BtaINT0031233 @ bosTau6
Intron Retention
Gene
ENSBTAG00000010230 | CAPN1
Description
Bos taurus calpain 1, (mu/I) large subunit (CAPN1), mRNA. [Source:RefSeq mRNA;Acc:NM_174259]
Coordinates
chr29:44064429-44064919:+
Coord C1 exon
chr29:44064429-44064695
Coord A exon
chr29:44064696-44064849
Coord C2 exon
chr29:44064850-44064919
Length
154 bp
Sequences
Splice sites
5' ss Seq
ACGGTGAGA
5' ss Score
8.94
3' ss Seq
GGACTCTGGGTCTCTTGCAGGAG
3' ss Score
7.69
Exon sequences
Seq C1 exon
ATGGCCGAGGAGTTCATCACTCCGGTGTACTGCACCGGGGTGTCTGCACAAGTGCAGAAGCAGCGGGCCAAGGAGCTGGGCCTGGGCCGCCATGAAAATGCCATCAAGTACCTGGGCCAGGATTACGAGCAGCTGCGGGTTCACTGCCTGCAAAGAGGGGCCCTTTTCCGTGACGAGGCTTTCCCCCCAGTGCCCCAGAGCCTGGGCTTCAAGGAGCTGGGCCCCAACTCCTCCAAAACCTATGGCATCAAGTGGAAGCGTCCCACG
Seq A exon
GTGAGAGGGGCCACCCTGGATGGGACTCAGTTTACCTCCTTCCTGAGTGAGGAGTGGGAATAGGACGCCAGGTCCCTAGAGTGGGGTCTGGGATGGCTGGGCTCCAGTTTCTAGGAGGGGCTGGCCCAGAGACAGGACTCTGGGTCTCTTGCAG
Seq C2 exon
GAGCTGTTCTCAAACCCCCAGTTCATCGTGGATGGAGCCACCCGCACGGACATCTGCCAGGGCGCACTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000010230:ENSBTAT00000011678:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0064816=Peptidase_C2=PU(11.3=38.2)
A:
NA
C2:
PF0064816=Peptidase_C2=FE(7.7=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:
CGGGGTGTCTGCACAAGTG
R:
CTGGGGGTTTGAGAACAGCTC
Band lengths:
253-407
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]