BtaINT0129475 @ 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
chr22:12098733-12101847:-
Coord C1 exon
chr22:12101522-12101847
Coord A exon
chr22:12098852-12101521
Coord C2 exon
chr22:12098733-12098851
Length
2670 bp
Sequences
Splice sites
5' ss Seq
AAGGTGACT
5' ss Score
6.64
3' ss Seq
AAGTGGCTCTCTGTCCGCAGACC
3' ss Score
10.25
Exon sequences
Seq C1 exon
CTTCCCTTCAGGCAGTGTGAGGACAGCCTGTGCCCCAGAAGCAGGATGAGAAGATGGCAGCCTTCCTGTTACCTCGGGGCACCAGCAGCTTCCGCAGGTTCACCCGGGAGTCTCTGGCGGCCATCGAGAAGCGCATGGCAGAGAAGCAGGCCCGGAGCTCGGCCGCCTCGCAGGAGAGCCGCGACGGGCTGCCCGAGGAGGAGGCGCCCCGGCCCCAGCTGGACCTGCAAGCCTCCAAAAAGCTGCCGGATCTCTACGGCAACCCACCCCGAGAGCTCATCGGGGAGCCCCTGGAGGACCTGGACCCCTTCTATAGCACTCAAAAG
Seq A exon
GTGACTGCCACCCACTCCCACCCCGCCTCCCCGCAGCATCTCAGTCGACCAGGCAGACAGGAAGAGGGTCTCACCTCCATACGGGGCTCTCTTTGGGGCTGGCTCCCTTGGGCCTCGGGGAAGTGAGTCATTAGTAATCTATATTCCAATCACCTTAACTTTGGAGTTCCAGAAAAAAAGCCCAGAATTATGCAGCCTGAGATGGTTCAGTGCTGTTAAGGAAAGAGCAGGCAGCCACTCTGGAAATCTTGCCTCCTGGTGGAGCATCTACTCAGGGGATAATCTGTGGTCAGATTTCCACCCCTGGAGGACTCCTGATCCTGTGGTGTGTATGTCAGTCAGAGTCGGGCCCTGAGTCCTGTCCTGAGTTGAGTTTTGGACCCAGAGCACAGCATGGGATCCCTCCCCCAAGCAGGGACAGCGTGTAGCCTCCGCCCCCCACCCCAGAGAATTTGCTGGGCATTGGCTGTGCCATCACGGCTTGGGGGCCACAGCGGCAGCATCTGGGCCTTGTGGGCTGGTGATGGGACTGTGAGGGCTCATGGGAAATCTGAAAGGAGTGGGAAGCCGGTGGCTCTGCCATTGTCCCTTCAGAGTGTGGGGAGAGGAATGGACTTTGGCCCACTCTTTGTGTGTCTTAGTCACGGCCGTGTCCGACTCCACAACTGTAGCCCGCCAGGTTCCTCTGTCCATGGGATTCTCTAGGCAAGAATACCAGAGTGGGTTGCCATTCTGTTCTCCAGGGGATCTTCCCGACCCAGGGACTAAACCTGGGTCTCCCACACTGCAGGCAGATTCTTCTACTGTCAGAGCCACCAGGGAAGCCCTTTGGCCACTTGGATGGGGTAACTCAAGCTTCCTCCAGCATGAATTTCTACCCAGGAGATAAATTCCCCCATCTGGGGCCCCTGCGCTGTCCTCACCTCTCAGGACCGTGTGCCGCCTGCACCCGGCCAGACCTCGGGCACACAGGGCTCCTGCAGAGGCCTGAGTCCCCACCCCAGCTGCCCACACTTTGGGCTACATGGCCAGGGGAAGGTGGGTTTCAATTTGGTGGAGGCCTATTCCCAGAAGGCTGGGTGCCAAGCAAGACGGGTCCTGCCCACATCCCTGCTGTCAGTGCCCGGGCTGAGGAGGCACTGAGGGCTGACAGGCCGGCATTTCCAGGGCAGGGCCAGCACCTGGTGTTCCTGAGTGTGTGTCAGTGTTACCAGGCGCCTGAGCGGTGTGTCACTATGCGCTGAGACTGCATCCAGGAGACCAGGGGTCTGCGAGTGGGAGTGATGCGCAGCTGTCTCCCCCTGTGCACGCACGTGTGCATGGGTGGAGGTCAAGCCCACCCAGGCTATGCGCACATGTGGGCGAAGAGACCATGAATTTGGCCTCACTCCCCACCCCCCAATTCAGGTGACTCAGGCTGGGTGAAGGTGAGGGCTCTGGCTATATTGGGATTAGTCAGGGTGGGTGGGCCTAGGTCCTGGTTGGTCAGAGCTGGAATTAGGGCTGGGGTTAAGGCCACGTCTGGGACGAGTCATGGTTTGAGTGGTGCATCAAAGTGGTGATGGGGTCGGAGTTCGCAGACTGGAGTCATGGCAAAGGGACCCAACTGAGAGTGGGCCAGAGCTGGGCTGGGCTTTGGGGGCTGGTGGCAGCTCAGCCCGGGAGCAGTCAGGGACACTCTCCTGTCCCTGTGACCGGGGACACTTGAGCAGTGGCCCCAGGTAGGATTCTGGTCTCTAACCTCCTGTCTTGCCTTGCTGACCCCTGGTCACACTGCCTGCAACCCCATGGGGTGACACAGGTACCACAGCAGAACTTTCAGTCCCGATCTTTCTGGACAGCTTGTCTCCCTAGCCCAGATTAAATAGAACCTTATCTCACCAGCTCAGCCCTGGGAGAAGCCCAGCCCCAGGCCTTGCCACCTCAGCAGTGCCTGCTGTAGCCAACGGGGATGGACCGCTGTCCTCAAAGACGGCACTGGACGCAGATGCCCACTCCATGTGCTGTGGCGCAGCCTCCAACACCCACTGTCCACTCCCATGCCTCACTGTGCTGTGTAGATAGAATCTTCCAGAAGCGTGAAGAGCAGGTTTACCCTGGGCAACACATGACCCTAGTGAGGAAGACACCAGGTCGTGGCCTCTGGTGTCAGCTGGGGCTGCCATCTGTCTGGACTCCAGGAGACAGGGTCCCAGGGAAAGTTTCTGTCTCCTGGGCTGAGTTCTGCATTTTCCTCATCCCTCTTTGGTTGTCCCTGCTGACCCAGCTCCCTCCTCGCACCCTCAGTCTTCGGTGGGCCCGGTGGGGAAGCACAGAGGGGTCAGAGGGAGAGGGGAACCAGGGGGGCATCAGCTGGGTCCTGGCCTCTGCTATGATAACAGCTCAGCTAGGATCATGAAAGGCCCCTTCTCACTGAAACGAAACTAAATCTACCCAACCTGACAATCCCCTGAACTTGCTCTTGTCCCAGCCCAGCCATGGGTGACCATATGAGGATCCACTCACCTGCCAGCTCCCGGTACCCCCACCACTCTGTCAGGCCCTCTCCTCTTCCTCTCACCCTACCCCTCTGCCAGAGTTCTAGACCTCTGAGCCCACACCTGCCCCCCAGGAGCTCCTCCATAAGGACCTAGGGCTGCCACCCTACCTAAAGTGGCTCTCTGTCCGCAG
Seq C2 exon
ACCTTCATCGTCCTGAACAAAGGCAAGACCATCTTCCGGTTCAGCGCCACCAACGCCTTGCATGTCCTCAGCCCCTTCCACCCCATCCGGAGAGTGGCTGTGAAGATCTTGGTGCATTC
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000009155:ENSBTAT00000012068:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.319 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
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:
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]