HsaINT0027386 @ hg38
Intron Retention
Gene
ENSG00000182472 | CAPN12
Description
calpain 12 [Source:HGNC Symbol;Acc:HGNC:13249]
Coordinates
chr19:38740051-38741910:-
Coord C1 exon
chr19:38741777-38741910
Coord A exon
chr19:38740220-38741776
Coord C2 exon
chr19:38740051-38740219
Length
1557 bp
Sequences
Splice sites
5' ss Seq
CAAGTGAGG
5' ss Score
5.85
3' ss Seq
CCCCAGATCTGCCCCCACAGGCT
3' ss Score
6.77
Exon sequences
Seq C1 exon
CTCTGGCAGTTTGGCCGCTGGATGGACGTCGTGGTGGATGACAGGCTGCCCGTGCGTGAGGGGAAGCTGATGTTCGTGCGCTCGGAACAGCGGAATGAGTTCTGGGCCCCACTCCTGGAGAAGGCCTACGCCAA
Seq A exon
GTGAGGACCCCAGTTCCAACCAGCTGCAGCCCTAAGTCCCCACAGCAGGCATCAAGCCACAGGGGGACCCAGAGTCCCCCAAGCTCTGCAATCCTCCAAACACCCCACCAAGAATCCCAAACCAAGTGACAACCGCCAGAACCCTCATATCACAACATCACCTGAGCAACTTCATGTTTTTTTTTTTTTTCTTTTTTTTTGAGACGGAGTCTCACTCACTCTGTCGCCCAGGCTGGAGTGCAGTAGCGCGATCTTGGCTCACTGCAACCTCTGCCTCCCAGGTTCCAGCGATTCTCCTGTCTCAGCCTCCCGACTAGCTGGGATTACAGGAGCGCACCACCATGCCTGGCTAATTTTTATATTTTTAGTAGAGATGGGGTTTCACCATGTTGGTCAGGCTGGTCTCCAACTCCTGATCTCAGGTGATCCACCTTCCTTGGCCTCCCAAAGTACTGGGATTACAGGTGTGAGCCACTGTGCTCAGCTGTACCTTCAAATCTTAAACCCCTCTCTCCATCAATATTTCACACAAAACATTCCTGGAGACCCCCAGTCACTCATAATTCTTAAGGATCCTGAAATCTCATATATCAGGCCCTGGATTCACCAAATCTGGGATTTATCCCCTCGGGTGAGCTGTATATCTTAGATTGTCTCTCCTGGTCCATTGAGAAATCTAAAGCACCCCCAAAATATTGGGGGTCACCCTGGGACCCTCAAATCTTTGCCTTTTCCCCATTCTGAGGCTCTGAAATTCCTGACAAGCCCCCATAGGGATGATCCCCCAAAGCGGACATCTACCAGAGGTTCAAGGTTTCAGACAGCACCAGGACTCTCAGAATTCTAACACAGCTCTCCCATGCCCCCCACCAAACCGAAGTCCTGGTCACCCCAAGGACCACAGGCCCAATCTCCAAGGGCTTCTGTATGTGCCACAGTTCCCCCCGTCAAGAGTCTGAATTTTTTTTTTTTTTTTGAGATGGAGTTTCACTCTTGTTGCCCAGGCTACAGTGCAATGGCGTGATCTTGGCTCACTGCAACCTTCGCCTCCCGAGTTCAAGCGATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGATTACAGGCATGTGCCACCACGCCCAGCTAATTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTATTGGCCAGGCTGGTCTCAAACTCCTGACCTCAGGTGATCCACTTGCCTCGGCTTCCCAAAGCGCTGGGATTACAGGCGTGAGCCACCATGCCTGGCCAAGAGTCTGAAATTGTTTTAGCTGGGTGTGGTGGTGTGCACCTGTGGGCCCAGCTCCTCGGGAGGCTGAGGTGGGAGGAGGATCGCTTGAACCCGGGAGTTTGAGGCTACAGTGAGATGAGATCACGCCACTGCACTCCGGCCTGGGCCACAGGGTGACCCTGGAAAAAGTCTCAAAACTTCAGGAATTTCCCCTGGGGATTCCACACCCTGAGACACAGGCCCCTGCAGATCCCAGGGCAGGGGTGCCTGAGACGCTTGTACTTGCCTCAACCCTCACCCCAGATCTGCCCCCACAG
Seq C2 exon
GCTCCACGGCTCCTATGAGGTGATGCGGGGCGGCCACATGAATGAGGCTTTTGTGGATTTCACAGGCGGCGTGGGCGAGGTGCTCTATCTGAGACAAAACAGCATGGGGCTGTTCTCTGCCCTGCGCCATGCCCTGGCCAAGGAGTCCCTCGTGGGCGCCACTGCCCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000182472:ENST00000328867:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF139001=GVQW=PD(15.4=8.9),PF0064816=Peptidase_C2=FE(21.6=100)
A:
NA
C2:
PF0064816=Peptidase_C2=FE(18.9=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTTTGGCCGCTGGATGGAC
R:
GACTCCTTGGCCAGGGCAT
Band lengths:
273-1830
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