RnoINT0131061 @ rn6
Intron Retention
Gene
ENSRNOG00000002104 | Scaf4
Description
SR-related CTD-associated factor 4 [Source:RGD Symbol;Acc:727896]
Coordinates
chr11:30390637-30391267:-
Coord C1 exon
chr11:30391133-30391267
Coord A exon
chr11:30390751-30391132
Coord C2 exon
chr11:30390637-30390750
Length
382 bp
Sequences
Splice sites
5' ss Seq
AACGTGAGT
5' ss Score
9.54
3' ss Seq
CTGTTCTTTGATCCCCTTAGATG
3' ss Score
9.17
Exon sequences
Seq C1 exon
TGCTGCTGGATTGTAACCACTGATTTACTTTCAGTTTGCAGCACCACACTGTGGGTGGGACAGCTGGACAAAAGGACTACTCAGCAGGATGTTGCCAGTCTCTTAGAAGAGTTTGGTCCAATTGAATCAATTAAC
Seq A exon
GTGAGTACTTATGGCTTGTAAGGTGCTGGCTAAGCAAGTGTGCTCAGTTGTCTTTGAGACTGAGGTCTTGAGCGCTCAGGTGCAGCTTCCTTCACATTCTCTGTAGTAGATGTTTCTCAGACAGCAATGTTTAAGTTAAACTACCTTTCTAGGAAAGTCTGTAACAACATTTGCATGGTTTAATTAAGACCAAATTTGAATTGCCAACATTGAACAGCACAGGTTCTTCCTGTTTCGGTGGTGGTACTGGGGTCTGAGACGTTGTTGTGCGTGTGTGCCTGTGTGCTTCAGTGCCTGGACCCTTCCTCGCACTGTAAAGCCCTGGTGAAGGAGAACGGCTGTGGCTAACTAAATCCTCTGTCCTGTTCTTTGATCCCCTTAG
Seq C2 exon
ATGATTCCTCCCAGGGGCTGCGCCTACATAGTTATGGTTCATAGGCAAGACGCATACCGTGCCCTGCAGAAACTGAGCCGAGGAAACTATAAAGTGAACCAGAAATCCATAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000002104:ENSRNOT00000002881:14
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.012 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0007617=RRM_1=PU(41.8=62.2)
A:
NA
C2:
PF0007617=RRM_1=FE(55.2=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGCTGCTGGATTGTAACCACT
R:
TCTGGTTCACTTTATAGTTTCCTCGG
Band lengths:
238-620
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]