BtaINT0129367 @ bosTau6
Intron Retention
Gene
ENSBTAG00000018520 | SCN1A
Description
sodium channel, voltage gated, type I alpha subunit [Source:HGNC Symbol;Acc:HGNC:10585]
Coordinates
chr2:30411994-30415283:+
Coord C1 exon
chr2:30411994-30412264
Coord A exon
chr2:30412265-30414105
Coord C2 exon
chr2:30414106-30415283
Length
1841 bp
Sequences
Splice sites
5' ss Seq
TAGGTAAGA
5' ss Score
9.14
3' ss Seq
CTCATCTTTTTTGTCCATAGGTA
3' ss Score
12.48
Exon sequences
Seq C1 exon
AACAAATTCCAAGGAATGGTCTTTGACTTCGTCACCAGACAAGTTTTTGACATCAGCATCATGATTCTTATCTGTCTCAACATGGTCACCATGATGGTGGAAACCGACGACCAGAGCGACTGTGTGACTAGCATTTTGTCCCGCATCAACTTGGTGTTCATTGTGCTGTTCACTGGGGAGTGTGTGCTGAAGCTCATCTCCCTCCGCCATTACTATTTTACTATAGGCTGGAATATCTTTGATTTTGTGGTGGTCATTCTCTCCATAGTAG
Seq A exon
GTAAGAAGTATTTCAAGCCTTTTAGCTCAATAAAAGAGCAATCACATTTAATTTAGAAGTCATCTGATCACTCAGAGAAAACCACTGTGAAAATTCTGATGTTTTTCATTCAGATGTGTTTGTCTTTCTTACAAAATTAAGCTCCTGCTATACACTGAGTATTGTATCCTGTTCTATCCATTTTAGACTAGGTGTATTATTTGTCAATATAGTAAGTCTCAGTCATTTGAACTAGAAATGTTCTATTAACTAAATGTGCTATTAAGATCGAAATGTCTTTGACATGTTGAAGTTGAATAGTCTATACAATATGTAAATGACTCTGTTGAAAAAAGGGATAGAAATTTAGTCTGATACTCAGGAGAGACAGTACATCAGAGACATAGAGTCATTGGCATACAGATAAGAGTGGAAGCTGGTACTAATAAGGAAGAATACAGAGTGAAAGAGAGTAAAGCAAAGAACAAAATGTCAGTGAAAATGGTAGGTTCTTTAATGCAGAGTATCAGAGATTTTCTAGATTACCTTGCAATGTATAATAATGATGCACAAAAGAAGTGATTTGGCATGGAACATCATTTCATCAGTCATACACTTCAAAGCCTGGAATGTCAACAGGTCACATGAGCAATAACCCATCTAACTGAAGATACAACTCCAGCCCCAGTGAAGTGAAGAGGTCTGTCTGTGGGCCTAAAGTATCCATTTTTTCCCTAAAGCAGATGATATGATTGAATAAATATTTTACCATCCAATATGGGGCACCTCTGTTGGGCAGATTTTTATGCCATTCCCCCTCTGAAGAAGTTGATCTTTTATCCAACTTATATGTTGTATGTACCCTTTGATTCCCATAGTATTCTGTGGTATTAACTAGTTGTGGATAGGGTACCTAGTTGTATTCACCTCTCTTTCTTTCTCTGTCTCTCTTTCCCTCTCTCATACAGACACAAACATGCTTATTTACTCTTTACAAAATGAGATAGTGTAATTCAAAGATACTTGGTTTCTTGAGCTCCTCTTCAGCTCATTCATTATTTCACTATTTCGAAGGTAAATGGATAAAGACGCTCTAAGTAAGAGGGCTAAGACACAGATGTAGGAAACCAGAAAAGGCATCAGCTTAAATCCTTTTAGAAATGCACCAGAGCATAATAAATATATACATCTATATATGAATATTATAGTGGAAACTTAGGAAAGCATCATGTTCATGGAGAGATGAATGCATTCAAAACTACAGATAGGTTTATATGGGGAAGGACTGAATACAGGTTATATGATTTAGTGTTTCAGAAAAAAATCATCGTGTTCACTGTATTTTTATAAACATTTACATATACTGTCAGCTACTGCTCTTCAGACAAACTTGAATTTTTAACTTGTTTTTTTAGATTCAGTCTTTGGATTTTCTGTAAGCAAAACTAGTCTATCAATACCCCTCAAGGATAAAATATACTATAAAATCCTTATTGAATTGAATACTATCTTAGTCACCTTGGAGTTTGCCAGGTAGTGCAGTAGTAAAGAGTCCTCCTGCCAATACAGCAGATGCAGGAAATGTGGGTTTGATCCCTGGGTTGGGAAGACCCTGTGGAGGAGGAAATGGCAACCCACTCCAGTATTCTTGCCTGGAGAATCCCATAGACAGAGAAGCCTGGCATGTTACAGTCCATGGGGTCGCAAAGAGCCAGACATGACTGAGTGACTAACACTTTCACTACACTTTTCAACTGAATTTTAGTACTCTGAAATTTACCTGTGAGCCTTAACAAAATTTGAGTATTAATTTAATGGATAACTTCTTCACTAGTCAGTACCCTCATCTTTTTTGTCCATAG
Seq C2 exon
GTATGTTTCTGGCTGAGCTGATAGAGAAATATTTTGTGTCCCCTACCTTGTTCCGAGTGATCCGTCTTGCCAGGATTGGCCGAATCCTGCGTCTGATCAAAGGGGCTAAGGGGATCCGCACGCTGCTCTTTGCTTTGATGATGTCCCTTCCTGCGTTGTTTAACATCGGCCTCCTGCTCTTCCTGGTCATGTTCATCTATGCCATCTTTGGAATGTCCAACTTCGCCTATGTTAAGAGGGAGGTTGGAATTGATGACATGTTTAACTTTGAGACCTTTGGCAACAGCATGATCTGCCTGTTCCAGATTACCACCTCTGCTGGCTGGGATGGATTGCTAGCACCTATTCTCAACAGTAAACCACCCGATTGTGACCCTAATAAAGTTAACCCTGGCAGCTCAGTTAAAGGAGACTGTGGGAACCCATCTGTTGGGATTTTCTTCTTTGTCAGTTACATCATCATATCATTTCTAGTCGTGGTGAACATGTATATAGCTGTCATCCTGGAGAACTTCAGTGTTGCTACTGAAGAAAGCGCAGAGCCCCTGAGTGAGGATGACTTTGAGATGTTCTATGAGGTTTGGGAGAAGTTTGATCCCGACGCCACCCAGTTCATGGAATTTGAAAAGCTATCTCAGTTTGCAGCTGCTCTTGAACCACCGCTCAATTTGCCACAACCGAACAAACTCCAGCTCATTGCCATGGATTTGCCCATGGTAAGTGGTGATCGAATCCACTGTCTTGACATTTTATTTGCTTTTACGAAGCGGGTTCTGGGGGAGAGTGGAGAGATGGATGCCCTTCGAATACAGATGGAAGAGAGATTCATGGCCTCCAACCCATCGAAAGTCTCCTATCAGCCAATAACTACGACTTTAAAGAGAAAACAAGAGGAAGTGTCTGCTGTTATTATTCAGCGTGCATACAGGCGCCACCTTTTAAAGCGAACTGTAAAACAGGCATCATTTACGTACAACAAAAACAAAATCAAGGGTGGGGCTAATCTTCTTGTAAAAGAAGACATGATAATTGACAGAATAAATGAAAACTCAATTACAGAAAAAACTGATCTGACCATGTCCACAGCAGCTTGTCCACCCTCCTATGATCGGGTAACAAAACCAATTGTGGAAAAGCACGAGCAAGAAGGCAAAGATGAAAAAGCCAAAGGGAAATAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000018520:ENSBTAT00000021951:25
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.122
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=PU(20.4=47.3)
A:
NA
C2:
PF0052026=Ion_trans=PD(79.1=42.5),PF0061222=IQ=WD(100=5.3)
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:
AGAGCGACTGTGTGACTAGCA
R:
ACATGACCAGGAAGAGCAGGA
Band lengths:
351-2192
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]