BtaINT0129336 @ bosTau6
Intron Retention
Gene
ENSBTAG00000017174 | SCN11A
Description
sodium channel, voltage gated, type XI alpha subunit [Source:HGNC Symbol;Acc:HGNC:10583]
Coordinates
chr22:12351959-12353134:-
Coord C1 exon
chr22:12353016-12353134
Coord A exon
chr22:12352061-12353015
Coord C2 exon
chr22:12351959-12352060
Length
955 bp
Sequences
Splice sites
5' ss Seq
TTCATATCC
5' ss Score
-14.87
3' ss Seq
GCCTTAACAGCCCCGCTCACGTT
3' ss Score
-9.27
Exon sequences
Seq C1 exon
ACATTTATGGTGTTGAACAAAAAGAGAACAATCTACCGCTTCAGCGCCAAACGTGCCTTGTTCATTTTGGGGCCTTTCAATTCAATCAGAAGTTTGGCCATTAGAATCTCAGTCCATTC
Seq A exon
ATATCCTTTTGTTGCTTCTTTTACTAAGTCCAGGTCATGGGAAGCGTGCACAAGCTCGGGGGGTTCATGTGTCTGTTGAGTGGAAACAACCCATTCTTTCAACAAATACTGGCTGAGTGGCCCCACTGCATGACAGGCAGGGCTGTGCTGGGGCTGGCCCCCGTCTGGGACCCTGAGGCCTCGGAGGAGAGGAGAGGCTCAGCTGGGCTTTGGAGGCATCAAGAATGGCCTCCTGAAGAAAGGAACATCTAAGCTGAGACCCAGGTTGGCAACCTGTGTACTGAGTTTAACTGATAAATGAGTTGTGGTAGAACTACAGTATTTAAAGCTTTTTTGGAAACACTTTCTAGTGTTAAAAGTACAGATTTACAGGGGATGAGAAGAAACCTGGCAGTTTCAGATGGGAGGCGGGGGAGATGTGAAAAAGACAGGCGTGGGTTGGTAGACATAATGAAGTACTCAGGAAAACGGGAAGGAATATCTATTTAAGTTGGGTTCCCTAGAAGCAGAGCCTGAGATGGGATTCTTAATTAAGTGATTTAGTGGAGGAGTGCCGTCTGGAAAAGGAAAAAGGGAAACATCATAGAGCAAAAGGAGGAGCCAAACAAGGACAGGGCCTTAGCTGAGGCTACATCAGGCATCAGCCTGAGCCCACAGGGATCTTCAGAGCATGGGTTGTATCACAGAGCTGCCCCACCTGGAAGCCAGACGGCGAGTTTTTGCAAGTCTGTGGGTCAGACGTGTGGCAAGGGCATGTAGCCTTGCAGGGTGAGAGGCTGCCATTCGAGGACAATTCTTCAAGAAAGGGGGCAGCTGTGGGTTGTTCCAGTCAGCACTCACAAAAGACAGATGCTTCTGCAGAAAAAGGGTCCTGCAGGGACCCCTGCAGCCTCTGCTACAATAACCAGTGACATGGGCCGTCCTGCAGTGCACCTGCCTTAACAGCCCCGCTCAC
Seq C2 exon
GTTGTTCAGCATGTTCATCATCTGTACTGTCATCATCAACTGCGTGTTCATGGCCTTGGCTCATCAGAAGAGCAGCATTGATGTGAAAACTGACCATGCTGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000017174:ENSBTAT00000022822:2
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:
NO
A:
NA
C2:
PF0052026=Ion_trans=PU(0.8=5.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGGTGTTGAACAAAAAGAGAACA
R:
TCAGCATGGTCAGTTTTCACA
Band lengths:
214-1169
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]