BtaINT0129365 @ bosTau6
Intron Retention
Gene
ENSBTAG00000018520 | SCN1A
Description
sodium channel, voltage gated, type I alpha subunit [Source:HGNC Symbol;Acc:HGNC:10585]
Coordinates
chr2:30408291-30410387:+
Coord C1 exon
chr2:30408291-30408428
Coord A exon
chr2:30408429-30410282
Coord C2 exon
chr2:30410283-30410387
Length
1854 bp
Sequences
Splice sites
5' ss Seq
AAGATAAGT
5' ss Score
2.82
3' ss Seq
TTTATTTTTCTTTTCTATACTTT
3' ss Score
0.99
Exon sequences
Seq C1 exon
GTGGAACTCCAGCCTAAGTATGAGGAAAGTCTATACATGTATCTTTACTTTGTTATTTTCATCATCTTTGGGTCCTTCTTCACCTTGAACCTGTTTATTGGTGTCATCATAGATAATTTCAACCAGCAAAAAAAGAAG
Seq A exon
ATAAGTATTTCTAATATTTTCTCTCCCACCAAGATAATAAATCATTTGGAGGGCTTTCAATACCAAATGAGTACTTTAACTCAGAAACCAAATGGGATTATATATTACAATCTATTTTTTGCATGCTTCCTCTCTGCCATTCACTGCCCATGTCTTTGCCAAGAATGACTGTGTTCCTTATTTCTGTGCATAGGCTCACAAAATCTCCTCTTTAAATAAAAACAAACAAACTTCAGGGACCACATTTTCTCTTTTGAAAAAAAAAATAACTAAAAAAGAACTGGAAGAGAACCCAGACATATACCTCTTTCCCAGACTCAGCTTATTGTTTATCCCTATGACATCTCCCCTTAAAATATATTGTCCAACAAAAACCTTTAGAATGCAACAAATTATACATGAGATGTAAGCTTCTTCTGGTGCTTCTTTTCACACTTTAAAATTCTTTATTGGCTCCATTTATATATTCCCACTTCATTCTCCCTGATATTAATTATAAGCTATCAGTTCTAGCTTTGAATTGAAAGTTCTTTATTAATTAGTATCATTTATAAAGCCCACTTATTATCTAATTATATATGTACATTATCATAAAATAGAAAGTAAAGAAATATCTTTACTCAGGAATAACCATTATTCACATTTTATGTTTTGCTGTATAAACTTTTTGTACACACATTCTTCTTACTGAAATTATTTTATCTATAATTATAAATTATTTTTGACTTAACATATATATTTCCCTTTTTAATCCTTCATATATACATTATCATAATTTACTTAACCATTTCCAAGTAGACTGATGATATAGGTTATTTTTAACCTTTAAGGATTAAATAGTGCCTGGTCAAAACTCTTTGTGCCAAAAAAACTGGAGCCTTTAACGATTTCTTTAAGATAAATTTCCAGAGTAAAGTGTTTTGCTTTCCTACTCATAGTACCAATATGGCTGTGCTCAGGTCACCACTGATACACTAGCATCAAGCATTCTCTCTGTTTTTTGATACTTGGTATTTGATATATGAAAATTGTATTTAATTTTCATTTTCATGTCTTTTATTATTAGTAGGTTTGAATATGTTTTCAAGGGCTTTTTTTTGCCATTTATATTTCTTCCTTCATGTACTGATCCTTCATCTCATTTGTTCAGTCTGTTTTCCTATTATATAATTGCTTCCATTGTATGAGGCTCTTTCATTATAGAACATGCCCTCCTTTGTTATTACTAATATTACTCTGTCATCATTATCAAGCTATTTCATTTCACTTATTAGCTTGAATTCCAGTTGTCTGTAACTACTGGCCTGTCACATACCTGCCAAACTTATGACTTTGACTTTTCCCCTAACTCTTCTACCAATTTCTCCAGTTTCCTTTCTAGCCTTTTGTTCCAATTCTTGGCAGAGTGACAGTGGCTCTTTATGAGTAACTCGAAACCATCACGCAATATACCTACTTTAACTCTTTGCTACATATGAATAAGAAAATCATTGTCTGAAAATTCTGAAAGACAGTGTGTCTAGTGTAAGGAACCAAGTATTTAGTGACTCAGTGAACCAAATAGTACTACTTCCTGAGTTTACAGTCTTGGGTAAAATACTTAACCTCTCAGTTTGTGGGATTGTTTTCCTCCATAAAATAATAATAAAAATCATAAAGTCAATTTTGGATGATTGAAATAAAGAAGATTATAGTATCTAAAACTAGTTTTAATTTTTCAATTTCAAATCCTAGGCAAATAATGCTAATTGGTTGAATTTTGTGTTTCCTTTTTTAATGGTCCCTTTTCTAAGTTTAACATTGAAAGAAGGAAGGTACACAGTTTTAACCAGTTTTTATTTTTCTTTTCTATAC
Seq C2 exon
TTTGGAGGTCAAGACATCTTTATGACAGAAGAACAGAAGAAATACTATAATGCAATGAAAAAATTAGGATCAAAAAAGCCACAAAAGCCTATACCTCGACCAGGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000018520:ENSBTAT00000021951:23
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=PD(15.3=76.1)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGAACTCCAGCCTAAGTATGAGG
R:
TCCTGGTCGAGGTATAGGCTT
Band lengths:
241-2095
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]