DreINT0018603 @ danRer10
Intron Retention
Gene
ENSDARG00000016188 | SBNO2 (1 of 2)
Description
strawberry notch homolog 2 (Drosophila) [Source:HGNC Symbol;Acc:HGNC:29158]
Coordinates
chr22:17684355-17686223:-
Coord C1 exon
chr22:17686090-17686223
Coord A exon
chr22:17684446-17686089
Coord C2 exon
chr22:17684355-17684445
Length
1644 bp
Sequences
Splice sites
5' ss Seq
ATGGTGAGA
5' ss Score
7.23
3' ss Seq
ATTGCTGATCTGTCCTGCAGGTT
3' ss Score
10.17
Exon sequences
Seq C1 exon
CAACATGAAGTGATTCTGCAGAACAGCCAGCGGGCAGGTTTCCTCATCGGTGATGGCGCTGGTGTGGGCAAAGGCCGGACAGTGGCTGGCATCATTCTAGAAAACAACTTAAAGGGAAGGAAAAAAGCACTATG
Seq A exon
GTGAGAAGCATCGACATCCAGCACAACTGACCGACTTTACTGGCACACTCATAACATGATAATCCTTCATAAGATCACTGTACACATAAACACATCTATAATTATTCATACTTATTTTAAGCATTCTGTTTTCCTGGATCTTATGCTGATTTTGCACACTTTTTTTGCTTTGTTTATTTACATGCGCAAGCGTGAAATGTTACAGAAAAAACATTTTTACTGTGGAAATAAACACTATATAAGAAATATAAGTCATTGTAGAATTATTGGCTAGATTTATTTATTCAAAAATACAGTAAATGTGTAAAACTGTAAAATTGTGGACTGTTATTACAATTTAAACTGTTCTTGTTGAATGTACTTATAAATGTTATTTATTCCTGCTATTTACAGCATCATTCCTCCATTCCTCAGTGTCAGATGATCCTTCAGAAGTCATACTTTGTTCTGTTATGATCAATTATTATCGGTACTCAATCACTAATAGTAAATCTTCTAATTATCAATGTAAAAAAAACTTTTTTCTTTTTTTGCTGCTTCAAAAATATGAGGATAGGATCAGACACTGAAAACAATTTAGGAAAATTAAGCTTTAAATCGCAGGAATAAATAACATTATAAAACAAATTCACTGAGAGAACAGTCAGTGAGTATGTTTACATTAACAACTATAATTCAATTTTAATATGATTAAGACAATACTCTGATTAAGAATCTACCATGTAAACAGCGATTTTGATGACCTTAATTTAACTAAAGTCAAAATCAAACTAAACAGAAATTGAATTAAGACATGTGAAGCATTATTAAAGTGCAGTTACAGACATTTAAACACCTTAAACAAACTATTACTGTTGTGTAGGATTTTGGCCGCATTTTGCTACAGTCTACACACATGGCTGTTTGACACTATTCTCTGCACCTACAGAGGCAGTGAAGGACCACAGACACTTGCATCGTGAAATACAGAGTTTCTTTTTCCCATACAGTGTGCGGTATCAAATTCCATTAAAACAAGACTCTTCCATCAATTCAAACTCACATCCAATATCTCATTTGTCACGGGGGCATGCATGAAATATTCCTGAATGAAAGTGTGAAAGTGCCAAACTGCAGTTAAAGTTTACAAATCAAAAATGAAACAAACGAAATTACATGAAACTCCGGAGGTTAATCTAATTATGTGCTATAACGTGTGAAATGGGATCATGAAAGGAACGACAAAAGGATTAAGACAAGTAATTCAATTACTGATGTCCTTGTAAATGTAGTCAGTGTTAAAATGCACTGTTACTGTATTTACTGTTTTTTCTAGGTGAGCAAAAGCGATTTCTTGTAAAAGCTGTACAAATCTTTTTAAAGCATTAATGTAGCTACAGCCAAAATACTGAATATAGAGAATAATAAATGAGCTGTAAGTGACATGTTCAGTAGGAATATTGTTGTTTAGTTGTTGTTGTTTTTTTTGTAATTTATTGACAACTGACAAATGAAATACCCAAATTATTAAGTTTTGATTTAACTACAGCGAGCACATTTTGCTTACATTTCCATTTCTTAATAAACCGGTACAAATGGTTATTTGTGAGCTGTGCAAGTCAACATGCTCATCTAATTTTTATTAATTGCTGATCTGTCCTGCAG
Seq C2 exon
GTTCAGCGTCTCCAATGACCTGAAGTATGACGCAGAGAGAGATCTCCAAGACATCGGTGCAGTCAGTATACGAGTGCACGCCTTGAATAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000016188:ENSDART00000137984:9
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:
PF138721=AAA_34=FE(14.8=100)
A:
NA
C2:
PF138721=AAA_34=FE(10.1=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:
CATGAAGTGATTCTGCAGAACAGC
R:
CTTATTCAAGGCGTGCACTCG
Band lengths:
222-1866
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]