BtaINT0092737 @ bosTau6
Intron Retention
Gene
ENSBTAG00000003600 | MGC151839
Description
Bos taurus calpain 8 (CAPN8), mRNA. [Source:RefSeq mRNA;Acc:NM_001081619]
Coordinates
chr16:27704326-27705281:-
Coord C1 exon
chr16:27705207-27705281
Coord A exon
chr16:27704487-27705206
Coord C2 exon
chr16:27704326-27704486
Length
720 bp
Sequences
Splice sites
5' ss Seq
TTGGTGAGA
5' ss Score
6.29
3' ss Seq
ACTGATCCCTTTGCCCCCAGGAT
3' ss Score
10.08
Exon sequences
Seq C1 exon
TGCACCGGAGTGGAATTACATAGACCCCAGGCAGAAAGAACAGCTGGGCAAGAAAGCCGAGGATGGAGAGTTTTG
Seq A exon
GTGAGAGGGTCTGCAGGAGTGCTGTCCTCCTGGCTGTGGGTTCCTTCCTGGATTGCGCATGGGCAGTTCTCTCTAGGTGTTCCAGGAATTCAATGTGGTTTCCTGCCAGGGGTCTTCTTTCTTCTTCCCCTTTTACTCCAGTAAAAGGTAGAAACCAAGATATCTGGGCCTCAAGATTAGCTATCAGCCTGACTTTCTCAGTTTCTGTATCTTTTCAAAGTCCAAAGTTTAGATTAGCATCAAAATACAATAACTTCCTTCACTCCCTAAGGAAGATAATAAGGACACGGTTAGACTGTGTGGCTTAGGGACCATCTCTAGGCTGGACACCAGAGTTAACCAGTCACCTCAAGGTGGTAACTTGGTTCATTTTACCTCCGAGGATCTCTGCAGTTTAGGGTTCAGTCTCTTTGCTGGTTGGTTGGATATAAGAGGGGAGCTTTTTAAGAGCAGAGATGCAAGCAATAGTGAGGAAGTTGCCAATACTGTACAGTTTTTTCACTGCTGTTAAAATACCATTGTTTGGTAAATTATAAGTCATTTAAAAAGAAATACTGAGACATTTGGCCAATGATCACTGCGTATTTGTACTGTGGGGTGTAGGAAAGATTTAGCTGGCCCACAGCCTCTGCTCTGTCCTGTGCCCACTGGGCCACACTTTCCACCACCTTTCCAGCCCAGCTCTCTTGACCAAGAGCTCACTGATCCCTTTGCCCCCAG
Seq C2 exon
GATGTCTTTTTCGGATTTCTTGAGGCAGTTCTCTCGGCTGGAGATCTGCAACCTGTCCCTGGACTCATTGAGCAGCGAGGAGGCGCACAAGTGGAGCCTGGTGCTGTTCAATGGGCGCTGGACTCGGGGCTCCACAGCTGGAGGCTGCCAGAACTACCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000003600:ENSBTAT00000011676:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.077 A=NA C2=0.030
Domain overlap (PFAM):
C1:
PF0064816=Peptidase_C2=FE(8.3=100)
A:
NA
C2:
PF0064816=Peptidase_C2=PD(6.3=34.5),PF0106717=Calpain_III=PU(15.2=43.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGCACCGGAGTGGAATTACAT
R:
CTGGGTAGTTCTGGCAGCCTC
Band lengths:
236-956
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development