RnoINT0028944 @ rn6
Intron Retention
Gene
ENSRNOG00000020935 | Capn1
Description
calpain 1 [Source:RGD Symbol;Acc:2267]
Coordinates
chr1:221346066-221347624:-
Coord C1 exon
chr1:221347566-221347624
Coord A exon
chr1:221346849-221347565
Coord C2 exon
chr1:221346066-221346848
Length
717 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGA
5' ss Score
8.68
3' ss Seq
ACCTTCCCCTCGCCCTGCAGTGG
3' ss Score
10.02
Exon sequences
Seq C1 exon
GGTTTTTCAAAATTCTGGACACAGACCTGGATGGTGTTGTGACCTTTGATCTATTTAAG
Seq A exon
GTGAGATGGTTCTCCTTGTTCACCTGCCCCTACCAGGACAGGGGTCCACGGCCTTGGAACAAGCCTTCAAATCTAGGGCCTAGTCTTGGAAGCCTTGGGACAGGGGCTTCTGGAGCTCCGGGGTGGGGGATGAAAAAGGGGAGACCAGGCTTCTAGAAGCTGGTGGCAACCAGCAGCCTGGTGTCCTGGAGTCTAGAAGTAAGATAGCTGCTGCTGGGTGTGTGGTGGAGACGCATGCCTTTAATCCCAGCCAGAGGGAGGCAGAGGCAGGTGGATTTCTGTGAGTTTGAGGCCAGCCTGGTTTATAGAGTGAGTTCCAGGACAGCCAGGAATTGTCCTTGGAGAGAGAGAGGGGGGGAGAGAGAGAGAGAGAGAGAGAGAGGGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGGGGGGAGGGGGGAGAGGAGAGGAGAGAGAGAGAGGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGCGCGAGAGCGCGAGAGAGCGCACCCCTGTCACCAGAAGGTCCCTCAAGGAGGGCATAAGCATGGCTGGTAATGGTTGACTTTGGGATGGGTGACAATGGGTGAAGGAGACTGACAAGGCCACGTGTCCTGCTGCTGCTCCCAGTAACCTTCCCCTCGCCCTGCAG
Seq C2 exon
TGGTTACAGCTGACTATGTTTGCATGAAGCGGGATGGCTCCGCTGCCTGTGTTCTTCCTTCTTCCTCTGCCAAGCCACACCTCCCCGCCATGCCGTACCAGACCATGTCAGCTGCCAGTGCCTTCCCTCAAAAAAGGAGGGCACCTTGTCCTCCTGTCCCCTTGTCCTCCTGTCCTTTCACCTCCCCACTACCTCTGTTCAATTGCTCTAGGCAGAGTCACAGGGCCCTTCCTGCCCCTGTAGCTAAGGCAACCCTGACCCCTGCTCATGGCTAAGAGCAGGAAGGCAGCTCCCTGCTTACTCCTTCCTGCCTCCGGGGCAGGAGTAGGCATCCCTGCCCCTCCCACTCCCTGCTACTGTCCAGATGTGTGTCTCACCTAATCTGTGGAGGCTCTAGCCCCTGTCATCCCCTAGACCTGCAGACTTCGTAACCACTAGCTAGTTCCTTGTCTGCACCTGGGTGTTGAAGGCCTCACCTCACTATGGGAGCCCCACAGCCAGTTCACCTTCCTGTGCCTTCATGTGCAGCAGCCAAGATCCCTCTGCAAACCAAAGTACACCTCTCCTGCCCGTGTGCCCACCAGGAACTTCCTGGCCGGGAGGGCACTCAGGCCCTCCGTATCCCCACCCCCCTTCCTCTATTTTTTAATATTTTTCAAGGAAATGCTTGAGGGACTAGTGTACTGGTTATGGAGGACCAGGACCTGGGGGGTGGGTTGGGGAGGTCCCATGTTTCAGTGCAGTGGGAAAATAAAATGAAAGGCCAGACATGTGTCTCCGGGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000020935:ENSRNOT00000028431:21
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF134991=EF-hand_7=FE(21.1=100)
A:
NA
C2:
NO
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:
CCTGGATGGTGTTGTGACCTT
R:
AGGAAGGAGTAAGCAGGGAGC
Band lengths:
343-1060
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]