GgaINT0091329 @ galGal4
Intron Retention
Gene
ENSGALG00000006112 | SCN5A
Description
sodium channel, voltage gated, type V alpha subunit [Source:HGNC Symbol;Acc:HGNC:10593]
Coordinates
chr2:5448588-5450561:+
Coord C1 exon
chr2:5448588-5448906
Coord A exon
chr2:5448907-5450440
Coord C2 exon
chr2:5450441-5450561
Length
1534 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGC
5' ss Score
9.6
3' ss Seq
TTCTCTGTTTTCTTTTCCAGACA
3' ss Score
12.32
Exon sequences
Seq C1 exon
CTGTTTCCACTACTTGGAGAAAAGACCAGTATAGACAAAGCAGGATGAAAAGATGGCTGACTTCTTGTTACCACCGGGTACTAACAGCTTCCACCGGTTCACGCCCGAATCCTTGGCTGCTATTGAGAAGCGAATTGCAGAGAAGCTTGCAAGGAATGCGAAGCAGGAGTACAGAGAGCAGCTGGGCGAAGAGGAAAAGCCTCAGCCTCAGTTTGATTTGCAAGCGTGCAAGAAGCTGCCTGATATCTATGGGACTGTTCCTCCAGAGCTTATTGGAGAGCCACTGGAGGACATTGACCCCTTCTACAATGATCGCAAG
Seq A exon
GTGAGCATCAGCAAGGCGTTCTGCTTCTTAGCGTTTGCTGAGCCATATTGTCTTTCTTTGTGTTGAGGGCTCAGGTTTTTATCTTTCTACAGTCAGTAAAAATATTTTTTTTTCCAGATTTTTGGCATGAGTGAGGCTCCCAAAAAACATGTAAGCAGTGCAAAGAAGGATAAAAAATATAATTAAAACCTGGGTGTTTTCAAGTGATGCTGATTATGAATATACATAATATGAAAAGAGCAGAGCAATAGCTGAAGGAAGCCAGAGGTTTTTATCTACTGTATCTTGCATCTTCATCAGATTTGACCCTTCACAGATGTGATGACCTTTTGAGTCCCTTAATTGAACTTGGATCTTGAGTCTTGGGTCTTAAGTAATGGGACTAAGGGCTCGAGCATCATGCTCATCACAAGAGGGAAGCACCTCCATGACCATTCTGAAGGGCAGTTGTTTTTCTGCTGAGGAATGATTTAACTCCATTTAAGATGGAGAGCGGGGCTGGTTGTTTACTACAGTTCATTCTCCTTTCCAAACATTTTGCAACATGGAGGATAAAGCAAGGCTTGGAACCTCAGAGTATTTTTAGGGAGCTTCATTTTCTTTCAGGTACTGATGTTCCTGGTTTTGGGCTAAGCTACTTCCTCTAAACAAAGGATTAATATGACTATGGTGATACTTTTATTAAAGTGATGTACAAACACCTACAGAATTAAAGTTAAGTGGACAAAGAGAAGGACCTGTAAAGGCAGAATTAAGTTGTAGATATTTATGGCTCTGCTGTTCCTGCTGTCTCCATGCACAAGCAGCGGGGTACAGATTTGGAATTTTAGGATCTCAAAGGTCTTAGTTTCCAGTGGATGACTTGCTTAGGAGTTTATCTACTGAGTGGCCTGCTCCTTTTGCTGAGTGAATTTTAGTCCTTCCAGGCATGAGTGGGCATTTCCAGAGCTGTGTAATTGGGTCAGCATCCAGTTCATCTTTGCTTTGGATTTAAGATAACTCATTATGGGTTTCCTCCCTCCATATTATATGAACACAGTGACAGTGCTTTAGTGCCTGGGTTAGATCCTCTTGTGGAGATGTGCCTCATGAAATCTTTGAGTCATTTAGGTTGGAAAAGACCAGTAAGTTCATCTAGTCCGACCGCCAGTCCATCACCACCATAGCTTCTTGAAAGATGAGTTGAGAAATGTTGACTGAGAGCAATAACATGTGCAAGGTAGGGAAGATGGAGTAACAACACAGCAGTAGAGATGTGGCATAAAAGTCTCTCTAAAGCATTTTAGTCGCCATGCCATCATTCACTGTTGTAAATCTAGTCCTGTTATGGAGGTAGGACTAGGAAGAGGGGGTATGAAAGGAACTGTAGGCAGTGAAGAAGATGACTTCATGGTGTGAAAAACAATTTGGGGATTTGGGATGGAGTGAGGAAGAGGTTTGGGATATTGGCAGGAGTTTCCTGGGAAAATGGGATGGGAAAAGCCTAACGTAAGTGCAAATATTGAATGTTTTTATTCTCTGTTTTCTTTTCCAG
Seq C2 exon
ACATTTGTAGTACTGAACAAAGGGAAGACAATATTTCGATTTAGTGCCACTCCTGCCTTGTATATACTTAGTCCTTTCCATCCAGTCAGAAGAGCAGCAATTAAAATTTTGGTACATTCAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000006112:ENSGALT00000031281:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.126 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
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACCGGGTACTAACAGCTTCCA
R:
GCTGCTCTTCTGACTGGATGG
Band lengths:
345-1879
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]