GgaINT1024543 @ galGal4
Intron Retention
Gene
ENSGALG00000000252 | SCN4A
Description
sodium channel, voltage gated, type IV alpha subunit [Source:HGNC Symbol;Acc:HGNC:10591]
Coordinates
chr27:1636890-1640060:-
Coord C1 exon
chr27:1639632-1640060
Coord A exon
chr27:1637020-1639631
Coord C2 exon
chr27:1636890-1637019
Length
2612 bp
Sequences
Splice sites
5' ss Seq
AAGGTGGGT
5' ss Score
8.23
3' ss Seq
AATCCCCCCTCCTGTTGCAGAAC
3' ss Score
10.7
Exon sequences
Seq C1 exon
GTGCTCAACCTGTTCTTGGCTTTGCTGCTGAGCTCCTTCAGCGCCGACAGCCTGGCGGCCTCTGATGATGATGGTGAGATGAACAACCTGCAGATCGCCATCGGCCGGATCACCAGGGGCATCGACTTCGTGAAGTCTTCTGTCCTCATGCTGATCCGGAGGCTGTGGAAGGGCAAAAAGGTGGCCCCGGAGGAAGAGCAGGAGCCCAGCAAAGGGGACAACTCCGTGCTGAACCATGTGGATAGCAGCCCGGATCCCAAGCCAGATTACATGGACGGAGTTGCAGGGAAGGAATATTTGTTGATGGACGAGTTGGACCACATGAATTTCATCAACAATCCCAACCTGACTGTGCAGGTCCCCATCGCCTCAGAGGAGTCCGACCTCTACGAGGAGACGAGCACTCAGTCTGACACTGAGGATGCCAAG
Seq A exon
GTGGGTTGCAGGGCTTTTCAGCCCCTGAACAATACTATTTGGGGTTACTTTTAGCTTTTCCACAATGTGGACCAAACTTGGGGTGTTTCAGCAAAAAATGACTCTGTTTCCCCCCCATGAGATGGGGGTCCAAGCAGAAGTTTGGATCAGGATATGGGGTTTTTGCTAACGCCTGCACCACCAGGCCAGTGCACTCCTTTTGGGGTTAAAGATGTTCCAGAGGAACTTGATGCCAGGAAATCTGCTGATGGCACTAACATTGGATCCACTGCTAATGCCTCCAAAAGCAGCATGGGGGAGGGAGGGCACGGAACCAGATGGACGGGCTTAGCACGAGCAAACATGAAGCGATGGATTTTGGATCCAAAGCTGACAAGACAGCTGATGTCGACTGCATCGGGTCAGGGCTCATGGGACACTGATCTGTGAGAATGAGAGGGAGAGGAGATGAGAAATGCAGAAAAACAATAGCAGGCACTCTAAGGAGGATGGTGATGGGATGGGATGTTGCTGCTAGCCATGGGGTTGCATCAAGAATATGGAGAAATGTAGGGCTGTGGGATTGCATATATTCAGGAAGGGAGAGCAGGGATGTGATGCTAATGCCCACATAGCCACTATGGGAGGACATGTCCAGCCTGGTCCATGCAGTCCTAAGGCCCTCAGTTCCTTTCTCATCCCATCATCTGTGCTGGATTGAGTGGAGAAATTCCATCAGTTATGGCCAACAGGGTGGAGGAGCATCTTCCCAGAAGGATGGGATGGGCTGGCAGCCATTGCATGAGATTCCTGCCTAGTAATTAGAAACGAGGTGTTAATTGATAGCAGCTCTGAGAAGCCTGCTGCTTGCTCACTGAGTTCGCATGCCGTTGATTAGCTCCAGATGGAGCCAAAGCCTTGCGCTGGGAACACGGTGACAAAGACAAGCTGGGAGATTTCTCTGGATGAGCTGCTCAGAAAATGCTGACAAACACTCTTCCCTTTAACAGCAGCTGCCTGCTGAGACCACACCACCAAATGTGCCCCGGGCACAGGGTGCTGTGGGGCTCCTGGCTTACAGCACTGTTTCCCAGCCTCCTGGTGGTTCTGCCCGCCATGTGTCCTGGAGGCGGGTGGTTTCCATCTGTCCTCCCCCAGGGTCACAGCTTGCATGGCTCCCAGCTGAGCTCTCCTAATCCCCCTGCCCCTCCTCTCCTCCCAAGGACCCAGCAGGGAGCTGCCCCCAAAGAAATGCCTTCACCCAACGGCATGCTGTGGTCGTGGGGCTGTAGGCAGTGATGATGCCCCATATTACCCCCATCTTGGGGTCTTCCCTGGCCTGCAGGAGGACGGAGCACCTCCTTTAGGCACCACCAACCTCAGGGCAGGATGATCTCCTTCCATGCAAGCTGACACCATCCTGCATTCATTCCTCCCTATGAGAACCCCATCCAAGATCTCCTGATTGCTCCCATTTGGATGGGCGGGTCTGGAAATTTGCTCCTCCTTCTCTAAAAGCCAGAAAAAAAGTAATAATAATTAAGAGGTAAAACAGTCCCAGGAGCGTGCCAGGGTTTTCTCTCATTATCAGCCCCTTCAGCCTTGCTGAGTGGTGTCTGGGAAGGCAGCCAAGCTGAGCGATGCAGGGAGAGCTATTTGGGACACCGGTTTTGAACTTGGGTGAACCTCAGCCTACAAGCCCTGTGAGCCAGCAGAGTGCCACGGTGGCCAACCGGGCTTCTGCTGGTCTAATTATGCCATAGGGTGATTAGAAGTGCATTCATTAGGGCACATGGAGATGGGGGTGGTGATGGGATGGGAGGAAGGATGAGGACAGTAGCCCCTCTGAAGCCAGATGTAAAGCAAAGACTGTCCAACTCCACGTATCTGTGATGCCCCAAGGTTTGCAGCCCTCATTATTCAATAGCTTTTCTCGGGGCTGTTTTCCCTGGAAAGAGATTCAGAGCAGCATCCAAGCAAAGGGCTCCCAACCCTTTGGGAACGGCTCCTGCCATCATATCAACTTGGGTGGACCAGTCCATCATAAAACCCCAACGGCAGATGACAGCTCCATCCTACTCACATAAAACCCCAACCTCAAATAATTCCTTTCTCTTTATGTTGGATTTAAATCGACTGCAAGGAGGGACCTGTGGTTTTGGGAACCAGCCAAGAGCTGGAAAGCTTTAGGAATATTGCCATGATAAAGAGGAAATGTGTAGAAATGGAATCAGAGACACCTGAGGATTAATTACTGGCAGTATCTCCTGAAAAGCACCCCACATTCCCTCAGCTTTCTAATTTCTTGTGTGTTTTGCCCCCATCAGGAGAAGGGCTGATGCCTGCACTGGCAGTACAGTGCGTTGGCTGGAGATGGTCAAAAACAAAAAATCCAGTGGCCAACACAGGCACTGTGTGGTTGTTTCCACACCAGAGGATCCAGTAGGTCTGTTCTTTCCATTGAGAAAGTCTTGATGGGGCCTCTCCGTGGGGCTCACCCCCCTTGGGAGGAAAGTTCAAAGCCATACATGAGCATTCCCTACAAAAAGTTTGTTCCCAACTCATCTCCTGTGGAGCATCCCCTGGCCCTGCAGCACCACCCTGACCATCCTGAATCCCCCCTCCTGTTGCAG
Seq C2 exon
AACCCCCTTTCCAGTGACAACGCCTCATCCCTGTGCAGCACTGTGGACTACAAACCACCGCTGCCCGAGGAGGAGGAGGTGGCCGAAGAGGCTGAAGAGAGCAATGAGCCCGAGGAGTGCTTCACTGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000000252:ENSGALT00000040680:19
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.399 A=NA C2=0.591
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=PD(4.2=5.6),PF065128=Na_trans_assoc=PU(57.2=83.2)
A:
NA
C2:
PF065128=Na_trans_assoc=FE(20.7=100)
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:
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]