BtaINT0129473 @ 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
chr22:12049374-12051345:-
Coord C1 exon
chr22:12050905-12051345
Coord A exon
chr22:12049536-12050904
Coord C2 exon
chr22:12049374-12049535
Length
1369 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGC
5' ss Score
9.6
3' ss Seq
AGCTGGGGGGGTCTCTTCAGCAG
3' ss Score
0.12
Exon sequences
Seq C1 exon
GTCCTGAACCTCTTCCTGGCTTTACTGCTCAGCTCCTTCAGCGCAGACAACCTCACAGCTCCTGACGAGGATGGGGAGATGAACAACCTCCAGCTGGCTCTGGCCCGCATCCAGCGAGGCCTGCGCTTCATCAAGCGGACCACCTGGGACTTCTGCTGCGTGCTCCTGCAGCGGCCGCCTCAGAAGCCCACGGCCCTCGCCTCCCAGGGCCAGCTGCCAGGCTGTATCGCCACCTCCAGCCCCCCACCCCAACCAGAGAGCGAGAAGGCGCCCCCAGCCCGCAAGGAGACGCGGTTTGAGGAAGGCCAGCGGCCAGGTCAGGGCGCACCTGGGGATGCCGAGCCTGTGTGTGTGCCCATCGCCATGGCCGAGTCAGACACGGATGACCCCGAGGAGGATGAGGAGAACAGCCTAAGCACAGAGGAAGAGTCCAGCAAGCAG
Seq A exon
GTGAGCCCCCAAACCCTGGCCCTCATGTGCATGAGCACCACCTCCTGTCCAGGGGACCCAGCTTCACTTGGAGCAGTTGCCCCAGTAGGGATTGGCCTGGAGGGGGAACACAGGCCACCCCCCCAGAACCAGCCTCTTGGAGGCATGCTGAGGCCAGCCGTCAACCCTCTCTCCCCAGCCCAGCCCAGGAGGGCATCTTCAAGGGACCGCTGTCTATCATTCATCCCCTGGCTGGACACAGGCAGCCAGTTGTTCAGAGAGGGAAACCGAGGCACGACAAGAGAGACAGACTTGCTAGGAGTTCCTCACAGGTCTAGGACAGAGCCAGGAAGCCTGGCTCCCAGACCCAACCCTGACCTTATCCCCTCCAAGACTAACAAGGCGGAATGTCTTGGTGAGTGGGGGAGAGCGGCCTCCTGACCCCGCCACTGCCCCTTCCCCTCCCCCGAGGCCCAGAGCTCATTCTAAGGTTTAAAAATAAGCATCCCTAAGATGGCAGGTGTCAGAGACAGCACTATCTTATCTCCCAACCTGTTATTTTTAACACTTAGGACTGGAGTCTGAACAAAAAGGACTGTACACCCCACCCCCACCCCGGCTCCCTCAGTGTTCTCACGGCCTGAGCCCAGCTCAGGTGGCTTGTCCCAAGGTCCTTGGTCAGACAGTGAGGACTGGGTCTCAGTTTCGTTGGGCCCACGCTGGCCACCTCCCTGGGGCCTGCACTGGGTGGGTCTGGCTGAGAAGAGCAGCTGCTCCCCTGCACGGAATTTGATCTGTGGCTCCAGGCTTGATTCCACAAACTCCTGCCTTCCTGTGGTCCCTGAGGCCAGCTCCTGCCCTTTCAGGCAGGCGGCAGGACAGCCACAGAGTCAGTTGGGGGAGGGGAAGGGTTGGTGTTGCCAGAACTGCGGCTTGGAATTAGTTCCAGGATGCTTCCAGCACAGGAGTGGGATTCCGGCTGTCCCTGCTTTTCCTCTTCTCCTTCTCTTGAGCCTGTTGGCCCTGAGACGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTAAGCAAGCTGAGCTGCCATGGGAACTCCTGGGAAAGCCTGTCCTTCCTAAGTGGAGCTGCCAGCACCTGGGAGCTGGGCATCATGGCGCACTGACACCCTTCAAGAAGCTAGAGGAGGGGAGATTTGTGCCAGCCAGGCCAGGGGCTTTGTTTAGCTTTAGGCCCTTTGCCTGGTCCTCTCAGGAGCTTTCGTCAGCCTTAGAATGAATGCCTGAGGGAGGGGTCTTCAGGGAGATGATGCCTCATGAAGAGAGTAGTGAAGCAGAGCCAGGATCCTAGAAACACTGGCTGGATAGCTCATAAGCTGGGGGGGTCTCTTCAG
Seq C2 exon
CAGGAATCCCAGCCGGCGTCCGGCAGCCCAGAGGCCCTCCCAGAGCCGAGGGTCTGGAGCCAGGTGTCGGAGACCACCTCCTCTGGGGCCGAGGCCAGTGAGGTTCAGGCAGACTTGCGGCAGCAGCGGCGAGCAGAGGCCCCCGCCCCAGGGTGCAGTGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000009155:ENSBTAT00000012068:18
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.571 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=PD(4.2=5.4),PF065128=Na_trans_assoc=PU(46.8=83.7)
A:
NA
C2:
PF065128=Na_trans_assoc=FE(20.2=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAGGCTGTATCGCCACCTCC
R:
GCAAGTCTGCCTGAACCTCAC
Band lengths:
342-1711
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]