BtaINT0031245 @ bosTau6
Intron Retention
Gene
ENSBTAG00000010230 | CAPN1
Description
Bos taurus calpain 1, (mu/I) large subunit (CAPN1), mRNA. [Source:RefSeq mRNA;Acc:NM_174259]
Coordinates
chr29:44065178-44067081:+
Coord C1 exon
chr29:44065178-44065296
Coord A exon
chr29:44065297-44066947
Coord C2 exon
chr29:44066948-44067081
Length
1651 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGG
5' ss Score
10.07
3' ss Seq
CTGTGCCCCTCCTCCCCCAGCTG
3' ss Score
10.67
Exon sequences
Seq C1 exon
GGGACTGTTGGCTCCTGGCTGCCATCGCCTCCCTTACCCTCAATGACACCCTCCTGCACCGAGTAGTTCCACATGGCCAAAGCTTCCAGGATGGCTACGCTGGCATCTTCCATTTCCAG
Seq A exon
GTGAGGAGCCCCACATGCACCTTGGACAAGGAGTGGGGCGGTGAGGGAGAGAGGGGTAGCAGGCAACGGAGATGGGCGGGGGACCCTGAAGTTAGGGTGGCGCGGGGCCGCACCTTGCAGGGCCAGCTCCCCGCACCCCCCCCCACCCCCCAGAAAGTATGTGACCTCTTGATTCCATCTCAGGTCTGTCATGTGTGAGAATCTGTCATGTGTGAAACGGTTGGGCAGGTATTTCAGCTGGCAGTTTTCCTGGCTGGTTGTGCACACTGGAGAAAAGAAAGTGCTTAGAGAAAATTCTCTGGGTTATGTCCTACGGGACAAATCCTTTTCCTCCTCAGGGTCTCAGTTTCCCTGTCTGAGAAATAGTGTTCTGCTGGGGAAAATCGGCTGTCACTTGTGGTCATCTACACCCTTGGCCTCAGTCTCCCCCCGACCCCCTCACCCCCAACTCCTCCTGCACTCTGTCAGTCTCCAGCCACTGAGAGCCCTGAGGAAAAGAAAGACTCTGGATAAAGTTTATTTAAACCAGCTTTTCCTGATGCTCTTTGCGCACAGGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGTTGAAGGATCTGGATCCTGCATCTTCATTCCACACCAATTTACCTAGGTATCCCCATCCCCCTACACACACACACACCCGCATTTTCATTCCACATCTAATTTACCTAGGTATCCCCACTCCCTACACACACACACACCCACACACACCCTGGCCTAGAATGGTGGGGAGGGGGAAAGTCTGGGGTCATGGTAGGGCCCAGCAGAACCAGGGTCCAAGGGCTTTGCAACGTCTCTGTACCTGAAGAGGCAACTTGGTCTGTTTCAAAAATATGAACAATGCTGCCTTACAAGTGTTGCCTGCCTAATCTTGTTTAGTTTTCCCATTAGGAAGGCATTATTGTTCCCTTTTGTGGAGGGGGAAACAGGCTCAGCGAGGACGACCTGCTCAGATCCTGTGTCTAGGATGCGTGGCCTAGAATCAGGTATCTAGTGAGTGGCAGAGCTGCTGAGGCCTGACCTCAGGCCTGACCTCAGGCCCGAGGGATCTCAAAGCAGGGATTCACTGTGCCCCTCCTCCCCCAG
Seq C2 exon
CTGTGGCAGTTTGGTGAGTGGGTGGATGTGGTGGTGGATGACCTGCTGCCCACCAAGGACGGGAAGCTGGTGTTTGTGCACTCTGCCCAAGGCAACGAGTTCTGGAGCGCCCTGCTGGAGAAGGCCTATGCCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000010230:ENSBTAT00000011678:3
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(13.0=100)
A:
NA
C2:
PF0064816=Peptidase_C2=FE(14.7=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:
GACTGTTGGCTCCTGGCTG
R:
ATAGGCCTTCTCCAGCAGGG
Band lengths:
246-1897
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]