BtaINT0031242 @ bosTau6
Intron Retention
Gene
ENSBTAG00000010230 | CAPN1
Description
Bos taurus calpain 1, (mu/I) large subunit (CAPN1), mRNA. [Source:RefSeq mRNA;Acc:NM_174259]
Coordinates
chr29:44089079-44089472:+
Coord C1 exon
chr29:44089079-44089195
Coord A exon
chr29:44089196-44089413
Coord C2 exon
chr29:44089414-44089472
Length
218 bp
Sequences
Splice sites
5' ss Seq
TCCGTGAGT
5' ss Score
8.93
3' ss Seq
CTCGTTTCTTGAACACACAGGGT
3' ss Score
5.87
Exon sequences
Seq C1 exon
GCTTCAAGCTCAACAAGAAGCTGTACGAGCTCATTATCACCCGCTACTCGGAGCCCGACCTGGCCGTGGACTTCGACAACTTCGTGTGCTGCCTGGTGCGGCTGGAGACCATGTTCC
Seq A exon
GTGAGTGTCCCCATGGGCGCCCCCTTCCCACGAGGGTCTCGGGGAATGGAGCTGGGGGTCCACACAGGCTGAGTGCCAGGAGATGAGGAGTATGGAGGGAACTTTGGAGGGGGCTCTCGGGCAGCAGGGGGAGGTGGAGGGTGAGGCTGGAGGTGGGGCTGGCCCTCGAACTCGTGTCTCACCGAGCCCTCCTCCCATCTCGTTTCTTGAACACACAG
Seq C2 exon
GGTTTTTCAAAACTCTGGACACTGATCTGGATGGAGTGGTGACCTTTGACTTGTTTAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000010230:ENSBTAT00000011678:19
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:
PF134991=EF-hand_7=FE(42.9=100)
A:
NA
C2:
PF134991=EF-hand_7=FE(20.9=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:
GCTTCAAGCTCAACAAGAAGCTG
R:
AACAAGTCAAAGGTCACCACTCC
Band lengths:
172-390
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]