RnoINT0028934 @ rn6
Intron Retention
Gene
ENSRNOG00000020935 | Capn1
Description
calpain 1 [Source:RGD Symbol;Acc:2267]
Coordinates
chr1:221352132-221354164:-
Coord C1 exon
chr1:221354153-221354164
Coord A exon
chr1:221352341-221354152
Coord C2 exon
chr1:221352132-221352340
Length
1812 bp
Sequences
Splice sites
5' ss Seq
GAGGTAGGT
5' ss Score
9.65
3' ss Seq
TGCTTCTTTCCTCCTGCCAGTTG
3' ss Score
10.05
Exon sequences
Seq C1 exon
GTCCCTCGGGAG
Seq A exon
GTAGGTGTGGCCCTCACCACTTTCTTGATTCATCAGCCCCTGAACTTAGCAGCCCGATAGAAGGAGAATGGCCGAAGTCACCGCTACCACGCATGAAGAAAGTATCAGGAAATGTCACCCTTTCACTGCCTTGAAAATGTTTCTCCCAGTTCTTCATCAGTAGGACAATCACTTCATGCCTGAGGCAGGAGCAGGAGCAAAGATCGGATTTGAACCCCTAGCCTCAGATCCCCTTCAGCCTGCACACAGGCCAGTTCTGTCTTGCAGTTTCACTCGGAGAAAGTGCTGTTCAGGTGTAGGGGTGGAGTTAGGAGCAGGAGTCATGAGCTGAGAGGTCTTTACTTCCCCCTCCCCCCCCCCCCCCGGAGCTGAGGACCGAACCCAGGGCCTTGTGCTTGCTAGGCAAGCATCTACCACTGAGCTAAATCCCCAGCCCCAGGTCTGTACTCTTGAATAGTTGCTTCAGCCTTGAGCCTTGGGGTTTGTATTAAGACATGGTACTTCCCAGATGTGCATGGTGGCTCATGCCTCACATTCCAGCACCTGGGAGGGATGGCAGGAAGATGAGGTTATCTTTGGCTATAAAGAGGGGTCAGGGCCAGCCAAGGCTACATGAGACTCTGTTTTAGTGGAGGGAAAGAATAACATTTCCTCTGGGGCCATCAAGATGGTTAGCAAAGTACCACCAGTCAGCTTCATGCAAGGCATGGTGACCCAGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGCATGTATGTGTACTTATGTATTTGTGTGTGTATGTGTCTGTGTGAGCATGTGCATGTGTGTGTGTACACTCATGTATCTGTGTATGTGTGTCTGTGTGTAAGCATGTGTGTGTATGTGTGCTTGTGTGAGCATGTGTATGTGTGTGTCTGTGTGAGCATGTACATGTTCGTGTGTTGCATTTGTGTGTTTGTGTGTATATGTGTCTGTGTGAGCATGTGGGTGTGGGAGTGTGTGTGTGTGTCTGTGTGTCTTTGTGAGTATGTGAGTAAGACACACATGCCACATTATGAGTGTAGAGATAAGAGGATGACTTTGTGGATTGGGTCTCTCTATCCTCCTTTATGTGGCTTCCAAGAATGGAACTCAGGTCACAGGCTTGTGTCACAAGTGTGCTCACTTGAGTGTCTGAACAATTCTGCATCACAGTGTTTGGAGCCCCTTATCTGCAGTCAGGTTTTCTTTTCTTTTGTTTTATTTAATTTCTTATTCATTTATTTTTGGGGTAGGGTTTTATGTAGCACAGGCTGGCCTTAAACTCACTGTATGGCTGAGGGTGACTTTGAATTCCTGATCCTCTGGCCTCTACTCCTGAGTGAGGGGCTGCAGGCATAACCCATCATACCTGGTTTAGTGCAGTGCTGGCATCAAGACCAGGGCCTGGGGCTGGTGAAATGTCTGGGTAGATAAAGGCTCATGTCTCCAAGCTTGATGAGCCGAGTTTGATCCCTAGAACCACATACTAAGAGGAGAGAACAGACTCCTACAAGGTTTCTTCTGACCTCCACTCACACCTTAGCACTCACATCCCCTCCCCCAACCACAAAAATAAATAAATGAATGAACCATGGTGGGAAGTAGCAGTGTTCTGTCCCTGTCTACCTTTAGATGCCAGCCCAGGCACTCACCTACAGGTGAGTGACTTATAGGGTCTTACAGGCTGTGGGCATTACCTAGCAGGCCAGGACTTGCAGCCTGGGCTCTGGGCCTGGGCCAGCATCTAAAAGTAGCTGGAGTGAATACTGCAGTACCCCCTTGCTTCTTTCCTCCTGCCAG
Seq C2 exon
TTGGCGGGTCAGCCTGTGCACTTGAAGCGTGACTTCTTCCTGGCCAATGCTTCTCGGGCACAATCAGAGCACTTTATCAACCTTCGAGAGGTCAGTAACCGCATCCGCCTGCCGCCGGGGGAGTATATAGTGGTGCCCTCCACCTTCGAGCCCAACAAAGAGGGTGACTTTCTGCTGCGCTTCTTTTCAGAGAAGAAGGCTGGGACCCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000020935:ENSRNOT00000028431:12
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=0.005
Domain overlap (PFAM):
C1:
PF0106717=Calpain_III=FE(1.9=100)
A:
NA
C2:
PF0106717=Calpain_III=FE(43.9=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]