BtaINT0129451 @ bosTau6
Intron Retention
Gene
ENSBTAG00000004770 | SCN4A
Description
sodium channel, voltage gated, type IV alpha subunit [Source:HGNC Symbol;Acc:HGNC:10591]
Coordinates
chr19:48797532-48798298:-
Coord C1 exon
chr19:48798161-48798298
Coord A exon
chr19:48797637-48798160
Coord C2 exon
chr19:48797532-48797636
Length
524 bp
Sequences
Splice sites
5' ss Seq
AAGATGAGT
5' ss Score
2.29
3' ss Seq
CGGGCCCCATCCCATTGTACTTT
3' ss Score
-1.03
Exon sequences
Seq C1 exon
AAGGAAGAGCAGCCACAGTATGAGGTGAACCTCTACATGTACCTCTATTTCGTCATCTTCATCATCTTCGGCTCCTTCTTCACCCTCAACCTCTTCATTGGCGTCATCATCGACAACTTCAACCAGCAGAAGAAGAAG
Seq A exon
ATGAGTATCTAGCCCGCCTTCCCCCCTGGGTTCTCCCTGCGCTGGGCTCCCTCCTCACACCCGCTTTGTCCACTCCTCCTTTCGTATGTTCACAAACACTGTCCGCGCACCCGATCGAGGCAGAGCCTGGGTTCCGATCCCACCAGGTGACCTTGAACTAGTGACGGGGCCAGTGTGAACCTTGGTTTCCTTCTGTACAAAATGAGGCTCGTGCTGCCTGCTTTGCCGGCTCATTCTGAGGACCCAGTGAAATACTGATGGAAGGTGGCCCAAAATGGGCCATGAGGGCTGTGCTGGCCCCTTCCCTCTGTCTGTCACCCACCCCCCTTTCTCTGGACCCTTCCGTCCCCCTTCCCTGCCTCCTTCAACCCCCATCTCTGGCCCTCTAAGCAGGTCTCCTTCCCTCTTCCCACCAGGCCCCCCTGCTGGGATGGGGGAGGGCTTTACACAGATGTTTGAGGTAGGCAAGTCCTGGAAGCTGAGAAGGGGGACTCTCCAACCTTACGGGCCCCATCCCATTGTAC
Seq C2 exon
TTTGGAGGGAAAGACATCTTCATGACAGAGGAACAGAAGAAATACTATAACGCCATGAAGAAGCTTGGCTCCAAGAAGCCTCAGAAGCCAATTCCCCGGCCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000004770:ENSBTAT00000006265:21
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=0.057
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=PD(15.4=76.1)
A:
NA
C2:
NO
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:
AGAGCAGCCACAGTATGAGGT
R:
CTGGGGCCGGGGAATTGG
Band lengths:
238-762
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]