RnoINT0087590 @ rn6
Intron Retention
Gene
ENSRNOG00000020871 | Ltbp4
Description
latent transforming growth factor beta binding protein 4 [Source:RGD Symbol;Acc:1307033]
Coordinates
chr1:84139871-84140592:-
Coord C1 exon
chr1:84140428-84140592
Coord A exon
chr1:84140021-84140427
Coord C2 exon
chr1:84139871-84140020
Length
407 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGC
5' ss Score
9.6
3' ss Seq
TCTCCTTGCCTCGTTCCCAGAGG
3' ss Score
8.94
Exon sequences
Seq C1 exon
CCCAACACGTGATCTCGGAGGCAAAGGGGCCCTGCTACAGAGTGCTCCAAGATGGCGGATGCTCGCTGCCCATTCTTCGAAATATCACCAAACAGATCTGCTGCTGTAGCCGCGTGGGCAAGGCGTGGGGCCGAGGCTGCCAGCTCTGTCCACCTTATGGTTCAG
Seq A exon
GTGAGCAAATCTTTCCAACCCATCCCTTCTTAACAGATATACACAGACCAGAGTCATAGGCCATGCTCTCCACCTCTAAAGTTCAGCGGCTTCAAACCGGGCAGTGCCTTGGCCACACTCCCAACACTTCATCAATGCTGGGCTTCTCTTTAGCCACGCCCATCCCTGAGACCTCAAAGCTATGCTGACCAGAGAACTCTGCCACCATCCCTAAAGGAAAACTCTCCCAGCTCCACCATTGGCTTCTGAAACATCTAATTCTTTGGTCGGTACACTACTCCATCCAGCATATGAGCCAGACTCCTGACACTATCTCAGTTCAAGCTCTGTTCCCAGCCAAGGCCTACTCACAACTCACAAGATTGCATTTGGTCTCCTCTCCCGCCCTCTCCTTGCCTCGTTCCCAG
Seq C2 exon
AGGGTTTTCGGGAGATCTGTCCAGCTGGCCCTGGTTACCACTATTCAGCTTCTGACCTCCGCTACAACACCAGACCCCTAAACCCGGATCCACCTCGAGTGACTTTCAATCAGCCACGTGCTCCACCTGTCACTCTTAGGCCACCCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000020871:ENSRNOT00000028322:10
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=0.627
Domain overlap (PFAM):
C1:
PF0068312=TB=PU(86.0=66.1)
A:
NA
C2:
PF0068312=TB=PD(11.6=9.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CACGTGATCTCGGAGGCAAAG
R:
CTGTGGGTGGCCTAAGAGTGA
Band lengths:
310-717
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]