RnoINT0131073 @ rn6
Intron Retention
Gene
ENSRNOG00000002104 | Scaf4
Description
SR-related CTD-associated factor 4 [Source:RGD Symbol;Acc:727896]
Coordinates
chr11:30401633-30402401:-
Coord C1 exon
chr11:30402266-30402401
Coord A exon
chr11:30401773-30402265
Coord C2 exon
chr11:30401633-30401772
Length
493 bp
Sequences
Splice sites
5' ss Seq
AAGGTACAG
5' ss Score
8.04
3' ss Seq
ATACCCTTTGCTTTTTTCAGGCT
3' ss Score
9.34
Exon sequences
Seq C1 exon
AGTAAAATAGTTCGTGTGCTAAATCTTTGGCAAAAAAACGGAGTGTTCAAAATTGAAATCATTCAGCCGCTTTTGGACATGGCAGCAGGAACCAGCAATGCTGCTCCAGGAGCAGAAAATGTCACCAACAATGAAG
Seq A exon
GTACAGTGACAGAAGCTCCTGCAAGTGCACTGCCTCTGCCTGCCTTCTGTCTGTGTGTCTGTCTGTGTGGTCCTGTTCCAGTTTGTTTCCTTTTGTCTTACCATATTTTCTTGTATTGTTCTTTAGCTGCCTGTTTGTTTTCAAAGGGTGTGGATTCAGATGAGAGGGAGGGAGGGAGGATAACTTGTCAGCACTTAACAAAAGCAAGCAAACAAACAGAAGAATAGTTTCTGTATGTGAAAGGTTTTGTTTCTTCGCTGGTAGAAATTCCCTTGGAAGAATTGATTTGCGTTTGGAAGGTACAGTTTTTCTTCCTGGAGTTTACTTTAGATGGGAATATGCCCTTTGTCATTTCTCATATAGTATAAGTCTTCGGTAACCACAATCAGTCCATCTTGCTGTATGTTAAACTAGGCAGAATTTTGTTTGAGCAGCAAAATTCAAAAGGCATTTTAAAGGGGAAGAAGTATGTGATACCCTTTGCTTTTTTCAG
Seq C2 exon
GCTCACCTCCACCCCCAGTAAAAGTCTCTTCTGAACTTCCACAAGCTCCCACAAACTCCATGCCTGCTGTCCCACAGCTGCCCAGCTCCGATGCCTTTGCTGCCGTGGCTCAACTGTTTCAGACAACTCAAGGCCAGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000002104:ENSRNOT00000002881:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.326 A=NA C2=0.596
Domain overlap (PFAM):
C1:
PF048188=CTD_bind=PD(24.2=34.8)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATAGTTCGTGTGCTAAATCTTTGGC
R:
CTGCTGGCCTTGAGTTGTCTG
Band lengths:
270-763
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]