BtaINT0129338 @ bosTau6
Intron Retention
Gene
ENSBTAG00000017174 | SCN11A
Description
sodium channel, voltage gated, type XI alpha subunit [Source:HGNC Symbol;Acc:HGNC:10583]
Coordinates
chr22:12297718-12298714:-
Coord C1 exon
chr22:12298445-12298714
Coord A exon
chr22:12297772-12298444
Coord C2 exon
chr22:12297718-12297771
Length
673 bp
Sequences
Splice sites
5' ss Seq
GTGGTAAGT
5' ss Score
10.36
3' ss Seq
TTTCTCTTCTTTCATTGCAGGCA
3' ss Score
11.92
Exon sequences
Seq C1 exon
GTGGTAGTTTATGCTCTCATAGGTGCCATACCTGCTATTCTGAATGTTTTGCTTGTCTGCCTCATTTTCTGGCTCATATTTTGTATCCTGGGAGTAAGTCTGTTTTCTGGAAGATTTGGAAGATGTGTTAATGCAACAGATGTAAAATCAGTTATAGATTATAACATTGTTGCAAACCGTAATCAATGTGAAAGTGGACATTTCTATTGGGACACCCCGGATGTCAACTTTGACAACGTGTTAATGGCTTACCTTGCGCTACTGCAAGTG
Seq A exon
GTAAGTGCTGTTGGTTTGTTTTTCACTCTGGGGAAAGAACCCTTAAAAGAATCATAAACCATTTCTCAGCTAATAAAAATATAATGACTCCATTGAAATAATGTAATCAAACCCCAGTTTCCTCATGGGAGCTAATGCCCTCTGGAGTTGTTCCCCACTGAGCATCGCCAACTTGATTGTCTACTGAGCTTCAACCTCCAAGACCCTGTAAGGGTTTGGACCTCACACTCTGTCCTGTGGTGCCTTGTTCTCCTTAGCTCCAGCCAGAGAGACATGGAGCCTCAGATGCCAAGCCACACCTGTAGTAACAGTTCCCTGTGGGAACAGTCCCATGTCAAACCATGGTTGCAAGGTCTTGGACAGATAGTGCAAATAGATGTGGCATCAGGAAAGAGCCTTAATCAGGTTCTTTGCATCAGCTGGTCCATAACTTTTCTAGGAATTTTTAAGGCAGAAATTTCTCTTGTCTTTAAACTTTTTATCTTGTGAAAATGAAGAAAAAATAATACAAAACACATGCCCATGACCTTTTTTCAGCTGTTCCTTTATGTAGGCATTCTGTCCAGGAAGGGTGGATCATCATCTTATATATATCTGCCCGCTGGACTTGCTGGCTTTTGTATGTTGATGACAAGCCTATAATGGTGTTCATGTTTCTCTTCTTTCATTGCAG
Seq C2 exon
GCAACATTTAAGGGCTGGATGGATATTATGTATGCAGCTGTTGATTCCACAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000017174:ENSBTAT00000022822:21
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=0.000
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=FE(40.8=100)
A:
NA
C2:
PF0052026=Ion_trans=FE(7.8=100)
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:
AGTTTATGCTCTCATAGGTGCCA
R:
TCTGTGGAATCAACAGCTGCA
Band lengths:
318-991
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]