BtaINT0129474 @ 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
chr22:12046410-12049535:-
Coord C1 exon
chr22:12049374-12049535
Coord A exon
chr22:12046531-12049373
Coord C2 exon
chr22:12046410-12046530
Length
2843 bp
Sequences
Splice sites
5' ss Seq
GAGGTAACG
5' ss Score
9.65
3' ss Seq
CCTTACAATCCTGCCTGCAGCTT
3' ss Score
7.71
Exon sequences
Seq C1 exon
CAGGAATCCCAGCCGGCGTCCGGCAGCCCAGAGGCCCTCCCAGAGCCGAGGGTCTGGAGCCAGGTGTCGGAGACCACCTCCTCTGGGGCCGAGGCCAGTGAGGTTCAGGCAGACTTGCGGCAGCAGCGGCGAGCAGAGGCCCCCGCCCCAGGGTGCAGTGAG
Seq A exon
GTAACGCACACCTTTGTCCCCGAAGCCAATGGGGCACTGCCGCTGGGGCTGGAGGCCGTGAGAGGCCCCCAGACACCAACCTTCTGGTGGGAGCCACAGCCGCTGTCACAGCCAGTGTGGGAGACCTGTTTGCGGAGTGGCCCCACACAGGGGAGGGATGGCTTGGGGCCCAGAGCCATTCGGAAATTAGGAAGCAGCCCCCCAGGAGCACGCCACAGGACTAACCCCAAACCCCTGCGTGTTCACCCCTTCCTCACTGGGTTCCTGTGCTTTGGTCCTGTTGGCGAAAGTCTGTCCTGTGAGTCAGCCCATCCTGGGGGACTGGGGGAGCTCTGAGCACAGGCTCTCAACACTCGAGCCACTAGCCGCTTCTCACCTGGACGGAAGCTGAGGCGGCGAATACAAGGCCTGTCAGGGGAATTTGTTCTGGACACAAAAGAGTTTTAATTTGAGCTCATTACCAATACTTTGGCCACCTGATACGAAGAGCCGACTCATTGGAAAAGACCCTGATGCTGGGAAAGATTGAAGGCAGGAGAAGGGGATGACAGAGGATGAGATGGTTGGATGGCATCACTGACTCAATGGATATGAGTTTGAGCAAGCTCCAGGAGATGGTGAAGGACAGGGAAGCCTGGCGTGCTGCAGTCCATGGGGTCACAAAGAGTCAGACACAACTGACCTACTGAACAACAAAATAACAATGACCAACATTTAAAATCCAGAGGCTTTTCTGTAAAAAGTCTGCATTCTGGCTTCTCTTGAAAAAAAAACATTGGAAGAAGAGCCTCCCTGCTGAAGAATGTAACCACCTCCTTGACTGGCCAGAATGCTGCGATTGGCCAGATCTCACCTGCCTGCCTTCATTCCATCACCTGCCTGGCCCCGTAAGCATTTGGGTTTGCAGCCCCTGAGCTAACTGGACTGTGGCGCTACTGTCTACACCCCACCCCTGCTCTGCCAAGCACCCAGGAAGGTGGAGGTCATGTGCTGAGACCATGCCCAGGGCCCTTGTCCTGCAGCCTGACCTCAGCCTCAGTCCGGCAGCTGTGACTTGCTCCAAGACAACATTTCTCCTTTGTCTCGTTCCTTTCATGGGATGGGCCCATGGGAAGCTTTGTTTTCATGGCCATTTTGGGAGTACAAGGGCCTAATGGAATCATTGCCCTGACTGTACACGTCACACTTGTCCTCCTGGACAGTCTGACACACCAAGGCGGGGGGAACAGGAAGACACGGGAGGGACAGAAGGTCATGGACAGAAGGGGCTCCCGTACTGGAATGCTGACCTTTGAGCAAGTCTGGTACCTTCATCACCTCTTCAGATCAAGTCCCAGTGGAAATGAGGAGACAGCCAGGTGGGCTGGGACTTTCCTAGGAGAAGGACCCCTCATCTCACTTGCCCGGGAAATCCTGAGAACTTGTCGTCACACGTGAAAGCTCTAGTGTCTGAAAAGAAAAGGCACACAAAGTCCCTCAACTGTGACTTTCCCAGCTCAGCACTGCACAACGAAGCTGGAGTGAGGACGCGACCCTCAGAGCCACAGAAGCCACCCTGCACACAGGGGCACTCTCTACATTTTCACCAGGATCCAGTTACTCCTTACGGCCAGTCTCAAGGTTAAAGAGGACTTTGAGACAGCAGTGGACTGAGTTGTGGAAGGAAGAGAAAAGAAGGCAGCTTTGAGAGCCAAGGCTGCCCAAGAACTCAAACCAGCTCTCCCCAGAGGAGCGGAGCCTGAGCAGCATGAGGTGGACGACTGAGCTGGGTGTTGTAGATGTGATCTGAAGCAAATGAAGGCTGCCCTCCTCCCCAGAACCCTCTTCCCTGCCATACTTGTCATTAAGGTGGATTCCCAGAGGCAGAGCCAGAGCCCGGCTTCCTGTGCAAATGATTCATTGAGAAGGTGCCCTCAGGAGAGACCCATAAGGAAGTGAGAAAAGCAGGCTAAGGCAAAAGAAGCAGCTCCAGATGTTATGCTGGCTGGACTCCAGCCTCAGCCGGGTCTCTTCCATATCAGTCAGTCACTGGGTGTCAGCCACCCTGGACTTGGGTTGTAACCCCCAAGCTATTTCCAAGGATGGCAGGTCCCTGGCTAAAGACACTTTTCTGGAGACGGGGTCGGCTAAACAGTATTCGCAGCAGCTGGAGACAGGTGCACTGGCCCAAAGAGGGGAACTGGGCAGAACTATAGCACACCTGTACAGGTGCCCACATGTGACACACACAGGTGCTCCTAGGGCAGTGGTACATACCTGTCATCATCAGGTTATGCGGGATCAGGGCCACAGAAGCCCGCGTGACCAGGCAGGGAAGGCTCCGGCACCTTCTTGCTCTAGGCTGTATGCCTCACACCAGCACCCGTATGAACTGAGTGAGAAATGTGGGCTGGGGTCCCTGGCCTGCTCTTTGCATGTCTGACCCGGTGCCTGTGTGTGCCTCTGACCCTGGCGCTGACTGTTCTGGGCGTGGCCTGCCTGTTTCCTGCGTGTGTGCTGGGCTGCCACTGTGTCCACATCCCAGTGTGTGTCCCTGTTGCTCCTCATGCCTGTTTCACTTCCACCTGGATGCCTTCCCCATTCCTGGGGTTTTCCCAGAACCCTTGTCCCACCCCTGCACCCCTGCTCTAGACACCAGCAGCCCAGAATCACAGATCCAGGGGCCCTAAGGCCCAGCCTCAATGACCTTTGTGGCAGGTTCCCACCCCACTGGGCTCAGATTCCCCAGGTGTGCTGTGGAGGGGATGGCCTAGGCACCTCCACTGTGGGACCCCCAGGCTGGAGGCTGCTACAGAGCCCACACTCATGCGCTCACCCTCCCCACCTTACAATCCTGCCTGCAG
Seq C2 exon
CTTCCCGAAGACAGTTACTCTGAGGGGAGCACGGCAGATATGACCAACACTGCTGACCTCCTGGAGCAGATCCCTGACCTCGGAGAGGATGTCAAAGATCCAGAGGACTGCTTCACTGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000009155:ENSBTAT00000012068:19
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=0.683
Domain overlap (PFAM):
C1:
PF065128=Na_trans_assoc=FE(20.2=100)
A:
NA
C2:
PF065128=Na_trans_assoc=FE(15.2=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]