GgaINT0000879 @ galGal3
Intron Retention
Gene
ENSGALG00000006060 | SCN8A
Description
NA
Coordinates
chrE22C19W28_E50C23:81841-83266:-
Coord C1 exon
chrE22C19W28_E50C23:83146-83266
Coord A exon
chrE22C19W28_E50C23:81929-83145
Coord C2 exon
chrE22C19W28_E50C23:81841-81928
Length
1217 bp
Sequences
Splice sites
5' ss Seq
CATATCCTT
5' ss Score
-20.06
3' ss Seq
TCCTTGACTTTGTTCCACAGTAT
3' ss Score
8
Exon sequences
Seq C1 exon
ACCTTTGTAGTACTAAACAGAGGGAAAACACTCTTCCGATTTAGTGCCACACCTGCCTTGTACATTTTAAGTCCTTTTAATCTGTTTAGAAGAATAGCTATTAAAATTTTGATACATTCAT
Seq A exon
ATCCTTTTTACTACCGTGGTATTTTTGTCTTTATTGGTTGAAAGATCTCTTGCCTATTGTCTTATTGCTCGATTCAATCATTATTTATTAACTACAGTTCTAGTGGAGTTGGGTTTGTTTTGAATGAAGAAGTGTGGCCCTTTAGTCAAATCCAATCAAGTAAATGTTTAATTTATGTATTCCTTGCTAAATTGTGCCTTTCTGTGTCCACTCCACCATCAATACATGGGTATTGCTAAGTTGGGCATGGTGGCCATGGGTTGATCATTGGACTGGATGATCCTAGAGGTCTTTTCTGGCATTGGTGACTCTACGAGTGGGCATTCTGGGGGTGGGTTGGGGTTGGACTTGATCTTAGAGCTCTTTTCCAGCCCTAATGACTCCATGATCCTAAGCACTGGAACAGACAGTTGTAAGATTGTGCTCTGCATGAAGAGCAGTTGAGCTTTAACTAGCTGCTGGGATGGTTAAATAGAATTAATATTTGGAGAAGGAGCCAAAGACACTTTACATGCAATTAGACACCGACTAATTTCCTGCTCCTTTGGCAACTCTTAAACCTCCTTCTAATGGGAAGGCACTTCCAAAATATTCTGCTGCTGGGCTCCAACTGCTCTGAAACATCACCTGCATGCACTATTAGGAGAGGAGGCACAGAGCAGCACTGGATGGGATGCACTGCTTTGGTGGTTTATTTTCAGAAGGTGACACTAAAACACATCTATGAAAGCACCTTCATTAGTTGCTTTAGGGGTTTCTCCTTACTGAATTCACACATCTCAAGAAGAAAAGGGTTTTCCATCTCCGGTTGCTTCAATCTCCACTAGGGAGCTGAGGCTGGGAATGGCATTTTGGTTCTGTGCTGCTCAAGAGTTTTTCCTCCTGTCTGGGGGAATGTATCAGCAGATTGTAGTTTTTGATGATACTGAACACGTAGAATTATTTGGGAATACATTTTTATTAAGGCATGTGATCTTTGCACTGCTAAGGCATGCCAGAAAGCAGAAAACAAAGAGACACAAGAGCACTGTTTGTATATATTCCCCCATTCTTATCTCCCATGACTGCAGGAAGCGTCTTGGCTGGTTGGTGTAGCACATAGGGAATAGAATGGAAATTGTTGTTGGGCTGTATTGTTATGCAGAGGTCTTTGGGAGCTGTGAGCTGATATGAAGAGCCACCCCAGTGTGCCTTTGATCCTTGACTTTGTTCCACAG
Seq C2 exon
TATTTAGCATGATCATTATGTGCACTATTTTGACCAACTGTGTATTCATGACTTTTAGTAACCCACCTGAATGGTCGAAGAATGTGGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000006060:ENSGALT00000009776:3
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:
NO
A:
NA
C2:
PF0052026=Ion_trans=PU(0.8=6.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACCTTTGTAGTACTAAACAGAGGGA
R:
TCCACATTCTTCGACCATTCAGG
Band lengths:
209-1426
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]