RnoINT0028948 @ rn6
Intron Retention
Gene
ENSRNOG00000020935 | Capn1
Description
calpain 1 [Source:RGD Symbol;Acc:2267]
Coordinates
chr1:221364745-221366635:-
Coord C1 exon
chr1:221366467-221366635
Coord A exon
chr1:221364829-221366466
Coord C2 exon
chr1:221364745-221364828
Length
1638 bp
Sequences
Splice sites
5' ss Seq
AATGTGAGT
5' ss Score
7.8
3' ss Seq
GCGCATGCTTCCTTCTGCAGATC
3' ss Score
10.1
Exon sequences
Seq C1 exon
AGTGAATGGCAGCTATGAGGCCCTTTCGGGAGGCTGCACCTCAGAGGCCTTCGAGGACTTTACCGGTGGGGTCACTGAGTGGTACGATCTGCAGAAGGCACCCAGCGACCTCTACCAGATCATTCTGAAGGCCCTGGAACGAGGCTCCTTGCTGGGCTGCTCCATTAAT
Seq A exon
GTGAGTGATATCCAACTTCCTCTGGCAAAGCCTAATCTCATCCTCAGTGCAGGTTCCGTCCAAGACACACCCCTTCCTCACCTCATTTCTGGCTGCAAATGAGCCCCGCCCCTCACCTCCTCCTATGGGCTACCTCCATGCGCACTCCCTGTTCCCCCCTTCTTCCTTCAAACCTCTGCCTTCAGCCATGCTCCAACTTGTTCCCCAGCTTCCTCCTGCTCCCTTCCCTTCTCATTCTTTTTTGTTTGTTTGTTTGTTTGGTTGGTTGGTTGGTTGGTTGGTTTATTTAATGTGCATTGGTATTTTTCCTGTATGTATGTCTATGTGACATCCAGGTGCCAAGTCCCTGGAACTGGAGTTACAGACAGTTGTGAGCTGCCATGGGGGTGCCGGGAATTGAACCTGGATCCTCTGGGAGAGCAGCCAGTGCTCTTAACACTGAACCATTTCTGCAGGCAGCACATATAGTAAAATTGAAACAATATAAAGTAGATTAGCAAGGCCCTTCATTCTTACCACCTTCCCATGTTCGGAGGCTATCACAGTCCAGTTCTTCAGCCTCCTGAGGCAATCTCTTTGCAATTCTCCGACTTCACCCACGCCTGGCTCCTCCTCCTGTCCTCTCCTTGCTCACCGTTATCTGCCCCACGATTGCCACAGCCACTTCTAGACTTCCCTAGTCCTGGTCTGGATCATTCCACACCAGCATCATGGCCACACACTGCTATGGAGCCCGACACAAAATCTTGGAATTTTACTTAACACATTGAGATTTTTAAAATCTGTGAATTAAGTGAGCCCTCCCCAAGGGTGAACTTTGTGAATGCCGTGTTACCATGTCTTAGGGTTGGAGCGAGAGATGGCTCAGTGGCTAACAGTATACACTGCTCTTGAAGGAGACCCAAGTTGGGTACCTGATGACTTGGCCTGTGACTCCCACTCCAGGAGGGGCTGACGCCTCTGGCCGCTAAGGGCATCTCACATACACACACCAACCCCGAGTCACATACAGAGAGTTACAGTTAATTAGGAAAGAAACTTTTAAAATAACTTACTTATTTCTATTTTACGAGCATTGATTGGCATTTCACCTGCACACGTGTCTGTGTGTGGGTGTCAGACCCCCTGGAACTGGGTTACAGATGGTTGTGAGCCACCATGTGGGTGCTGGGAATTGAACCCAGGTCCTCTGGAAGAGTAGCCAATTTCTTAACTTAGCCACCTCTCCAGCCCCTAAACTAAGCTTTTTTTTTTTTTAAAGGGCTATATGACTCTGTAAGTTTATCCCCACTGGATCCGTCCTCCCCCCCACCCGACTCCATCCCCTCGCTGCATCCCTCGGGGGTGCTCCTGATTATCAGAGTGTGTACATGTGCACATTCACTACCTCGCCAGCCCTAGCCAGTGCTAGCTTGGTGAGAGCATCGGTGAGGTATCTAGGCTTGACCCTGCTCCCTAGGAGGAACAGCATTTGTGTGTAACAGTGAGTGAACAGGCGAGGAGTCTCTAACAGTTTCTCCCATCAGCTTTTGTGGGGGTTATGTGCAGGGGGGTAAGGGGTCCTGCCTGCGCCTCCCGAATCCTCCAAGCAGGAGTGGTACTCGATCTCCTGACCACAGCGCATGCTTCCTTCTGCAG
Seq C2 exon
ATCTCCGATATCCGTGATTTGGAGGCTATTACTTTTAAGAACCTGGTGAGGGGCCATGCATACTCTGTGACGGATGCCAAGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000020935:ENSRNOT00000028431:6
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(18.7=100)
A:
NA
C2:
PF0064816=Peptidase_C2=FE(9.0=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:
GTGAATGGCAGCTATGAGGCC
R:
GGCATCCGTCACAGAGTATGC
Band lengths:
246-1884
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]