DreINT0131549 @ danRer10
Intron Retention
Gene
ENSDARG00000005775 | scn8aa
Description
sodium channel, voltage gated, type VIII, alpha subunit a [Source:ZFIN;Acc:ZDB-GENE-000828-1]
Coordinates
chr23:27325085-27327284:-
Coord C1 exon
chr23:27327014-27327284
Coord A exon
chr23:27326912-27327013
Coord C2 exon
chr23:27325085-27326911
Length
102 bp
Sequences
Splice sites
5' ss Seq
TTGGTAGGT
5' ss Score
7.03
3' ss Seq
CTTTTCCCCAAAAACAACAGGTA
3' ss Score
5.03
Exon sequences
Seq C1 exon
AACAAGCTCCAGGGTATGGTGTTTGACTTTGTGACACAGCAGGTCTTTGATATTTCCATCATGATCCTCATCTGTTTGAACATGGTCACCATGATGGTTGAGACAGATGATCAATCACAGGAGACGGAAAACATTCTGTACTGGATCAACTTCATCTTTATTGTGGCCTTCACTTCAGAGTTTGTCCTGAAGCTCTTTGCGCTGCGTCATTATTACTTCACCAATGGCTGGAACATCTTTGACTGTGTTGTGGTCATTCTCTCTATCGTTG
Seq A exon
GTAGGTGAACATAGTTTCTTAACCTTCTTCATTTTGGCTTTGAAACAATACAAATTTAGCTTATGTTGTGTTCTGCTTGTTTCTTTTCCCCAAAAACAACAG
Seq C2 exon
GTATGTTCCTGGCTGATCTGATTGAGAAGTACTTTGTGTCACCAACATTGTTCAGGGTAATCCGTCTGGCTCGAATTGGACGTATTTTGCGTCTGATCAAAGGAGCAAAGGGCATTCGGACTTTACTGTTTGCCTTGATGATGTCACTGCCGGCCCTGTTCAATATTGGCCTTTTGCTGTTCTTGGTTATGTTCATTTTCTCTATTTTTGGCATGTCAAACTTTGCCTACGTGAAGCGGGAGTCTGGCATAGATGACATGTATAACTTTGAAACATTTGGCAATAGCATGATCTGCCTGTTCATGATAACCACCTCAGCCGGATGGGACGGCCTTCTCGCTCCCATTCTCAACTACCCGCCAGATTGTGAGCCAACTAAAGAAAATCCAGGTACTAGTGTTAAAGGTAACTGTGGAAACCCTTCGGTGGGCATCTTCTTCTTTGTCATGTATATTATTGTCTCGTTCCTCATCGTGGTGAACATGTACATCGCCATTATTCTGGAGAACTTCAGCGTCGCGACAGAGGAGAGTGCTGACCCTCTTTGCGAGGACGACTTTGAGTCCTTCTATGAGATCTGGGAAAAGTTTGATCCTACTGCCTCCCAGTTTATCACTTTTGCCAAGCTGGGTGATTTCGCCGACACTTTGGAGCACCCACTACGTGTTCCTAAGCCCAACACTATAGAGCTGATCGCCATGGACCTGCCAATGGTGAGCGGCGACCGCATTCACTGCCTAGACATCCTGTTTGCATTCACCAAACGCGTGCTGGGTGATAGCGGCGACCTGGACATGATGCGGCAACAGATGGAGGAGCGTTTTATTGCTGCCAATCCTTCCAAAGTGTCTTTTGAGCCCATCACTACCACCCTGCGCCGCAAACAGGAGCATATGTCTGCTGGAGTCATCCAGCGTGCTTTCCGTGCCCATCTGATTCGGAAAGGCTTCATCTGCAAGCGTTTACTCAGCAGCAGCAGGCTGGAGAATGGTGGTACTAATCAGGACAAGAAAGAGGGCACACCTTCCACTGCCTCACTGCCATCCTACGACAGTGTGACCAAACCTGAGAAGGAGAAGTTGGAGGAGAGTGACAGTAAGGGCAAAAAGGGCAAAAACCAAAAAGATGTCAAGGAATCCAAGTTTTAGGAACGATGGACACTGTCTAGTTGAGACTTAAACTATCTATTCCAACAAAATGTATAGAAGAAAATTTGCAACAAAAAACACTGATATCTTTGAGCAAAACAGTTGTTTACATACAACAAATGCACCGGTGCAACAGGAAAGCAGCTTGGTTTTTACAAGATTCAATGATGACCAAACCAACTTATGAGCTTACTGTCTTACATTTTGTGCTAAGTGACCAAGATTTTACTGTTCCAACTGCGGCCAAAAGGCACTTACAAGGACAAACTAAATAACAATCCATGGCAGAAATCTTTGATAGGGACCACCTGCCAATGGACAAACTAGTACAAAGCAAGCTCATAAGATGGCTTCCTTTGCACTCACATGTGTGTGGAGTTCAGCATTCCTCCGCTACGGACATCCCGTTCAAACACTACACTGCCGAAATCCGACGGAAACCTCCCACTCATCCCAGGAGGATTCTGGGACTTTGTATTTTAACCATAGGAGAACCAATAATAATGATGTTAACTCAATCATGTGGAGTGTCTGCCGAAAAAAACAAACAAAAAAAACAGAACATTATGCAAGGGTTTTCAGTTGTTGTGATGAATATTTCACCTTATTTGATCCACAGAAAGTAGGGGAAAACGTTCAGCCCATTCATCTCGTCATCATCTCTTTGTTATACTAAAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000005775:ENSDART00000022042:26
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.196
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=PU(20.5=47.3)
A:
NA
C2:
PF0052026=Ion_trans=PD(79.0=43.3),PF0061222=IQ=WD(100=5.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCTCTTTGCGCTGCGTCATTA
R:
AATATTGAACAGGGCCGGCAG
Band lengths:
247-349
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]