BtaINT0129467 @ bosTau6
Intron Retention
Gene
ENSBTAG00000009155 | SCN5A
Description
Bos taurus sodium channel, voltage-gated, type V, alpha subunit (SCN5A), mRNA. [Source:RefSeq mRNA;Acc:NM_174458]
Coordinates
chr22:12072477-12073648:-
Coord C1 exon
chr22:12073469-12073648
Coord A exon
chr22:12072849-12073468
Coord C2 exon
chr22:12072477-12072848
Length
620 bp
Sequences
Splice sites
5' ss Seq
GTGGTAACC
5' ss Score
3.88
3' ss Seq
TCCTCTCTCCGTGCCTTCAGAAT
3' ss Score
10.71
Exon sequences
Seq C1 exon
GCCCTCGCCATCAGGGGTGTGGACACCGTGTCCCGCAGCTCCTTGGAGATGTCCCCATTGGCCCCAGTAACCACCCACGAGAGAAGGAGCAAGAGAAGAAAACGAATGTCTTCAGGGATGGAAGAGTGTGGGGACGACAAGTTCCCCAAGTCCGACTCAGAGGATGGTCCCCGAGCAGTG
Seq A exon
GTAACCCCCAGCTGCGGCTCTGCCCCTTTCAGGATGGATCTGGCATCCAAAAGCCATCATGCTAAGCCTAGTGCTGTCAGAGCCCCCATGGTTGCTCCCCAAGGAAAATATTCCTTGAGCCCCCTCCCAGCCCCTCCTGTTTCCCATGGCCACTCTTAGAGTGGAGAAGCCCTGGGCAGAGGGATAGGGTAGGTTTGGGTGTTAGCATATCCCCAACCTCAGCTAAGTCCCAGCACTGGAGTTGGGGGCACCCCCGTCGTGTGGATTGGTAGGAGCTCACAGACATGCCCAGATGAGCAAGGGATGTGGCTGATTGCCGAGGTCCTGCTCGGGCCAGGCCTGTCTATACCATCAGGAGCCTTCTGCTGCTTCTTTCCCATATGAGCTTCAGTCTCAGAGCCCCAGGAGCCCAGGCCTCAGGTGAGCAGAGACCCTAGAAAATGCAGGATTGCCTGTAATCTGCACCCCTCCTCGGAGCACCCCTAGTTCAGCCCCCTCGGTTCCTATGTGGCAGACAGAAGCCCTCAGTGCTCCAAGTTGAGCCGGGGCCGATACCGTGAGTGACAGGCCGGGAGCACGTGAAACGCTGTCCCAGCCATGTCCTCTCTCCGTGCCTTCAG
Seq C2 exon
AATCGTTTCAGCATCACCCATGGCCTCAGCAGGACCTCCATGAAGCCGCGCTCCAGCCACGGGAGCATTTTCACCTTCCGCCGACGGGACCTGGGCTCCGAGACAGATTTTGCGGACGATGAAAACAGCACCGCCGGGGACAGTGAGAGCCACCGCACATCACTGCTGGTGCCTTGGCCCCTGCGGCGGCCTAGTACCCTGGGACAGCCCAGTCCCGGAACCTCAACTCCCGGCCACGTGCTCAACGGCAAAAGGAACAGCACTGTGGACTGTAACGGGGTGGTCTCCTTGCTGGGGGCAGGAGACCCCGAGGCCACCTCCCCAGGGAGTCACCTCCTCCACCCTATGAAGCTGGAGCGCCCCCCAGACACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000009155:ENSBTAT00000012068:12
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.717 A=NA C2=0.968
Domain overlap (PFAM):
C1:
PF119333=DUF3451=PU(21.6=75.0)
A:
NA
C2:
PF119333=DUF3451=FE(59.1=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCAGGGATGGAAGAGTGTGGG
R:
CCGTTACAGTCCACAGTGCTG
Band lengths:
347-967
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]