HsaINT0027413 @ hg38
Intron Retention
Gene
ENSG00000162949 | CAPN13
Description
calpain 13 [Source:HGNC Symbol;Acc:HGNC:16663]
Coordinates
chr2:30753053-30754364:-
Coord C1 exon
chr2:30754290-30754364
Coord A exon
chr2:30753199-30754289
Coord C2 exon
chr2:30753053-30753198
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:ENST00000295055:9
Average complexity
IR
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