GgaINT0000902 @ galGal3
Intron Retention
Gene
ENSGALG00000006060 | SCN8A
Description
NA
Coordinates
chrE22C19W28_E50C23:51092-53007:-
Coord C1 exon
chrE22C19W28_E50C23:52737-53007
Coord A exon
chrE22C19W28_E50C23:52240-52736
Coord C2 exon
chrE22C19W28_E50C23:51092-52239
Length
497 bp
Sequences
Splice sites
5' ss Seq
TGGGTAAGT
5' ss Score
10.24
3' ss Seq
ATCCTTTTCTTCTCCTTCAGGAA
3' ss Score
11.75
Exon sequences
Seq C1 exon
AACCGCATTCAGGGAGCTGTCTTTGACTTTGTCACTCAGCAAGCATTCGACATCGTCATCATGATGCTCATCTGCCTCAACATGGTGACCATGATGGTGGAGACGGACACACAGAGCAAGCAGATGGAGGACATCCTCTACTGGATCAACCTGGTGTTCGTCATCTTCTTCACCTGCGAGTGTGTGCTGAAGATGTTCGCCTTGCGGCACTACTACTTCACCATTGGGTGGAACATCTTTGACTTCGTTGTTGTGATTCTGTCCATTGTGG
Seq A exon
GTAAGTGCAACACCCATTTTTCTTTCTTGGTGTTTGCAGAGAAGGTGCATTCAAAGAGGATGTGTAGGTACCCGGACTTCTGGCTTCTCTTTTCACCCATGGCAGAGTTTGGCAGCTCAAAGGCCCAACTTGCCTGCCTTCCTCCCTCTGTCCTGGCGTTCATTTCCAGTTGTATGGAGTAAAACACTTGACAATTACTCCCCGTATCTTTAAAAGCAGACTTTTTACTCACCTCCTTGGAATGTTATAATGCTTACCAACCACTGAAAATAGCATTGCAGCACTTCCTACATCAGCATGTGATTTGCACTCCTGCTTTCTGTTTGGTTGGATGTTGAATCGAGTGGTTTCCTCCAATAAATTTTTCTTTTTAGTGGCTAATCTGTGAGATGCCTGTAACTTCACAAATACAAGTTATACAAACACAACTTAAGGGTCATTTAAGCCTGGCTGACCAAGGCATGCTGACAAAAGCCAATCCTTTTCTTCTCCTTCAG
Seq C2 exon
GAATGTTCCTGGCTGAAATCATCGAGAAGTATTTTGTATCCCCCACTCTCTTCCGAGTCATCCGCCTGGCTCGTATTGGACGTATCCTGCGTTTGATCAAAGGAGCCAAAGGGATCCGCACCTTGCTTTTTGCCTTAATGATGTCTTTGCCTGCCTTGTTCAACATCGGCCTCTTGCTGTTCCTGGTCATGTTCATCTTCTCCATCTTCGGCATGTCCAACTTTGCCTACGTCAAGCATGAGGCTGGCATCGATGACATGTTCAACTTTGAGACCTTTGGCAACAGCATGATCTGCTTGTTCCAGATCACGACGTCGGCCGGCTGGGATGGCCTCCTGCTGCCCATCCTAAACCGGCCTCCAGACTGCGACCTGGACAAGGAGCATCCCGGGAGCGGCTTTAAGGGGGACTGCGGGAACCCCTCAGTGGGGATATTTTTCTTTGTGAGCTACATCATCATCTCCTTCCTGATCGTGGTCAACATGTACATCGCCATCATCCTGGAGAACTTCAGCGTGGCGACGGAAGAGAGCGCAGACCCGTTGAGCGAGGACGACTTCGAGACCTTCTATGAGATCTGGGAGAAGTTCGACCCCGACGCCACGCAGTTCATAGAGTACAGCAAGCTGGCGGACTTTGCAGATGCTTTGGAACATCCTCTGCGCGTCCCAAAGCCCAACACCATCGAACTCATCGCCATGGACCTCCCTATGGTAAGTGGAGACAGGATCCACTGTTTAGACATCCTGTTTGCCTTCACCAAACGCGTCCTGGGGGACAGCGGAGAGCTGGATATACTGAGACAACAGATGGAGGAAAGGTTTGTGGCTTCCAACCCTTCCAAAGTGTCTTACGAGCCCATCACCACCACGCTGCGGCGCAAGCAGGAGGAGGTCTCGGCCGTGGTGTTGCAGAGGGCTTACAGGTCGCGGTTGGCGAGGCGGGGGTTCATCAGCCGAAGACCCCTCCCCACCAAAATGGAAAATGGTGGAACGAACAGGGAGAAGAAGGAAGGGACGCCCTCCACTGCGTCGCTGCCGTCCTACGACAGCGTCACCAAACCTGAGAAGGAGAAGCAGCAGCGGGCGGAGGAGGGAAGACGGGAACGGGCAAAAAGGCAAAAAGATGTCAGGGAATCCAAGTGTTGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000006060:ENSGALT00000009776:26
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.199
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
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CACAGAGCAAGCAGATGGAGG
R:
GAACAGCAAGAGGCCGATGTT
Band lengths:
344-841
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]