BtaINT0129556 @ bosTau6
Intron Retention
Gene
ENSBTAG00000002425 | SCN9A
Description
sodium channel, voltage gated, type IX alpha subunit [Source:HGNC Symbol;Acc:HGNC:10597]
Coordinates
chr2:30168201-30169459:+
Coord C1 exon
chr2:30168201-30168482
Coord A exon
chr2:30168483-30169401
Coord C2 exon
chr2:30169402-30169459
Length
919 bp
Sequences
Splice sites
5' ss Seq
GTGGTAAGT
5' ss Score
10.36
3' ss Seq
TATCAATGTTATATTTACAGGCA
3' ss Score
7.82
Exon sequences
Seq C1 exon
GTGGTTGTGAATGCACTCATCGGTGCAATTCCTTCTATCATGAATGTGCTACTTGTGTGTCTCATATTCTGGCTGATATTTAGCATCATGGGAGTAAATTTGTTTGCTGGCAAGTTTTATGAGTGTATCAACACCACAAATGGATTACGTTTTCCTACAAGTGAAGTGGAAAACCGTTCTGCCTGTCTTGCGCTTATGAATGTCAGTCAAAATGTGCGATGGAAAAACCTAAAAGTGAACTTTGATAATGTTGGACTTGGTTACCTGTCTCTACTTCAAGTG
Seq A exon
GTAAGTGACTCGTTTTATGAATGCTTGATATTTTAGTGCACGTTGGATGGAGGAGCTGTCGTTATCATGTAGCTATTAACTAAAAATTAAAGATAAAGTACTGTGTGACAAAAAACAGAAGTGGTCTTTCGTAGAACATGTGCCTATAAACATGAGTTAAGAAGCATGGGCTCTATTGCACTGTTGTACAGGTGATTAATCCATAATCACCTTTTCAGAGTCACCTGACCCCCTGCCATTGTGCCTTCTGAATTGTTCCAAAAATGAATAGTCATTTTTTGGACTACTGCTTTCACACTACAAGGAAATCAGAAGGACTTGCCACTGGTACAGAAAGTCCTTAAGATATGGAGAAAAATTGCTTCTTTCCTTAGTTGTAAAACTCTCTACCCCCTCTGGAAAAATAAAAGTTCAGGTACAAAACTCACAAGCAGTTCTAACAACCTGGAAATTCACTGCTGCTGCTAAGTTGCTTCAGTCATGTCCAACTCTGTGCAACCCCATAGACAGCAGCCTACTAGGCTCCCCCATCCCTGGGATTCTCCAGGCAAGAACACTGGAGTGGGTTGCCGTTTCCTCCTCCACTAGGACTGAGATTTAGAACGTGACTTGGCAATGTGCCCCCCCTCTTTTTCTTCTTGACACAGCATCTTTATGTTAAGTTGATATCTTGAAATATAATGGGCTCTCTTTATCCATGGCTTTGCATCTGCATGATGCAAGGGCTTGAGCATGGGCAGATTTTGGTATTTTCAGGGACTGCCCTGGAACCAGTCCCCCCTGCATGTACCAAGGGATGACTGTATAGTTCACTCACTTAATATTACTTAAAAGTTGTAATATTAAATACACTTACTCATTTATGGCTATTTTAGACTATGAGCTTTACATTCAGAGTCTATCAATGTTATATTTACAG
Seq C2 exon
GCAACATTTAAGGGATGGATGGATATTATGTATGCAGCAGTTGATTCTGTTAACGTAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000002425:ENSBTAT00000003146:22
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(40.6=100)
A:
NA
C2:
PF0052026=Ion_trans=FE(8.3=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGTTGTGAATGCACTCATCGG
R:
CGTTAACAGAATCAACTGCTGCA
Band lengths:
335-1254
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]