BtaINT0129553 @ bosTau6
Intron Retention
Gene
ENSBTAG00000002425 | SCN9A
Description
sodium channel, voltage gated, type IX alpha subunit [Source:HGNC Symbol;Acc:HGNC:10597]
Coordinates
chr2:30158681-30161314:+
Coord C1 exon
chr2:30158681-30158835
Coord A exon
chr2:30158836-30161140
Coord C2 exon
chr2:30161141-30161314
Length
2305 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGT
5' ss Score
10.65
3' ss Seq
TTCAAATGTTATTTTCACAGGCT
3' ss Score
7.68
Exon sequences
Seq C1 exon
GTTGCGTACAGAGGTTCCCATGCTGCCAAGTTAACATAGAATCAGGGAAAGGAAAAATCTGGTGGAACATCAGGAAAACGTGCTTCAGGATAGTTGAGCACAGTTGGTTTGAAAGCTTCATTGTTCTCATGATCTTGCTCAGCAGTGGTGCTCTG
Seq A exon
GTAAGTGATCTGACACCTAATGCTTAAATGGATGGTCATTATTTTTAATAAATGTGTTGGAAGTTAAAAATATTGTGGCATTTTTTTTTTTTTACTTAAAAATTAATCCCTCTGATCAGTAAAGGACAACATGTTAGTTACCTTAGTAAATACTTACTACATGCCAGGCATTATTCTTCCTCCTGGAATGCAATGATGTTTAAGACCCACAGACTTTTCTCAAGGAGATCAGAGAGCTTTAGGGAAGTAAGAAGCACGAGTGGTACAGAACTGGGATATGTTTGTAAGTGAAGTACATGCACGTTTAAGCTCTGGAGCAAGAAGAGTCATCTGCTTGGGAATTCAGAAAGGTAGATGATGTTTTGCAAAATCCAGAAAGATGAATAGGAATTTTCCAGCCAGGAAGGTGGCCTGAGGGGAATGAAGCATGAAATAGCATGAGACATTTAGGAAATTGAAAGTTGTCAAACTGTAGAAAGTGTTGTGGGAGGAAGAGCAAATCCAGAGAGGTGGGTGGTGACCAGAGATACTGTGAAAAAGATAGACAGTGTCAATTTAGGAAGCATCTTGCATAAAAGAAAATACTGTAGTTTTAGGACGAGAATGGGATAGGTCTCTCATTCTTATACATGTGCTAACACTTTCTATGAGATTTGAAAAGGATCTGGGAGAGTTAGAGGCTCCCTGAGCTTTTTCTTGACTTAGAGAAGGGAAGCAAGAAAGTCCTGAGGGCTTGACTTTAATTCTTGCATTTCAGTTCCACTGTCATTCAGAAACTCTGCCAACTGCTGGAACCTTCTCTCAACATCTTAGTAGGTCTGTCCATTCTCTATATCCCAACGTCTGTGTTTTCCTCAATATTGACAATAAACTTTTGTAAAAAGTGCTAAGGATTATTTTTAAAGTATCAATAGAAAAACTTGGAATAAGAAGAATAAGAATGGCACAAGTCCATAACTGTGGACAAGTAGACCACTGTTAACCACTAAAGATAAAGGTCCTTTTGCTTTAATTTTCTCTAACAAGGTGAATATTGTTTAAACTTGAAAGAGAAAATTCTAATCCTTTAGACCTGTCTAGGTCAGCAGTCATTTTCAGTGGCTTCAGTTAACTCAGTTCTTAAGTCCTTTCAAACTATTTCTCAAGGACTTTGTGGCTGTAACCACAGTATCATCATCTACCACTCACTGAAAGTTCTTGGGAAGGATCAAAAGGTGTCACATTGATGGAATGAATATAACAGATATTAGTAGAGCTGAAGCTTTTAATGAATGATAAAGGGTTGGTGAAAAATTCAAAGAAAGAAACCATCTTCTGTGCTCTATAGCCCTGTTAAGCTACAGCACTTGATTTTACAAACCTTTCCTGCTGTGTTCTTGACATAGAGCTAGGTACTGAGAATTCATAAGCACATAAGAGCTGAAGGAGAGGCTCTAAATCCTACTGCTGGCTTGAAGAAGAGTGCAGGGTGAGAGAGATTTATAGGAGGGGCTGACCCTGGAATCATGTCTTAAATTATTAGGACTTACTAGTTTGCAGGAGCGTTTAGGGGTGTCAGATAGTGGAAATCACTGAAAGAGTCAGAGATCATGGTTCTTTTATAGGACTATAGTAATTGCATTTTTTTGCACCCTATTTCTCTTGACCTCTGGTGACCAGCCACCTGTATTGATGAGAACTGAGTGTTACACCTGCGTGTGTGCTTGTGTGCTAAGTCACTTCAGTTATGACTGACTCTTAACAACCCTGTGGCCTGTGGCAAGGCTCCTCTGTCCATGAGATTCTCCAGGCAAAAATACTGGAGTGGATGAGAATGGGATAGGTCTCTCAATCCTGCAGGATGCAGGATCTTCCCAACCCAGGGGTCAAACTGGTGTCTCTTACGTCTACCTGCATTGGCAGGCAGATTGGTGACTTAGTGGTAAAAAAAAAAAAAAAAATCCGCCTGCAATACAGGAGATGCAGGAACCCAGGTTTGATTCCCTGGATTGGAAGATCTGGAGGAGAAAATGGCAACCCACTCCAGTATTCTTGACTGGAGAATCCTATGGACAGAGGGCTGCAGACCTTGGGATTGCATAGTAGGAAACTTAGCAACAGACTTTCTTTCTTTTTCTCCCTTTGCCACTAGCGCCACCTGCGAAGCACATGTGCTCCACTGTAACTGTAAACCAGAAGAAAGCCAGCAGCCCCGTAATAGCATAATACGTCAGTGATCTCTTTATCAGAATTTCAGTTCCTGTTTTGGTCTTGAATCATAAGCTTTAAGTTGTACCGAATTTAAATTCAAATGTTATTTTCACAG
Seq C2 exon
GCTTTTGAAGATATATATATTGAAAAGAAAAAGAACATTAAGATTATCCTGGAGTATGCTGACAAGATATTCACGTATATCTTCATTCTAGAAATGCTTCTAAAATGGGTAGCATATGGTTACAAAACCTATTTCACCAATGCCTGGTGTTGGCTGGATTTCTTAATTGTCGAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000002425:ENSBTAT00000003146:19
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:
PF065128=Na_trans_assoc=PD(19.9=84.6)
A:
NA
C2:
PF0052026=Ion_trans=PU(17.0=67.2)
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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]