HsaINT0027413 @ hg19
Intron Retention
Gene
ENSG00000162949 | CAPN13
Description
calpain 13 [Source:HGNC Symbol;Acc:16663]
Coordinates
chr2:30975919-30977230:-
Coord C1 exon
chr2:30977156-30977230
Coord A exon
chr2:30976065-30977155
Coord C2 exon
chr2:30975919-30976064
Length
1091 bp
Sequences
Splice sites
5' ss Seq
TTGGTATTT
5' ss Score
2.39
3' ss Seq
TGTATATCTGTTTTTAACAGGAT
3' ss Score
9.63
Exon sequences
Seq C1 exon
GTCTCAGGAGTGGGAGGAAACCTGTGATCCGCGGAAAAGCCAGCTACATAAGAAACGGGAAGATGGCGAGTTTTG
Seq A exon
GTATTTACCCTTCTTATACAATGGTGTTTTAAATCTTTTATTGCCCAAGTCTTCAATCCCTACCCTTTTCCCTGAACATTTACGAAGGTGGAAAATAGCTTTGCAGAGACCTGTTTAGAGGGAGCCTATTTTCTCTACCAAGACACAAAAACTTTGGATGAAAAATTATTGTAGGCTCCCTCTTGGTGGGAAAGTTATTTCAGTTATGAAATGCTGAACTTTCCAGGACATTTTAATAGTAAAAGAGAACATTGGCACCAAAGGCTTGAAATCTGTGGTTTCCTGGAAGCTAGGATGCATGGTTGTCATGCCCATATCCTCTGTACCATCTTGCTGGGACCCTCGAGCTCCCCAGTTTCCTCTAGCATGACGTCAAAAACAGCAGCAGGATGCAGACTCTATAGCTCTGGGTGAGACATGGACTTCATCACCCAGAAGTCACACAGGACTAGATGTTTTGAAAACACGTTCTCGGCCATATGCTCACATCTTAGAGCATGACGTGTACATTCCTCAGAGGGTTGTCTGGTTTACGGAGTGATGCATTTCAATGGAAATTAGCATGTGTGGAAAGGAGCATGGATCTAAATAATTAAGAATCAGAGGGACAAATATAAATTAGAAGGAAATCTTTCCCAGTATCTCTGGTTTAATCACAGTAGGAGGTGGGATTTTAGGTGTGGAATCCATTTTAGGCTGATAAAGACCTCAACAATAAATTTGGCAAAACACCCTAGGGGAAAAGCAATTTTCCTAGCAGCTTAGAGGACCCAGAGCAGAGAGAGACTGGCCGTCGTCCCACTGATCATGAAAGGGCTCACCATCGGATCAATGGGTTAAGGAGATGGCAGTAAATGATAAAGCTGCTGCCAGGTGACCGGCAGACCCCAGAACTTGACTGTGTCCTTGCCTTGCCCTCCCAGCCACTGGAGCAGAAGGACTGAAAAGATAGAAGGGTGCTTGATGGTGAATGAGCCAGGATCAGACACTGGCCTCTGGGCAGGACAGTGGCTATGCTGTGAAGTCATAGGAACCCCCACCCTGGGGACACAACCCCTGGTCACTGAGTGATGTATATCTGTTTTTAACAG
Seq C2 exon
GATGTCGTGTCAAGATTTCCAACAGAAATTCATCGCCATGTTTATATGTAGCGAAATTCCAATTACCCTGGACCATGGAAACACACTCCACGAAGGATGGTCCCAAATAATGTTTAGGAAGCAAGTGATTCTAGGAAACACTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000162949-CAPN13:NM_144575:9
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.615 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0064816=Peptidase_C2=FE(8.4=100)
A:
NA
C2:
PF0064816=Peptidase_C2=PD(6.0=36.0),PF0106717=Calpain_III=PU(12.4=34.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCAGGAGTGGGAGGAAACCTG
R:
GCAGTGTTTCCTAGAATCACTTGC
Band lengths:
216-1307
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)