RnoINT0028931 @ rn6
Intron Retention
Gene
ENSRNOG00000020935 | Capn1
Description
calpain 1 [Source:RGD Symbol;Acc:2267]
Coordinates
chr1:221369333-221370322:-
Coord C1 exon
chr1:221370227-221370322
Coord A exon
chr1:221369601-221370226
Coord C2 exon
chr1:221369333-221369600
Length
626 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGA
5' ss Score
10.77
3' ss Seq
CAGGCCCATGTGTCCCCCAGGAT
3' ss Score
6.9
Exon sequences
Seq C1 exon
GGAGGAGCGCTCTTCCTGGTTGGGCCCTGCCCTGAGCTGCCACCAAGGAAGCCAGCCCCAGGGACCGCAGCAATCTCCCAAACTCCCCTTCCCCAG
Seq A exon
GTAAGAAGTTGGGTGTCCAAAACTGTCTGACTCAGGCCACTGCTTCTGGGGCTAGGGGGCTGTGGCTGATCGGCCCCTGTTTCAGGTCTTCTGTGTGCTTGCGTGAAGGGTAGGGGTTAGGAAGCAGCTCAGCCCAGGCGCACAGCTCAACCTGTCCGCCTGAAGCCGGGCCACTGTCCAGTGCTCTGATGTTCAGCTTGCGGGAGGACATCAATGCTGGGAGTTTTCAGTTCCTAAGCCGAGGAAAGGGGCAAATGAACTAGATACTTGGCAACTTTGTGAAGGGGGTTACAGGCAGGGAAACAGGGTCAGAGATCTTAAATGAAGTACCTTTGCTCTCCCGTGCTGTGGCTGGCCTCCACCCAACTGCCTGGATGAGTGACACCAAAATGTCAACTCTGGATAGTAGGGATAGGAGAAGGAGAGGTGGTGGCCAGGTATCTAAAGACTGGGCACCCTTTTCCAGATTCTGGGAGCCTAACAAGGTGGCTCAGAGTCCCAGGCTCTGTAAAGGGGGCAGTGAACTATGTCTGGGGAGAAATGAGTCCAGGAGGACTGCTAGCAGGCAGGCATTGTGTTTTATCCCGGGAAGGCCTGTATTTCTACCAGGCCCATGTGTCCCCCAG
Seq C2 exon
GATGGCAGAGGAGTTAATCACACCTGTGTACTGCACCGGGGTGTCAGCCCAAGTGCAGAAGCAACGGGACAAGGAGTTGGGCTTGGGCCGCCATGAAAATGCCATCAAGTACCTGGGCCAGGATTATGAAAATCTTCGTGCAAGATGCCTGCAGAACGGGGTCCTCTTCCAAGACGATGCCTTCCCTCCAGTTTCTCATAGCTTGGGCTTCAAGGAACTGGGTCCCAATTCCTCTAAAACCTATGGCATCAAGTGGAAGCGTCCTACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000020935:ENSRNOT00000028431:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=0.022
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
PF0064816=Peptidase_C2=PU(11.3=38.2)
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAGGAGCGCTCTTCCTGGTT
R:
GACGCTTCCACTTGATGCCAT
Band lengths:
358-984
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]