BtaINT0129453 @ bosTau6
Intron Retention
Gene
ENSBTAG00000004770 | SCN4A
Description
sodium channel, voltage gated, type IV alpha subunit [Source:HGNC Symbol;Acc:HGNC:10591]
Coordinates
chr19:48794399-48796918:-
Coord C1 exon
chr19:48796648-48796918
Coord A exon
chr19:48795625-48796647
Coord C2 exon
chr19:48794399-48795624
Length
1023 bp
Sequences
Splice sites
5' ss Seq
TGGGTGAGC
5' ss Score
7.23
3' ss Seq
CGAGGCTTCCTCCCTTGCAGGCC
3' ss Score
9.43
Exon sequences
Seq C1 exon
AACAAGGTCCAGGGCATGGTGTACGACCTGGTGACCAAGCAGGCGTTCGACATCACCATCATGATCCTCATTTGCCTCAACATGGTCACCATGATGGTGGAGACGGACGACCAGAGCCAGCTCAAGGTGGACATCCTGTACAACATCAACATGGTCTTCATCATCATCTTCACGGGCGAGTGCGTGCTCAAGATGCTGGCCCTGCGCCAGTACTACTTCACCGTCGGCTGGAATATCTTCGACTTTGTGGTCGTCATCCTGTCCATTGTGG
Seq A exon
GTGAGCAGGGCCGGGCTGGGCTGAGTCGTTCGGGAAGGCCCGGGGTCGCCCTCCTCATGTCCACACGCACACCTGCTCATGCACTTGGTATGCTTTTGCACACACACAGACACACACACACACATGCATTTGCACCCGGTGTCTACACTAAATGCACAGAAGCACAGACGGTGGGTTCCCAGGCAGCCTGTTACCTGTGCACACACGAGTACAGCTCCAGAAGCATTCACCTGACCTGAAGATGCACGTTCAGGTCCCAGTGTGCTTTGGGAAAGACATAAGAAGATGGTTCCAGGACTTTCCTGGTGGCCCTGTGGCTAAGACTCTGCACTCCTGATGCAGGGGCCCCAGGTTCGATCCCTGGTCAGGGAACTAGATCCCGCATGCCACAACTAAAGATCCCACATGTTGCAACGAAGACCCATCACAGCCGAATAAATAAACTAAAAAAAGAAGATGGATCTAGCAGCCTTACGCACAGGAGAGGTGTGTGTAATTATGACAGTAACTAGCTGTCATTTATCCATCACTTACAGTTGGCCTGAACTAGGCCATGCACTTCACAGTATTAGCTGTGTAATTAGTAACTGTTCCTAACAAATGTCCTGAGACTGGGACTGTTGTCATCTCCATCTTACAGATGAGGAAACTGAGTCACAAACCAGGTAGGCGACATGCCCATCATCACACACCCAGAGCTGTTCTCCCCCTCACTCTCATCCATGGCATCTGTGAACAGCCTTGGCAATGGGCCTTACCCACCCCCCCATCCACTTTGGCACATCCCACCTCCACTGGGCTGCGTCAGGGCAGAGATGGAGCCCAGGACCCCAAGAGCCCTGGGAGAGTCTAATGGGTCAGGGCACTCAGGCTGTGCACTGAGCGATGAATTTCTACTGCTCCTTCCTGGGGTAGACGAGCCCAGCACTGCATGCCCCAAGGAGCTGCGCCTTCCCCCTGCTCCCCGACCCTGCCGCCCACCCCCAGGGCAGCAGTGCTTCCTCGAGGCTTCCTCCCTTGCAG
Seq C2 exon
GCCTGGCGCTCTCCGACCTGATCCAGAAATACTTCGTCTCACCCACGCTGTTCCGTGTGATCCGCCTGGCGAGGATCGGGCGGGTCCTGCGGCTGATCCGCGGGGCCAAGGGCATCCGGACGCTGCTCTTCGCGCTCATGATGTCGCTGCCCGCCCTCTTCAACATCGGCCTCCTCCTCTTCCTGGTCATGTTCATCTACTCCATCTTCGGCATGTCCAACTTCGCCTACGTCAAGAAGGAGTCGGGCATCGACGACATGTTTAACTTCGAGACCTTTGGCAACAGCATCATCTGCCTCTTTGAGATCACCACGTCGGCCGGCTGGGATGGGCTCCTCAACCCCATCCTCAACAGCGGGCCCCCTGACTGTGACCCCAACCTGGAGAACCCGGGCACCAGCATCCGGGGCGACTGTGGCAACCCCTCCATCGGCATCTGCTTCTTCTGCAGCTACATCATCATTTCCTTCCTCATCGTGGTCAACATGTACATCGCCATCATCCTGGAGAACTTCAACGTGGCCACGGAGGAGAGCAGCGAGCCTCTTGGGGAGGATGACTTCGAGATGTTCTACGAGACATGGGAGAAGTTCGACCCCGACGCCACGCAGTTCATCGACTACAGCCGCCTCTCTGACTTCGTGGACACCCTGCAGGAGCCGCTGAGGATCGCCAAGCCCAACAAGATCAAGCTCATCACGATGGACCTGCCCATGGTGCCGGGGGACAAGATCCACTGCCTGGACATCCTCTTTGCCCTGACCAAAGAGGTCCTGGGTGACTCCGGGGAGATGGACGCCCTCAAGGAGACCATGGAGGAGAAGTTCATGGCCGCCAACCCCTCCAAGGTCTCCTATGAGCCCATCACCACCACCCTCAAGAGGAAGCACGAAGAAGTGTGCGCCATCAAGATCCAGAGGGCCTACCGCCGGCATCTGCTGCAGCGCTCCGTGAAGCAGGCCTCTTACATGTACCGCCACAACCATGACGGCGGCAGGGGCGGGGCCCCCGAGAAGGAGGGGCTGATCGCTGACACCATGAGCAAGGTGTACGGCCCCGACAACGGGAACAGCGGTGTGCCGAGCAAAGAGGAGGAGAGGGGCTCCACAGGGGACCCCGGACCTGCCATGGGGCTCAGGCCCATCAGCCCCTCTGACGCACCCCTCCCTCCCGCCCCACCCCTGGGGCAGACGGTGCGCCCAGGGGTCAAAGAGTCTCTCGTCTAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000004770:ENSBTAT00000006265:23
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.260
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=PU(20.4=47.3)
A:
NA
C2:
PF0052026=Ion_trans=PD(79.1=40.8),PF0061222=IQ=WD(100=5.1)
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:
CATCATCTTCACGGGCGAGTG
R:
ACTCCTTCTTGACGTAGGCGA
Band lengths:
353-1376
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]