BtaINT0031387 @ bosTau6
Intron Retention
Gene
ENSBTAG00000008868 | CAPN3
Description
Bos taurus calpain 3, (p94) (CAPN3), mRNA. [Source:RefSeq mRNA;Acc:NM_174260]
Coordinates
chr10:37861124-37862825:+
Coord C1 exon
chr10:37861124-37861242
Coord A exon
chr10:37861243-37862691
Coord C2 exon
chr10:37862692-37862825
Length
1449 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGG
5' ss Score
10.07
3' ss Seq
TGCTTGATGCTTCTGTGCAGTTC
3' ss Score
6.1
Exon sequences
Seq C1 exon
GGGACTGCTGGTTTCTTGCAGCCATCGCTTGCCTGACCTTGAACAAGCGTCTGCTTTTCCGGGTCATACCCCATGATCAGAGTTTCACCGAAAACTACGCGGGGATTTTTCACTTCCAG
Seq A exon
GTGAGGTCAAGGGACTGTAGTTAAGAGGACCAGCGGGCTGTCCACCTACCGCTGGTCTCCCAGGCTTGACTTCCCCGTGGCTCCAGGAAAGATTCCCACCCACCCAGCCAGCTATGGCTGTGGGCAGTGACCCTCTTCAGGCCTCAAGCCTGTGAGGAAGTAGTTGTTTATTTCTTCCTACCCTCAAACCCCTACACCTTCCGTTAGGCCCCAGAAAGGTTAGAAGATATCCTGTTTGCTGGCCTGTTGGTCTATTTTTACCTTTCCAGCTGTCAGGCTTCTGTGTGATAACCAGAAGTCCTTCTCAAGTAAATCCCTAAGACACTAGCACTGGGAATCCAGAGGGCCCTTTAGGCTGCAAAAGAAATGCCAACACAGGTCTATACCCACACTATCATTTACCCCTTCCGGGCTCTGGAAGAAAAGTCTGGTTAATCTGGGGACCAGGCTTCTGGCTTGGCCCAGCAATGAGTCTTTTGGTTTCAGAATAAGTTCAGACACTGGAAACTTTCTGGATCCAAATTGTCCTAGCAAAGAGCCAAACCCCATGCTGTCCCAGAACTGAAATGAGCTTTGTATGTGGGCACTTGTATCTACGGGTGTTCTGAGGCTTCTGAACAGCCCTGAAGGCTCCCAGTGTCCTGGACTGACCCAGATCATCAGTTGATCTTGTATCCCAGGATGGAAGGCCTCAGAAAGTGTCTTCTCTGAAGGTTTAGGATCAGACTCCTGCTGCCATTCCAATGCAGACAGGGCAGCAGGGTCCCAAGTTTTGTTTTTCCCCTATGCCATTGAGCTGCTCACTCCCCTTGGGTATTTAAAAGATCTGAAACCAAAAGGATCATAAACACAAAGACCACACGGATTTTTGCCTTCTTGTTCATAGGAGAGTAAATGTCATTAGAAGGAAATTAAACTACTTTTGGCTTTCTTGGGTTAAAACCGATTTGTTCAAGAAAGATCATCTAGAATTGGGATTACTGGACAGTGTTCCTGGTTTAACCAGAGTATATTCTGGGTCACCTTCCATTTCCATGTCAATCCTTCTTCTTCAACAACCATTCCTACCTTATTTGTCATCAAGAAGTACATAAATTATATGTCACCTTCTCCTAGACCAGTGCTTCTCAGCCCTGACTGCATATGAGGATCAGCTGAGATAACAAATGATACTGATACCTAGGCCCTCCCAGACCTACAGAGCAGAAGGAAAATCTCAAGCCCTCAGATACACACGGAGTACTTACCATCCCCTGTACTGAGCTGGACTGTGTGGGAGAGACATAATGGTTTGTAACATACTTGCTGCCCTCAAAGAGCTCACAGTCCACTTAAAGACAGATTCACCTTCTCTGAACCCAGAATAGTGTGAACAAAAGGAATGTGGGGTAGGGACACATTTCCCACTGGTAATCTGAGGATGGCACTGTGCTTGATGCTTCTGTGCAG
Seq C2 exon
TTCTGGCGCTATGGAGACTGGGTGGACGTGGTTATTGATGACTGCCTGCCAACCTACAACAATCAACTGGTTTTCACCAAATCCAACCATCGCAATGAGTTCTGGAGTGCTCTGCTGGAGAAGGCTTATGCTAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000008868:ENSBTAT00000011677:3
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(19.1=100)
A:
NA
C2:
PF0064816=Peptidase_C2=FE(21.6=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGGACTGCTGGTTTCTTGCAG
R:
TAAGCCTTCTCCAGCAGAGCA
Band lengths:
247-1696
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development