GgaINT1024546 @ galGal4
Intron Retention
Gene
ENSGALG00000006112 | SCN5A
Description
sodium channel, voltage gated, type V alpha subunit [Source:HGNC Symbol;Acc:HGNC:10593]
Coordinates
chr2:5559002-5565282:+
Coord C1 exon
chr2:5559002-5559148
Coord A exon
chr2:5559149-5565161
Coord C2 exon
chr2:5565162-5565282
Length
6013 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAAA
5' ss Score
7.3
3' ss Seq
TTGCTCTTGTTGACAACAAGCTT
3' ss Score
0.09
Exon sequences
Seq C1 exon
CAGGAAAAGCAGCTGCAGCTGAGGGGGCAGCGATGCCAAAGCCCAGGCGCCCGAAGTCAGAACTCTGAGATTTGTGAAGAGTTAAGTGAGTTGCACGTGGATAAGCAGTTGAAGGCTGAGCCACCACCTCCAGTAGGGCAAAAAGAG
Seq A exon
GTAAAAGAAACCACTTTCCTGCTTGATGCTGCATGCCATTCGTCACGCCAGCTCCATAGTGCATGCCACCAATTTATGTGGGGGTCTGGGGCATATTACCTGTTCTTTTTTTCGTGTTAAAGGTATAGGGCCATGCGAAGTGCAAGAATTTATTTACCTGACATGAAAGCTTTGGTGTCATTCAGTTCATACTGGCCAAAGTGTACATCACGTTTGCTTCTCGTGTTGGTAAGCCTGTGCCCGGCAGGAGAAATCCCATGTGAAAATCCTGACAGGGCAATGGAAACAGGGCTGCCACAGAGCAGCTCGTCTTCTGCTGAGTCATATTGTCACGTGGGGTGGACATCTGCTTCTAGACTTGTCATATGAGACCCTTTTATAGTCAGTGAAGATCTGGAGCCAATAAAGTTAGGTGAAAGTGTCTCACATCCTGCTGAAATCAACATTTAAATTAGACCAGATGAAGCATATTTTATAAGCACCTGTTTTTCTCCTTTGGCTGTGAGGGGGGACCAAAGTAACTAACTGAGCTGTGGATGTCTGTGTCATGTAGATTACACTTAGGTGAGCTGAACTCCATCCCAGTCACCAGAAATGCTCTGGCCATAAAAGGTTTCTTTCAGGAGCAATCCTTTTTACCAGAATACTTATTGGCGTAATGGATTTTGTATTCAGCAAAAAAAGGTCCTAGACCTTAGAGGAGGGAAGCTTGAGCATTTCATGTCACAATCTCAGAGGAAAAGAATTTGTACGTACTTAAGAGAAACCCCAGATTTCAAACTAATGGGATGAAGCGTTGTAACTAGGATCAATTGGAAGACCACCTCCAGATTTTTTCTTACAGTGGATTTCCTATCCTTCCTGTTTAACTGTATTTTTAAGATAAATAAACCCTGATGTGTTAGCACGAAGGGCGGAAAACTGCATCCTTTTTTAGTGCTACAATGAAATGTCATAAGACAGGAACATTCTAGCTCTGATATATTCAGCAACACTGCGATAAAGTAATAATCCCCATTTCCTCCCTCAACTTTCAAAGGGTCCTGGAACACAAATGTCACCTTTCTATAGTGGAGTATAATTGATTCTATTTGTGGCTGCTTAAAAAGAGGTGGAGGAATATGGCAATAATCCAGGGATGACTTGAAATCAAACGGAAGTTCACATGAGGCTGTGAATGCCAACATGAAAGAGCAAAGCCCAAAGGATGCTATTTTTGAAGGCTAAATCTTGTGTGGACATTGCATCCTTACAGTCCTCCCGTTCAGAAGTAATCTTTGTGCCGACACACGAGGACATGCTAATCTTTTTTATGAATGTCCCAAAAACTTGGGGCTAGCCAGATAAAGCCAACAACTGTGAGGAAGTAACTTAAGGGATTTGATATGCCCCAGAGACGAGGCTCTGAGTTGTTTGGTCAATAACAGGAAGCATCGAATGTGTTCTGACTAAAACACTGTTCATGTCAGTAAAGGATACATTATATGATTAAAAATTCATCCCATACAAATCGCCAGTAAGGCACCACAGAAATAAAATCAGTGGTGGCACAGAACTCAGAGAACATACCACTTGATTTCTTTGCCAGAACACTGCTCCATGAAAGATTTTGCATGGCTGTGTGGAATCTGCCTTTAAATAACTTCTTTATTTATCAAAGGGAATAGTTCTCTAATTTAGAAAAAAAAAAAAAAATGTGGCTGGGTGTAATGCCTTAATAATCAGACTATTTTTTTCCTTTCAAAGTACTATTTCATTACTCTCTTTTACCAGTTACTATGCCATTTTAATTTTATGAATTAATAGCAATTAAGAGAGCATTACTAGCTTCCTTCTGCATTTAGTTTACTCCCTACAGTCACATGCCATTGTTCTTTCATTATTTCTTGTCACTGAGTATCTCTGCACCCTTCATCTAATTCATTTATCTCGTTTTTGTTTTTACAACTCTCTCAATTAGAACTGTTGTGCCAAGAACTAAACAGTGTTCCAAATACAATTCCCACAGAACCATATGGAGGAGAAATAGTACCTTATTGCCTAGACGTGATGTTTCCAAGTAGGATACTTGCATCACAATATCCCACTACAAAATCCTGTTTGATTTCTTTATATTACCCCAGGTGACTTGAGGTTACAGCTTTCCAGGTCTGTTGATGTTCTATCCCTGGACTCATTCGTTTGTAGTGCTTTGTAGTCTCATTGTGCTATATATTCTTTCCATGTATCACTTTTCACTTTCTCCTCAGTTTCAGTAGTCTCTCAAATTCAGTATTATCCACCAGTGTGTGAATTATATTGGTCAGTTCCTCTTCTATATCTTTGGTGCTAACTCTAATCCCTGCAGGTCTCCTCCTCTGAAGGTAAAGTTTCTGTTACATTTGGGTCCTTAGCGTGGGTTTTCTCCATGAAGCAATGGGGGAATCCAAGCCAATGCCTTTATTTCAAAAGTCAGCTTTTCTATCACAGAAACACAGATATTTTACCCAAGTTTACATTATCATCTGTCAGTTTGACAGATTAAGACTGCGATCTCCGAAGGTTAGGGAGAGAGGGAGAAGGCGGATAAGAGAGATAAATCTTGAGCAAACACCAACTTCCAGTGAGATTGCAGCTTCTCACCGTTACAAGCTTTCTGGAAAAAAAAAAAGAATAATAATTCAGATCAGTTTGCCACTACTGGAGAGCCAAGCAGTGGGTGAGTAAACTATTCCAGAAACACATTAAAAACTGCCTCGACAGTGTGACTTTGTGCTCAGGTGGGAGATCTTCCAAAGAGGTTTCTGTTGTTGCCTTTGCCTGGTACACCTCTCCAACAAGAAGAGGGGATGTTCTTTGTCCTGTTTTTGGCCTCATTGTTCCCGTTTGTGCACAGACCAGTGGCAGACAGGAGAGCTGCCTTGCTGTCTTTATGTCTGTTTGATGTGTCACTCAGCTGCCCTCCAAGAAAGTACTCTACTTTTCTCCACTGAGTTTATTTAATTCACTTTAATTACAAGCTGCAGCAAGAGTTCGGTGATCTGTGATTCCCATGATTATTCCCTCTTCCTCTTCTCTAAGCTCAGTGTTGTATGTACTTATTGATGCTCTCCTGGGCTCTTTCCAGCTTTCCATGAGCATTCACTATTGATTGCTAATGGTGTGTTAACGTAGTGTGTCAGATCCCTGCACGCCCATGCTCTGCCATGTGCATTTGCTGGATCTGCTGATTTACATTTGTTTTAGGTTTTCTAGATATTTCCCTGCTTACATTTCCGCTGATTCTAACAAGCCCTCATTCCCTTCTTATTGATTGCTCTGTTGGTCTTTTAAAAAGCTTTTATTTTCTTAGGCAACTGAATTTTCATTAGTCCCATCTCCCTCATAAGTTACTTTTATGCCTCTTTTCTCACAGCGTCCATGAAAACATTAATCCCTTTCACCTTTCTGGCAAAGAGTGACTTTTGCTTCTTTTCCCACAAGCTTTCCTAACCTTTCCCTCCTCTCTCACATGTATGAGTTCTTTTTCTAGTCCCTGTTCAGACCCCAGAACCTTTGCCTCGTGTTTTCTGAATCCACGTTCACTGCCTCTTCTTCCTTGAAGGCTTTTCAAAGCAAATCCCGTCCGTGTCGTCTTGCATGTTCCCCATCTCCTTTTGACACTGATGGATTCTAATAATTTCTGAAAACTCCTCCCCGTAGATAACTCTCGAGCATTCTCGACTCTTTTAAGATGCTTTCCCTGTAGTCTAATAGAATTGCACTGTGTCCTGCAGTTGCGTTCTCTGAATTTCCCAACCTGTCTCTGCTAAATGCAGCACTCTCAATGACAACGCTATTGAGCTGACATTTTTCTCACAATGTTCTTTGATTTCTCTCTGTTGGTTAGAATTGTGTCCAACAAGGCTTCTTTTCTCATCGGGACCCCTATTTTCTGCATCCTGCAGTTGTGTGTGATTTAGGACTGCTTCGGTGTTCTGTCTGTTGATGACTTCGTAACAGAAGAAATAATGACTAAATGCATTCCGTAATGAACAGTAACAGAAAGTTCTGATTGTATGAAAACCTGACATTTTTTCCACCATCATGTATTGTTTGTAGCCTGTGGAAAACTGGCTGTTCTCTGTACAACAGCTGCATTCTGAATATGGATTTTTTAGAAGCTTCAGCCATGTCTTTGACCTGTGCTTTCTGGCCCGACTCTCTTTTTAAATGATCTCTTCTCGATTGTTTGCTCTTCTTCTGAGCAGAGCATTAAAAGCCCTAGCCAAGACTATGACCTTTGGGATGCTGCAGCTAATTGCAAACACGTAGCTTCCATCCTGCTTACAAGTATTGCTGGAATGTTCAGCCTTGCTCGTTTTACCCCAGGTTCAGCATTTCTCTGAATTCAGCTATAAATTTTGCATTGCCTCTGTATACTGGAAAACAGAGGGCCCATTTTCACATTAATAATAAATACACAGAGCTGTACCTATTCTCTGACTCTGTCATCTTCATGAAAATAATAATTTATGTGTACGTGCCATCTTTCATATAACTATCTCACAGGTTGTTTAAAAGCATGGGTAAGTATTATTGTCCTCATTTTTAAAATGAAGACAATAGTATTACGAGATAAAGCACAGCAGTGTTTAAGTAGGTGCTCAGGGAAGAAAATAAGACAGTTTGCAAATAAACCCCCTTGTGCCAGATATCTCTTTTACAAAGTCAAAAGCAAATACTGAGCAGGGCTGAGTAAATAATAGGCCTTGAACTATAATGGCCTAGCTGAGTAATCCAGGCAAATATAATTCTGGATTAACACAAACCTATAAAACAATTATTTTGACCACTAAAATTAAAAAAAAAAAAAAAACCAAAAAACAACTCCTGTTGTATTCTAAAAAAAAAAAAAAAAAAAAAGTATTTAATGTCAGAAGAAAGCTTTGACCTGAAATGAAATTTTTGTTTCTTATTTGATTGGCTTATGTTATCATGCATCTCTATTTTAGCAACAAATGCAGCCAAATTTCAAAAGCCAAATTTCAAAAGCCAAATTTCAAATTTCAAAAAAATTTAGGCATCAAGTTTTCATGAAATCCATTGCTTTATTTAACCCTATTTCCTGCATAGCCTTAAAACCAGTTTTTCTTCGATCATCCATTCTCCAGACTTTTTTTCCCAGATTACCTGAGACTTCTTGCTCTAAGAAGATAAAATGAGTATATAGGAATATATAAAGGAATATATTTGTCCCCATTTTGCAGAGAAGGATTTGAAGTGTATTTAAACAACATGCCTTAGACTGGGGATCAAACATTTGGGGCAAACGACAGGTCCTCCAAAAAGCCTTGAAATCCTTGTGTCCCTCCTTCTTATATCTCAAGAGCAGAAGTGTGCATCTGAAAGACGAGTGGTCCCATCCCAGGGTGGGGATGTGGGATGGGGAAGGTGAAAGAGCCTTCCCACATGTGCATGTGGTGTCATTGTGTGAGCAGAACGTGATGTCAAAAGGGCTTCTGCTCATCCCATAGGAGAAGCCACAGCAGAAGAGAGGATGATGCGGTCCTGGCTGACCGGATACAATATGAACCCATCAGGTGTGGGTACAGAGCCTCATGTCCAGGAGGCTGGAACCCAGCATGAGTCCTCTAAGTCCTCCTCCAGCTGTTTAGCAGCTGGGTTCTACCCATTTGAATCCACCAGATAGGAGGGAAGGATATAAAAGATTTATAGTTCTGAATGGTTTGGTCATTCCAGACTTCCACCTACCATTAGTATTCAGTAGTCGTTCACAGTCTTTCTTGAGTTATTCCTTTTTACTTTTTTTAAAAAACAAATATGGTGTTTTAGGCTTTTTTGCCGTTCTTGAGGATGGGTCCACTGTTAGCTCACCACTGTTAGTGTAGGTAGAGCTGTCACTCAAGCATGGCCATTTCACTGTCGTGACTGCTTTGGCTGGGATATTGGTTAGTGGAATAAGAACTCAGCTACTTCCTTTGGGGCGATTGATCAATTTGTTTTCCTCATCTTTGCTCTTGTTGACAACAAG
Seq C2 exon
CTTGATGAAATCAGTCTTTCTGAAGGCAGCACAGTGGATTTGACAAATCCTGCAGAACTGCTGGAGCAGATCCCTGAGTTTGCTGAGGAGCTGATGGAGCCTGAAGATTGCTTCCCCGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000006112:ENSGALT00000031281:17
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.776 A=NA C2=0.122
Domain overlap (PFAM):
C1:
PF065128=Na_trans_assoc=FE(17.9=100)
A:
NA
C2:
PF065128=Na_trans_assoc=FE(14.9=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:
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]