BtaINT0129443 @ bosTau6
Intron Retention
Gene
ENSBTAG00000004770 | SCN4A
Description
sodium channel, voltage gated, type IV alpha subunit [Source:HGNC Symbol;Acc:HGNC:10591]
Coordinates
chr19:48802269-48804507:-
Coord C1 exon
chr19:48804019-48804507
Coord A exon
chr19:48802402-48804018
Coord C2 exon
chr19:48802269-48802401
Length
1617 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGC
5' ss Score
10.22
3' ss Seq
TGACCCTGTGGCCTCTGCAGAAG
3' ss Score
8.18
Exon sequences
Seq C1 exon
GTCTTGAACCTGTTCTTGGCCCTGCTGCTCAGCTCGTTCAGTGCCGACAGCCTGGCGGCCTCGGATGAGGATGGCGAGATGAACAACCTGCAGATTGCCATCGCTCGCATCACGTGGGGCATTGGCTTCGCCAAAGCCTTCCTCGTGGGGCTGCTGCATGGCAAGGTGCTGAGCCCCAAGGTTATCATGCTCAGCCTTGGAAGCATCGGCGAGGATGGGGAGGCCGGCGAGGCTCCAGAAAGCGCCCCCGAGGATGAGAAGAAGGAGCCTCCACCCGAGGAGGATGGCAAGGACCTCAAGAAGGACAACCACATCCTGAACCACGTGGGTCTGGCTGACGGCCCTCCCCCCAGCATTGAGTTGGACCACCTCAACTTCATCAACAACCCCTACCTGACCATCCACGTGCCCATCGCCTCCGAGGAGTCTGACCTGGAGATGCCCACAGAGGAGGAAACTGACACCTTCTCTGAGCCTGAGGATGTCAAG
Seq A exon
GTAAGCCCGTAGCAAGGTCCAGATTCAGGGCTTGGGAGTCAGACAGAGACGACTCTGCATTTATGTATGACCTTGAACATGGCACAAAGCCTCTCCAAGCCTCAGTTTCTCCATCTGTAAGGTGGGGTAATGGTACCTACCTTGTGGTGTTACTGTGAGCATTAGATGAGATGCTGTGTGCAGAGCATCTCTGTGAATGGTGACATATAAATACCATTATTATGACCCGCTCCACTTGTCTGAACACCCCAGGCCTTTCCCTGCACTCCTGCCCTGCAGCTCCTCCTGGGTCCCCTCTCACCAGCAGGTGGCGCTGTGAGATAGCATATTCTCACCTGAGAAGCCTGAATCCAGGGCTGGAACCCAAGGGGCCTCTCTTAACCCTGCCCTGGGGTTAAGAAGCCGCTACCAAGTTCTTGCTATTATCGTCTGTTTCTGTGTAGACGCCCCCTGGTGGTGGTGGGGACCCGGTCCCAACTTCCCAGCGTGGGCCAGAGTGCCAGGTCTGGGCTGGAGACACTGAGGAGAGGGGGGTCAGAGATCCAGTGGGGTGGAGCCGAAGAACTGGAGAGCTGGGCCCCAGCCTCAGTGGGAGCTCTGATGCCCACCCCCTGCCCCTGCCCCTCCCCTGTAAGGGTTGGGGAGGCCCTGGCGGTTGCCCCCAGAAGCTCAGGTTGAGCCCCTCACCCACCCTCCAGCTCCATCAGGGGAAGGATCAGCACATAAGCTAGGGCAGGGCCCCCTGACCACCCCCACCCTGGCAGCGTGGGCCCAGCAGGCACCAGAGCCTGAATAAACTTTGCCCTGAAAGCTCTTGACTCCTTATTCCCCCCAAATACGTGGCATACTAAGTTACCAGGGAGCCGAGCGCCTGCCAAGCTATAAATACCCCTGGAAACGTGGCACCAACCTCGGTATGAGGAGTGGGGGTGGAGAAGGGCCGGACAGCAGCCGGGCCAAGGTGCTGGGGACTCTGGAGGGGGCGGGCACAGCTTCCGAGGGGCGGTGAGAAGTGGGGGGCATAGGCAGGGCCAGTGGCTCAGCGGGCATCCTGCCCGACCTAATGCCCCGTGCCTCAGTTTCCCTTTCTGTCAACTGGGCACCAGGCCCTCCCTTTCTGGCCACCATTCTGACAGCTGCCCCCGCCACCATCCCATGACCCTCTCCATTTTCCTTTTCAGGGGCCTCACCCCAGCCATAAAGGGGGCCCCTTGAGGAGTGGAGGCTGGGCCAGGAGGAGGTGAGGGAGGTCTGGCCAGGCTGGAGTACCAGCCCCCTACCCCCACTCTTTCTGAATCCCCCCATCCTTCCTGGATTCCTCAGCTGAACAGAGCGTAAGAGGGCTCGGACCTTGCTCCATCCTGACCCCTTCCCTTCTAGCCAGCATCTCTGAGCCTCTTCAAATCCAAGTGCCCTGAGGATAGGGCCAAGGCCTGGGTCCTTCTGCACAGAACCCAGTGCTGGCTCCACAATCCAGGGCTGAATGAATGAATGAGTCTGTGAATGAATGAGTCTGCTCCACCCCCCACCCCCGCTTCCCCTTCTCCCTTCTGGGCCCTCCCCTCGGGGCTCCCATCTGGACCCCCTCTGCCCCACGTGACCCTGTGGCCTCTGCAG
Seq C2 exon
AAGCCGCTGCAGCCCCTGGATGGGAACTCCTCCGTCTGCAGCACTGCTGACTACAAGCCCCCCGAGGACGACCCCGAGGAACAGGCCGAGGAGAACCCTGATGGGGAGCAGCCTGAGGAGTGCTTCACCGAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000004770:ENSBTAT00000006265:14
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.472 A=NA C2=0.822
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=PD(4.2=4.9),PF065128=Na_trans_assoc=PU(60.7=85.3)
A:
NA
C2:
PF065128=Na_trans_assoc=FE(19.2=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:
ATCATGCTCAGCCTTGGAAGC
R:
GACGGAGGAGTTCCCATCCAG
Band lengths:
342-1959
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]