACCCAGTCCAGGCTCCCTCAAGCCCCACGGGTGCCTTTTAGACCTGAGGAGGTTGCAAACCTGATCCCCCATACCTGCCCCACCCATCCGCGGACAACCCGCCCTCGCAAACTCAGACCCCCACCCGGAGGCTTCAGATTCCTCCCAGGTCCAGCTGCCGGAAATGCGTGTTTGAAGGGAGGGTGTGGGCTCAGGGGCGAAGCACCCACTGGTCCCCTTTTTTCCCCCCAG
Seq C2 exon
CAGTGAGTCGCAGCCATGTTCCTGGTTAACTCGTTCTTGAAGGGCGGCGGCGGCGGCGGCGGGGGAGGCGGGGGCCTGGGTGGGGGCCTGGGAAATGTGCTTGGAGGCCTGATCAGCGGGGCCGGGGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGTGGTGGAGGCGGCGGTGGCGGTGGAACGGCCATGCGCATCCTAGGCGGAGTCATCAGCGCCATCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000126247-CAPNS1:NM_001749:1
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=0.214
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
NO
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Conservation
Rat
(rn6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGTGTCCGACCCGAGAGTTG
R:
CTGATGGCGCTGATGACTCC
Band lengths:
342-1181
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
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)