GgaINT0000888 @ galGal3
Intron Retention
Gene
ENSGALG00000006060 | SCN8A
Description
NA
Coordinates
chrE22C19W28_E50C23:69636-71965:-
Coord C1 exon
chrE22C19W28_E50C23:71573-71965
Coord A exon
chrE22C19W28_E50C23:69772-71572
Coord C2 exon
chrE22C19W28_E50C23:69636-69771
Length
1801 bp
Sequences
Splice sites
5' ss Seq
AGTGTAAGG
5' ss Score
5.2
3' ss Seq
TCTGCATATGAATGTTGCAGGGT
3' ss Score
5.24
Exon sequences
Seq C1 exon
TCTCTCCTCAGCATCCCGGGCTCCCCTTTCCTCTCCCGACACAACAGCAAGAGCAGCATCTTCAGCTACAAGGGCCGATTCCGCGACCCGGGCTCGGAGAACGAATTCGCCGACGACGAACACAGCACGGTGGAGGAGAGCGAAGGCCGCAGGGATTCCCTCTTCATCCCCATCCGCGGCCGCGACCGACGGAGCAGCTACAGCGGATACAGCGGCTACAGCCAGGGCAGCCGCTCCTCGCGGATATTCCCCAACCTCCGCCGCAACATCAAGAGGAACAGCACGGTGGATTGCAACGGCGTCGTGTCCCTCATCGGCGGCCCGCCTTCCAGCATGCCCGGCGGGCGCCTTCTGCCTGAGGTGAAAATAGATAAGGCAGCTCACGATGACAGT
Seq A exon
GTAAGGAGGCTGATGTGTAGCTAGTGTAGGCATGGCGGCCTTGTCGTCCTCCTCTACTTCCCCGTATGCCGCCCTCCGAGCCGTCTGGGCGCCCCGATGCGTTGAGTGTTGGTTTGATTGACCGCAGGCGGCAGCATCTCTTTTGGGTTCCAATCCTCACGCTTCGGCTTTCCCCTTTCTTCCCTTAATCAGACTTAATGACCCCACCTCCTTTCTCCCATCTGCCAAAAAAAGGGCTTGGAATGTAACGACCCTCAGTACGTCAGGGTGCTTCTCATGGAGCTTTTTTGGATAGGGGTCAAACAAAACTTCTTGCAAATGCTCTGCACAGTAAGATAAACCTGGGAGCTTAAAGGGAAGTAGAGACAGTCATTTACCCTCACTAAAAGGCCTCCTTTCTTCAGAGGAAATGGCGGTACCTTGGAGTATCAACACAGAACTTGTCTTACCAGAGAATAGATTGGGTTGGAAAAGACCTCAAAGATCATGGAAGCGTGGAATGGGTTGGGCTGGAAGAGACCTTAAAGAACATCCAGTTCCAACCCCTTCCATGGACTGGGTTGCCAACCACTAAGCCAGGCACTTGGTCAGGTTGCCCACCTTGAAGTATGTCTAGGGAAATACCTGAGGGATTCTACTAGTTTCAGAGCTGTTATGGTTTCAAAGGCTTGATTTTCCAAGGGAGGCTGTTAATATAACAAGAAACTTCTTTAATTTTAATTTTTGAGTTTTCCTGGGTTTCGGTTTTTCTTCAATTAGTTGACTGAATTGGTATTGAGTAACCTTCTAAGTGTATCAACAACAATTAGCTCAGTAAGGGAGGGCTGATGAGAATACTGAGAAGATCAAAACAATTATTTCTGAGCAAAGTCTGGTTACCACGCCTATAAATTCCAAGCAATTTTTAAAATCTGTTTCAGTTCTTGCAACCTAATTGACCCTAATGAGTTATGTTAAGCATTGGTTGCTACCACTTTTATTTTTCTTCCCCCATTAGCATGTTAATACAACGTTTTGCTTCAGTATTTAATTATCTTTTTAACACAGCATGAGCGTGGTAGGAATCGTAACCCGCATGATGCATGCGTAAAGGAGAAAGTTTTAGTTGGCAATCCAAGAACTGCTTTTATTGCTGTTTTCAGGTGCAGATTTCGAAATGAATGTCAATTCCATGAAATATTCCAGTGGTAAACTGTAACAGTTGCCTCTAATGAGGCTGGGGTTGAATTCTCACTGACCAGACAGGATGAAGCATGGGCTTGTTAGGAGTCATTGCTTGCCTGCTGTTAGTAGTAGAGTAGAAACTGCTTTGCGCTGTAGCAGGGCTCATTAGAAATGATTCTTAAGATATAATCCTCCCTTTGCCTGAGGCTGCAAAGCAATGATATGAGCAGAAATGAGGGCTTGAGTTTTGAATTGACCACTTATGTCGTATCATCATCTTCATCATAGAATGGGTTGAGTTGGAAGGGACCTCGAAGACCATAGAACCATAGGATGGTTGGGTTGGAAGGGACAACAGAGATATCCAGTCCCAACTCCCTTGCCATGGGCAAGGTTGCTACCCACTAGATCAGGTGGCCCAGGGTCCCATACAGGCTGGCCTTGAGCACATCCAGGATTGGGGCATCCACTGCTTCTCTGGACTGCCTGTAGGAAAGTGGAAAGACTAGCAATAATTTAAGATATTTGTTGATTTTTTTTTTCTCTCTTGGCTATACCTTGCATATTCCTAGGCTGGTAGCACGTGAAACACCGGGAAGATGAAAAGCTCATATTAATCTGCATATGAATGTTGCAG
Seq C2 exon
GGTACGACTGAAATTGAAATTAAGAAGAAACCTGGTGGGTCTCTCTTGGTCTCGATGGATCAGGTGAACGCCTCCTATGGAAGGAAGGATCGTACCAACAGCGTGATGACCGGCTTGACCAACACCCTCGTTGAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000006060:ENSGALT00000009776:12
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.523 A=NA C2=0.101
Domain overlap (PFAM):
C1:
PF119333=DUF3451=FE(55.1=100)
A:
NA
C2:
PF119333=DUF3451=PD(15.3=78.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTCCCTCTTCATCCCCATCCG
R:
CACGCTGTTGGTACGATCCTT
Band lengths:
343-2144
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]