GgaINT1024512 @ galGal4
Intron Retention
Gene
ENSGALG00000027702 | SCN11A
Description
sodium channel, voltage gated, type XI alpha subunit [Source:HGNC Symbol;Acc:HGNC:10583]
Coordinates
chr2:5327499-5330205:+
Coord C1 exon
chr2:5327499-5327573
Coord A exon
chr2:5327574-5329950
Coord C2 exon
chr2:5329951-5330205
Length
2377 bp
Sequences
Splice sites
5' ss Seq
AAGGTACGG
5' ss Score
10.26
3' ss Seq
ATTCATTTTATTTATTTAAGGTT
3' ss Score
7.58
Exon sequences
Seq C1 exon
GGTGCCCTGAAGTCTCTCAGGACGCTCCGAGCACTGAGGCCTCTACGAGCACTGTCAAGATTTGAAGGGATAAAG
Seq A exon
GTACGGATATTGGGAGGGATACGTATGTTTTGGAATAGGTGCATTTGAAGTTTTTGTAAGATTACATCCCTATCTGGGGACTTGAAATAGCATAAAGATGGTGTAGATGGTTGTCATTTCCAAAATAATTTCATAGAAATATATAAATTCAAGTGAAAGAAGGAAATTTAATTATAGTGTGCGGATACAATGAATTATGGTGTTTATCAAAGAGACTACTTAAATATTTTCTCATGTTTCCAAAATTTCACTGCAATTTGTAGAAGAAACTTTTTTTTAATGAACTTATACATTTCTGAAGCCTGTTGCTTATTTTACTTTAGACATGGAAAACATTCATCCAATTACCCCAAACAAACTGTTACACAATGAGGATACTGTACTGTGAAAGTTGTCTTTTCTATTGATCTCCATGGCCTAAGAAGTGTAGTGACTGCAGCTCTTTTGTATTTTTTTCCTCCCTGCCTCAGACAGTAAGTTAGGAACAGGAAAAATGTTAAATAATTCATTGCTTCAGCTGAAACTATTCACTTTTTGTAGCTCCTTTCCATATTTCCCCTTCTTTAAACTGCTGTGATTGTATCAACTTATCTTGACAGGTATCTCTGGGTAGGGTCCCTGTTCTGGGTGAACATGACAGAGAGCAATCCTTTGCATAATTAAATTGGGTGGGATTTTCTTAACAGAGGAGGAGATTCTTCTTATTTAACCTTAGAAACTTCTCTGAGTGGACTATCTGGAGCATTTAAAGCCAATGGGAAGAAATAAAATGTGATGTGATGTAATATAAGTTATCTGACCTATGTTAAATTACAGAATGTGATGAGATGCTAAAGTAAGGCCCCAGGATGGATATCGAGCAAATTCTCCTTACAAATATGAAGGACAAGAAATCAGATGGAAACAACCATTGTGAATTTATGAAAGTTGTCTTGGTTGTCTTCTATGGCAAGATGTCTGAGGGAGGGAAAAGTTAACCATGGTCTCATATGGAGTTTAAATATAGTTCTTTATAGATGAACTATAAAGAAAATTGGCTGAACTGCTAAGTTCAATGTGCAGAATTACATTCAATCGCTAGACTGTCATTGATGGCTCAGTCCTGGGGTCTGTACTATTTAAAGCTTCGTTGGCAATCTGAATAATGTGGCTGCAGAGGTGAAGGGTATAGCTTGTTCTGTCTGGGGAAGAGAAGATTAAAAGGAGGATCCATTGAGATATAATTAGGTAACAGATCTAATTGTTGCCTTTAATTACCTAAGTTACAGGAAATTGAACTAAAGTTTTCTGATAGGACTGCATTGGGGAGATGAGAAAGAATGAGTTGGCAGTGTCTGATATTCCTATTAAATAAAATAATTGTCATGCAGATGTAATTGGGAGCCTAGAAAGGTTGTGGAATCCCCATCCTTGGAAAAAAATCAGAACGTGATTGGTTAAGACCCTGAACAACGTAATCTCGGTTGGAACAGCTAATGTGTGTTCCTAGTGTATTACATACTTCTAGTGAATATTATCCAAGGCCAAGATAAAGTTCTTGGAATTGTCTCATAATTCTAGCAGTGATCTATTTCCAGAGAACTCTTCATTATGCTCCACCACAAAATGACAAAAAAAGGGTGAAAAGAAATTGAAGATAGTCCCAGAATTCCTACTGGCAACAACCACGGTCCTTCTTGTCAGCATTAATGTGGGGGATTCCTGAATGTGAGTTCTTGTTGCTGCTTGAGACAGATCCACCAATGTTACCAGCAGAGACACTAAAAACTGGAATCTCTTTTTCAGTGGTATCATTTCTGTAAGAGATCTAATGCATACCACAGTCTTGCATTCACCTTGTCCTCAAGCAAACCTAAATGAAGGAAGAGTGCTAACCAAAAAAATTCAGTCACCTTGGAAACCTAACTATTTTGCTTCTTGTACTGTTTGCAGCCAGTTCCTGATGGTTATCATGTGAGGCTCATTTTGTTCTGGAGGTCAAGCTCTTGTTCTCTTACAAAACTTATCCAAGATAAATGAGGATTATTTATGGCATGGTAGTATATGAGGACAACCTGTTCTCCTATACCTGCTTTTAGGTTCCAGAGCCACTATAGACTCTTTTTTTTTTTTTTTTTTAATGTATGTCTTTTACTCAAGGATAATTCTAGTTGCCATCTGTTCTGCTTCCTCAGAATGACAAGATAGATAGCACAGGATGTTAAGACAAGCTTGTCGGCTGAGGGTTGGCTTTAAATATGTCTTCTGCTAGTTTTTCTGTGAGTGAGAAGCTGCAATAGATGCCGAAGAAAAAAATGAATGTTTTGGGGGGAGAGGGAAAGTGTTCTATTGAATGTGAAAAGTTATTCTTTCTTTTCATTCATTTTATTTATTTAAG
Seq C2 exon
GTTGTTGTGAATGCACTTTTGGGAGCTATCCCCTCGATCTTGAACGTTTTACTCGTCTGTGTTGTCTTCTGGCTCCTGTTTAACATTGTAGGAGTAAAACTACTTGGACAAAAATTTTGGAAATGCGTGCTTAAGACAGGAGATAACAGAGAAGTTCAGAACATAAATGACTGTAGGAATTATGGTGGAAAATGGACAAACAGTTATGTAAATTTTGATCATGTTGGGATGGGATACTTGGCTCTTCTCCAGGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000027702:ENSGALT00000042757:20
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=FE(10.9=100)
A:
NA
C2:
PF0052026=Ion_trans=FE(38.2=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]