RnoINT0145657 @ rn6
Intron Retention
Gene
ENSRNOG00000020392 | Stxbp3
Description
syntaxin binding protein 3 [Source:RGD Symbol;Acc:619968]
Coordinates
chr2:211603335-211604107:-
Coord C1 exon
chr2:211603969-211604107
Coord A exon
chr2:211603442-211603968
Coord C2 exon
chr2:211603335-211603441
Length
527 bp
Sequences
Splice sites
5' ss Seq
ATGGTAATG
5' ss Score
5.46
3' ss Seq
CTCCTATCTCACTTCCTAAGGAA
3' ss Score
7.07
Exon sequences
Seq C1 exon
GACCTGGCACTTGGAACAGATGCGGAAGGCCAGCGGGTAAAGGACTCCATGCTGGTGCTCCTCCCAGTGCTGCTCAACAAAAACCACGACAACTGCGACAAAATACGGGCAGTCTTGCTCTACATCTTCGGTGTTAATG
Seq A exon
GTAATGGAGTGCCTGCTTGGCTCTAGGACAGTACTAAAGTCCTGACTCACTTTACGTGTAGTTGCTACCTGTAATTTATGTGTGTGGTAGGGATGTGTCACAGACTGACTGGAGGTGATTCTGTATTCAGATTATAGCACCACAGACACTGGCCAAGTCCCCACATGGTATCTTGATCTCGCAGTTTGGGTTACATTTTGAGTTTCCACTTTTTCTTCACCATGAGGGTTCCAGAGATTAAGCCCAGGCTGTTGGTGTTGGCAGCAAGTGCCCTTAGCCTCTGAGCCCTTTCCTACCCCTCACGTCATAGTTTAATAACGAGCTTCTTACTACTCAATGTAAGGGAGTTGTGGGGACCTCAAAAGTAAATGCCTAAGTAAGGTAGAGACAAAGGAAATTCCTGAGAAACTGAGAGAAGCCTGAGGGTTATAGCTTTCCCTTAAGCTTTAGTCCCTGTAATAAGAACTCAGTCCTAGAAGTAGTCACACAAGCAGGTGTCTGACCACACTCCTATCTCACTTCCTAAG
Seq C2 exon
GAACCACTGAAGAAAACCTGGACAGACTGATCCACAATGTAAAGATAGAAGATGACAGTGATATGATTCGGAACTGGAGTCACCTCGGTGTTCCCATTGTTCCCCCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000020392:ENSRNOT00000027666:14
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.043 A=NA C2=0.083
Domain overlap (PFAM):
C1:
PF0099518=Sec1=FE(8.4=100)
A:
NA
C2:
PF0099518=Sec1=FE(6.4=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:
ACCTGGCACTTGGAACAGATG
R:
AGGTGACTCCAGTTCCGAATCA
Band lengths:
223-750
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]