RnoINT0028998 @ rn6
Intron Retention
Gene
ENSRNOG00000020389 | Capn12
Description
calpain 12 [Source:RGD Symbol;Acc:1307341]
Coordinates
chr1:87070245-87070940:+
Coord C1 exon
chr1:87070245-87070413
Coord A exon
chr1:87070414-87070865
Coord C2 exon
chr1:87070866-87070940
Length
452 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGA
5' ss Score
7.54
3' ss Seq
ACAATCTTGGCCTCCTCCAGAGT
3' ss Score
6.27
Exon sequences
Seq C1 exon
GCTCCACGGCTCCTATGAGGTAATGCGAGGAGGTCACATGAACGAGGCATTTGTGGACTTTACGGGAGGCGTGGGCGAGGTCCTCTACTTGAGACAGAACACCCCAGGTGTCTTTGCCGCCCTTCGCCATGCCCTGGCCAAGGAGTCCCTTGTGGGTGCCACTGCCCTG
Seq A exon
GTGAGAGCTGAGCTCCCGTGTAGACCTCCACTAGGCCAGCGTAGTCGGGGATGAGGTGGGAGGGGAGCCTAGTATTCAGTGTCCTTCTTACCTTCTGCTGTTGTCCCTCAGATCCTCAATGGTAGATTCTAGGCTAGAGCCCTCCATGTAAGCTACATCCTTCCACCCCCTCCATTTTACATTCCTTCCCAGGCAGGGTCTGAGTTACCCACACTGGCCTTGAACTTGTGATCTTTCCGTATCAGCCTTCTGTGTAGCTGGGATCCCAGGCCTGTGATGCAGAGCCCAGGCTTCCCCCATCTCCTTTATTTTACCCCAACTGTTCACCTGAGTCCCTTGGCATTTGATGCGGCTTGGAGAGCTCCTGGGTCAGAAGCATGAGGCTGGATTGGGATGCTAGGGAGAGATGCTTGTATCGCCCACCCGACGCTCACAATCTTGGCCTCCTCCAG
Seq C2 exon
AGTGATCGGGGTGAGATCCGCACAGATGAAGGGCTTGTGAAAGGACATGCTTATTCTGTCACAGGCACACACAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000020389:ENSRNOT00000027645:5
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:
PF0064816=Peptidase_C2=FE(18.9=100)
A:
NA
C2:
PF0064816=Peptidase_C2=FE(8.1=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg19)
No conservation detected
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGGCTCCTATGAGGTAATGCG
R:
CTTGTGTGTGCCTGTGACAGA
Band lengths:
238-690
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]