DreINT0131495 @ danRer10
Intron Retention
Gene
ENSDARG00000098738 | scn4aa
Description
sodium channel, voltage-gated, type IV, alpha, a [Source:ZFIN;Acc:ZDB-GENE-051201-2]
Coordinates
chr12:4856175-4858535:+
Coord C1 exon
chr12:4856175-4856445
Coord A exon
chr12:4856446-4857162
Coord C2 exon
chr12:4857163-4858535
Length
717 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGT
5' ss Score
10.86
3' ss Seq
GCAATTTCCTCTTTCCCTAGGTC
3' ss Score
10.75
Exon sequences
Seq C1 exon
AATATTATCCAGGGTTTGGTGTTTGACTTCATATCAAAACAGTTCTTTGACATTTTTATCATGGTGCTAATCTGCCTCAACATGGTGACCATGATGATAGAGACGGATGACCAGAGTGCTGAGAAAGAATATGTCCTGTACCAGATCAATCTGGTCTTCATCGTCGTCTTCACAAGTGAATGTGTACTTAAATTATTTGCACTCAGACAGTACTTTTTCACTATTGGCTGGAACGTCTTTGATTTTGTTGTAGTCATCCTTTCTATTGCAG
Seq A exon
GTAAGTGTAGAATACAGCAGGTTCATTAGAAAGACGTGTGAAAGGACATTATTAAATTGACATGTTTCGTTGCACTTTCTAAATGAAGTGTGCAGAGATTTTATGTTAAGTTTGAACCGAAACTGTTAAATGTGAAAGTGTTTTATCAGCTTATGGCTCATTCTCTTTAAATAAACCATGTTCTTAATATAAATATAATGCAATCAACTGTGAGATAAAAATATAACCATTTTAACTTGCTTTTGCAAGTATTTAGAACATTTCATGGAACTCACACCCAAATGCCACACATTGCAAGCGTGGTGTTATTTTTCCCCCAATGTGCTTATACTAGTATAAAATTAGTTGTTCAAGATTCAATTTCGTTCATCATAGAGATTTGGAAAATTGTATGTATTAAATGTTCTAAAAGGGTGTGTTCACACTTTTTTTTTGGTCGGAACTGAAAAAGAAAATTATACATTTAGTTCTGTTTGCTTAGGCTTCACACTTAAACTCTGTAAATAGGGTAGTAAAAAGGATGCCTGTAGTCTGTATTTACATGTGATGGGTACATCATGACTATGATGAGAACAAACAGATAAGTTCACACTTACCCAAATGAACCACAATAATTGAATCAAACCTGCCAAGTGTGAATACACCCTGAGTGTGCCTCTGTGTAAACTCTCCTACTGTTATTGCTCTAAGTAAAACCGCAATTTCCTCTTTCCCTAG
Seq C2 exon
GTCTAATGTTATCAGACATCATTGAGAAGTACTTTGTGTCTCCTACTTTGTTTCGTGTCATCAGACTTGCAAGAATCGGCCGTGTGCTGCGTCTCATCAGAGGGGCGAAGGGCATTCGGACCCTTTTGTTTGCCTTGATGATGTCACTTCCTGCCCTTTTCAACATTGGACTGCTTCTGTTCCTGATCATGTTCATCTTCTCCATCTTTGGCATGTCTAACTTTGCCTATGTGAAAAAGCAGGCAGGCATCGATGACATCTTCAACTTTGAAACATTTGGTGGCAGCATTATCTGCCTGTTTGAGATCACAACCTCGGCAGGCTGGGACGGCCTTCTGCTGCCTATTCTAAACAGTGGCCCTCCTGATTGTGACCCTGACTTTGAAAACCCTGGTACAGATGTGCGGGGAAACTGCGGGAATCCTGGCATGGGCATCATGTTTTTCTGCAGTTACATCATCATGTCATTCCTGGTGGTCGTGAACATGTACATCGCCATCATTCTGGAGAACTTCAACAATGCTCAAGAGGAAAGTGGAGACCCGCTCTGTGAGGATGACTTTGATATGTTTGATGAAACATGGGAAAAGTTTGACGTCGATGCTACGCAGTTTATTGAATACGACCGCTTGTTTGACTTTGTCGATGCCCTGCAGGAGCCTTTACGAATTGCCAAACCCAACCGTCTCAAGCTGATCTCCATGGACATCCCCATTGTAAACGGCGACAAAATCCACTCTCAGGATATACTTTTAGCAGTGACCCGGGAAGTACTTGGCGACACTATTGAGATGGATGCCATGAAGGAGAGCATCGAAGCCAAGTTCATCATGAACAACCCCACATCTGCCTCGTTTGAGCCAATCATCACCACTCTCAGGAGGAAGGAGGAAGAGCGAGCAGCCATTGCGGTTCAAAGAATATACCGTAGGCATCTTCTCAAGCGTGCCATCCGCTATGCCTGCTTCATGCGCCAATCAAAGAGGAAAGTTAGGAATCCCAACGACAATGAACCTCCTGAAACTGAAGGGTTGATTGCAAGGAAGATGAATACCCTATATGGCAGCAATCCAGAACTTGCCATGGCTCTTGAATTGGAGACTAGGCCAATGCGGCCAAATTCACAGCCTCCTAAACCAAGCCAGGTCACACAGACCAGAGCATCAGTGACCTTCCCTAGGCCGCAAGGACAGCTCATCCTCCCAGTGGAGCTCACCAGTGAGGTGATCCTCCGGTCTGCACCCACTACACACAGCTTCAACAGTTCAGAGAATGCAACAACGATAAAGGAGTCAATAGTATAACTAGCAGACAATTCCTGTGGACTAAAAGACAATCCTTGTGGTGTTAAATGGAGTGTCATCTGAACAACA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000098738:ENSDART00000170961:24
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.207
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=PU(20.4=47.3)
A:
NA
C2:
PF0052026=Ion_trans=PD(79.1=38.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTGCCTCAACATGGTGACCAT
R:
GGGCAGGAAGTGACATCATCA
Band lengths:
356-1073
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]