RnoINT0087604 @ rn6
Intron Retention
Gene
ENSRNOG00000020871 | Ltbp4
Description
latent transforming growth factor beta binding protein 4 [Source:RGD Symbol;Acc:1307033]
Coordinates
chr1:84131996-84132342:-
Coord C1 exon
chr1:84132211-84132342
Coord A exon
chr1:84132122-84132210
Coord C2 exon
chr1:84131996-84132121
Length
89 bp
Sequences
Splice sites
5' ss Seq
AGGGTGGGT
5' ss Score
5.37
3' ss Seq
CGGCCTGCTGGTGCTTGCAGATG
3' ss Score
8.13
Exon sequences
Seq C1 exon
ACGTGGACGAGTGCCGAGAATATGGCTCTGCGATTTGCGGCGCCCAGCGCTGTGAGAACACCCCTGGCTCCTACCGATGCACGCCAGCCTGCGACCCTGGCTATCAACCTACTCCAGGGGGCGGGTGCCAGG
Seq A exon
GTGGGTGTTCATAGGGTAGTAGCGGGGAAGGGGGAAGGGGTGAGAGGTTTAGAAATGACCTTACTGAAACGGCCTGCTGGTGCTTGCAG
Seq C2 exon
ATGTGGATGAGTGCCGGAACCGGTCTTTCTGCGGTGCCCATGCTATGTGCCAGAATCTGCCTGGCTCCTTCCAGTGCGTCTGTGACCAAGGCTACGAGGGGGCACGGGACGGGCGTCACTGCGTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000020871:ENSRNOT00000028322:23
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:
PF0764510=EGF_CA=WD(100=95.6),PF0764510=EGF_CA=PU(0.1=0.0)
A:
NA
C2:
PF0764510=EGF_CA=WD(100=95.3),PF0764510=EGF_CA=PU(0.1=0.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAGAACACCCCTGGCTCCTAC
R:
CCTCGTAGCCTTGGTCACAGA
Band lengths:
178-267
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]