RnoINT0087573 @ rn6
Intron Retention
Gene
ENSRNOG00000020813 | Ltbp3
Description
latent transforming growth factor beta binding protein 3 [Source:RGD Symbol;Acc:62057]
Coordinates
chr1:221113096-221113626:+
Coord C1 exon
chr1:221113096-221113224
Coord A exon
chr1:221113225-221113458
Coord C2 exon
chr1:221113459-221113626
Length
234 bp
Sequences
Splice sites
5' ss Seq
AGGGTGAGT
5' ss Score
9.25
3' ss Seq
AACTGTCACCCTCTCTCCAGAGG
3' ss Score
8.32
Exon sequences
Seq C1 exon
ATATAGATGAGTGCAGCCAGGACCCAGGCCTGTGCCTGCCCCACGGGGCCTGCGAGAATCTCCAGGGCTCCTATGTCTGTGTCTGCGATGAGGGTTTCACACTCACCCAGGACCAGCATGGATGTGAGG
Seq A exon
GTGAGTACACTCCCTTGGTAACCCTTGGAGCTACAGCTGGCTTGGAGGTGTGCCCCAGTTCCACCCTTTTGAATTCCTGAAACAGGAAGAAATCCTCTTTGCTTGGGAGAAGTGGGTGGGGCTAGACAAGGAGGGCCAGGGCAAGTAAAGGCCAGAGTACGTGCAGTTTTGGGGTACAGTAGACAGGGCCAAAGCTACTACCTCCATGAATTTGAACTGTCACCCTCTCTCCAG
Seq C2 exon
AGGTGGAGCAGCCCCACCACAAGAAGGAATGCTACCTTAACTTTGATGACACAGTGTTCTGTGACAGTGTATTGGCTACCAATGTCACCCAGCAGGAGTGTTGTTGCTCTCTGGGGGCCGGCTGGGGAGACCATTGTGAAATCTATCCCTGTCCAGTCTACAGCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000020813:ENSRNOT00000028262:19
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=95.5)
A:
NA
C2:
PF0068312=TB=PU(86.0=64.9)
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:
TAGATGAGTGCAGCCAGGACC
R:
TGAGCTGTAGACTGGACAGGG
Band lengths:
293-527
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]