RnoINT0145624 @ rn6
Intron Retention
Gene
ENSRNOG00000015420 | Stxbp1
Description
syntaxin binding protein 1 [Source:RGD Symbol;Acc:3785]
Coordinates
chr3:11831543-11833279:-
Coord C1 exon
chr3:11833194-11833279
Coord A exon
chr3:11831698-11833193
Coord C2 exon
chr3:11831543-11831697
Length
1496 bp
Sequences
Splice sites
5' ss Seq
GAGGTAGGT
5' ss Score
9.65
3' ss Seq
GTGTGTGCTCTCTCCCTCAGTGC
3' ss Score
11.39
Exon sequences
Seq C1 exon
GACACCATTGAAGACAAACTGGATACAAAGCACTACCCATACATCTCTACCCGCTCTTCCGCATCCTTCAGCACCACTGCTGTGAG
Seq A exon
GTAGGTCAGTGTGGGGGTGCAGGCTGTGTGGCTCTCCCTTTGGCTCCAAGCCTTCAAGAACTCCCTCCCTCCCTTTCCCTTCATGCACCCTCAGCCCTTGCTCACCCTGGAACAAGCCAGGCCTACTTGTATAGCCAGGTCAGCTGCACACCCTTTAATCTGTAGGTCTCTCTTGAGTGTTCCTCTTCTCTAACTACCTGCTGAGTCTTGGAAGGCCAGCATCCATTCATAGCAGTTCTCCTCATAGCCGCCTGACGTGGATGGCCCAGGCCAGCAGACAGGCATTGGGACTGTGTCTCTAGAGCTGGAGCTGTCGGAGCTGCAGAGAAGACAATCACTGTGCTTCCCAGGGCTGACTCCTTCTTTGTTTTGTTTGGGGGTTGTTAATTTATTTGTTTTGTTGGGTTTTGTTTTCTTTTCTGAGGCCGGGTTGCCCTGGATGACCTGGAACTCACTCTGGAAACCAGGCTGGCCTTAAACTCAGAGAGATCCTCCTGCCTCTGCCTCCTAGCTGCTGGGACTAGATGTGTTCACCACCGCCTGGCTTCTTTTGTTATTTTTTTGAGATAGGATCTCTGTGTAGCTCTGGCTGTCCTGGAACTCACTATGCTGACCAGCCTGGCCTTGAACCCACAGAGATCCACCGGTAATATCTGCCTCCCAAGGCTGGATTGAAGGTGTGCTCCACCATGACCAGAAACACTCTAGAGTGCCAGACGCTGTCCGATGACTCTGGCTTTTCTTCTTTCTGTTTTCACCGTTGGCCTTTGACCTGGGCAGGTCTGCAGTGGCGCCTGTGGCATTGGCTTCCCCTTGTATGGCAGCCTGGGTGAAAAAGTCATTGCCAGCTGGGCAGTAAAATACAGCTGGCTCCAAGTGCTGCCCTTGCCAGGCCCGAGGGGCACGGGAGAGACGGAGTGCCCAGCTGCGCCCGGGCCTCCATGAGGAAGCAGGGTGGAGCATTCTGGTGTCCAGAGGGGATTCGCTTCCTCTTTCATGTTTTTCATTGTCCCGGCCTGTGTCTCAGTCCAGGCCCCTACTAAGGAAGTGCAGGGACAGAGAGACCTGGCAGCAAAGGCTCAGCTGCTCTTTACCTCCCTGGTAATGCCTGAGCAGTGCCGTGCGGCCCTGGTTCCGTCACCTGGCATTCAGCATCTCCCATCCTGTTAGACTGTGACTTCTGAGTAACGAGTGCTGTCTGTCCCTGGAGATACAGTACCAGGAAGCCTGGCCCCCACAGAGCTTCTTTACATGTGATCAGTGTGCAGGCTTGATGGGGCCCCTCTGCCTCTGCACACTGCAAGCCCAGACATCTGAATGAGAGCCATCCAGGCAGAGCTGCTGTGAGACAAGCCAGTCTGGTGCCTGAGTATTCATGAGAGCGTGGCAGTCACAGCTCAGGCACCTGCAGTGCAGCTCAGCTTGGCCAGCATTGATGAGCAGTGCTGCTCTGTGAGGCCCTGGTACGAGTCATCTGTGTGTGCTCTCTCCCTCAG
Seq C2 exon
TGCCCGCTATGGACATTGGCACAAGAATAAGGCCCCCGGGGAGTACCGCAGCGGCCCCCGCCTCATTATTTTCATCCTTGGGGGCGTGAGCCTGAATGAGATGCGCTGTGCCTACGAAGTGACGCAGGCCAACGGCAAGTGGGAAGTGCTCATAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000015420:ENSRNOT00000021178:17
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=0.019
Domain overlap (PFAM):
C1:
PF0099518=Sec1=FE(5.0=100)
A:
NA
C2:
PF0099518=Sec1=FE(9.4=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GACACCATTGAAGACAAACTGGA
R:
TATGAGCACTTCCCACTTGCC
Band lengths:
240-1736
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]