BtaINT0031303 @ bosTau6
Intron Retention
Gene
ENSBTAG00000008946 | CAPN13
Description
calpain 13 [Source:HGNC Symbol;Acc:HGNC:16663]
Coordinates
chr11:69116930-69118429:+
Coord C1 exon
chr11:69116930-69117132
Coord A exon
chr11:69117133-69118392
Coord C2 exon
chr11:69118393-69118429
Length
1260 bp
Sequences
Splice sites
5' ss Seq
CAGGTACAG
5' ss Score
8.68
3' ss Seq
ACTGTCCCCTGGTTTTCTAGGAA
3' ss Score
11
Exon sequences
Seq C1 exon
TTCCAGCACTTCCAAGACAGATTGCCATCCACCTTCTTCTCCCAATTCAGAATTGCTGAGAAGGGCATTGTGTCTGAAACCACGTGCAACCTCACAGAGTGCTTCAGTCTGAGCCCCGGGACCTACGTGGTGGTCGTCTCCGAGGGCAGAGAAGCTGTTGAATTCTTGCTCCGAATCTTCCTGAAGATGCCAAACAGTGACAG
Seq A exon
GTACAGAACTTCTGGGATTCTAAACGTTTTTATCCTACTTAATTTTATAAGAACACATCATATCATTCTGTGCGGCAATGCACTGTGTCAGTGGGGGACACAGAATGGCCCTCACTCTGGAGAAACTCAACGCCAAGTCTAATGCCAAGACAAAAAAGAGGGTGGGGATGTTGCTTGATGGAAGGCAGGGTCACATGGGAGACTGGAGGGACCCATCTCTGGCAAGAGGGCCGGAGGAAGGCTTCTTGGGGGCATGGCATGTGAGCTAGTCCTTGAGAAAAAACATAACTCAGAGTTTCAAAGGGGAGGGCAGTGCTGTTGTTCAGTTGCCCAATCATGTCTGACTCTTTGCGACCCCATGGACTGCAGCACACCAGGCTTTGCTGTCCTTCCCCATCTTCCAAAGTTTGCCCAGATTCACGTCCATTGAGTCGGTGATGCCATCAAACCATCTCATCCTCTGTCGTCCCCTTCTCCTGCCTTCAGTCTTTCCCAGCATTAGAGTCTTTTCTGATGAGTTGGCTCTTTGCATCAAGTGGCCAAAGTATTGGAGCTTCAGATTCAGCATCAGTCCTTCCAATGAATATTCAGGGTTGATTTCCTCTAGGATTGACTGGTTTGACCTTCTTGTAGTCCAAGGGACTCTGGCGGAGGAAAAAAGCATGAGGAGAAACAGGGAAGTGGGCGAGGATGGGGCTCATTGAAGAATCAGCAGAGCTGTCCGTAATGCGCAGGAAGGTGGTACATGGCATGCGTGGTAGTTGTCTGAAATGTGGCCAGAATGTGGAATCACTGCCAAGTCGGCAGTTAAGACTGGGACCAACAGCACACCGGCTGCTGGGGCACCGAGGCAGGTATCGCTGCTGCCATGGCAGTCTTCACAGTTGAGTGCAGATGAGGCTGTCTCAGTCCAGCATTCCATGCGGTCACTGTGCCATGACTCAGAGTTGGAACCTAAGACAAATCTTACTTGCCATCTTGGCAATGGGGGTCACTAAACACCCATATTTGGGTGTGAAAGGAACAGTTTACTAAATGATTTGAAGGCCAGGGGAGGCCCGCCCTGAAGACTGGACATGAGGTCACAATGTTCATCTGTCTCCTGACTGCCCACTTCACAGCCCGCTGTGCTGTGGGCTCTCCACGCATGTCCTTGGCATAGATGCCCAATGCTTCCAGAGGTGCCCACCATATGTAAGCATGAGCCTCCTTTGAATAGTGAGCTGGTCATCCTTGTCACACTGTCCCCTGGTTTTCTAG
Seq C2 exon
GAACCTGGATGGCAGTCTCAACCTGAGAGCCCTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000008946:ENSBTAT00000044473:13
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:
PF0106717=Calpain_III=FE(49.3=100)
A:
NA
C2:
PF0106717=Calpain_III=PD(0.1=0.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
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:
TTCCAGCACTTCCAAGACAGA
R:
CTGCAGGGCTCTCAGGTTGAG
Band lengths:
240-1500
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development