RnoINT0087572 @ rn6
Intron Retention
Gene
ENSRNOG00000020813 | Ltbp3
Description
latent transforming growth factor beta binding protein 3 [Source:RGD Symbol;Acc:62057]
Coordinates
chr1:221111511-221113224:+
Coord C1 exon
chr1:221111511-221111630
Coord A exon
chr1:221111631-221113095
Coord C2 exon
chr1:221113096-221113224
Length
1465 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGA
5' ss Score
10.57
3' ss Seq
GGTCTCCTTGCACCTCCTAGATA
3' ss Score
4.98
Exon sequences
Seq C1 exon
ACATTGATGAATGTGACTTCCCCGCGGCCTGCATTGGGGGTGACTGCATCAATACCAATGGTTCCTACCGATGTCTTTGTCCCCAAGGCCATCGGCTGGTGGGAGGCAGGAAGTGCCAAG
Seq A exon
GTAAGAGGAGTTGGCAGAAGGCTTCTGAAAGGAGCAGTAGGGCAGTGTATTTGACACGCTGTAGCTTTTCTGTATCTATTTGACACACTGAGGCTTTTCTGTTACCTATTTGACACACTGTAGCTTTTCTGTATCTATTTGACACACTGAGGCTTTTCTGTTACCTATTTGACACACTGTAGCTTTTCTGTATCTATTTGACACACTGTAGCTTTTCTGTATCTATTTGACACACTGTAGCTTTTCTGTATCTATTTGACACACTGAGGCTTTTCTGTTACCTATTTGACACACTGTAGCTTTTCTGTATCTATTTGACACACTGTTGCTTTTCTGTAGTCTTTGTATCCCTCCATTCCTCCATCAATCCATCTAACTGGTTCACCAGTGCATTTGTTCTCTGACAAGGATCACCCTGCTGGCCGCAGTGTTTCTGTGTTCCTTGTTTTTACTTTTTGTGCATGTGTGGTTGCCTGAATCATGTCTGTGAACCACATGCACACATCTCTGTGGAGGCCAGAAGGGGGCGTTGGAGCTACAGATGGTTGTGAGTGGACGTGTGGGTGCTGGGTCATCTGGAAGAGCAGCCAGTGCTCATAAAGGCAGAGCCACCTCTCCAGCCCCTCCGCTCAGCCCCTTACAGATGTGACAGTCTGACCCATCAACTGCCTGACCTCTATGTACATTCATCACCATGTGATACCTGCATCCCTGTCTGCCAAGTGGTGTACTAGGTATTTCAGCAATGAACTGGGGCCCTAGATTGGAAAGCGGGCCTCAGGTTCAGGGTGAGGGTACCCAGAAGTTAATTAAAGGGAGTTGACTGTAGAGTTGAGATTTGAATCATAAGGAGTCTTTCAGCAGGGGCTCTGGGAGGGAAGAGCTCTCTCAGTAAGGAACTCTGGGTGGGAAGGAGTCTCTCTGGGTGGGAAGGGGTCTCTAAGTAGGGGGTTGTGGGTAGGAAGGGGGTCTCTGGGTGCGAAGGGTCTCTCTGGGTGGGGTTCTACTCCATGAACAGGAGTTGCAAATTACTCAGTGTGTTTTTAGAGTGGTGGGGACAACTCTAACTTGAGCAAAAATTTGGGAGGAATGAAAGTGTGGAGCCAAGTTTGATAACATGTATCTGCCATCCCAGCAACACAGGAAGCTGAGACAGGAGGATAGCAAGCAACAGACATTGCCTCAAGGAATGGCAAAACTGAAAGGTAGTGGGAGATGAGCAGGAAGGTCTGCAAATGTCAGCTGAGGGTCAGAAGCTCATTCCAGTGCCAGGGGGACCTTAGGGTTTACACAGGCTGACAGCGGTGTCACAAACCTCCCCACACAGATGGGTCCAAGGGGACTTCTGTGGTATGCACAGGTTCTGAGCCTGTGTAAGGGCTTTAGACACACCCCAGGGAAAGAGGGGCTGGGTCTCTCCACAGCCGAGCTTGCCCTTGCTTCCTGGTCTCCTTGCACCTCCTAG
Seq C2 exon
ATATAGATGAGTGCAGCCAGGACCCAGGCCTGTGCCTGCCCCACGGGGCCTGCGAGAATCTCCAGGGCTCCTATGTCTGTGTCTGCGATGAGGGTTTCACACTCACCCAGGACCAGCATGGATGTGAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000020813:ENSRNOT00000028262:18
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=95.1),PF0764510=EGF_CA=PU(0.1=0.0)
A:
NA
C2:
PF0764510=EGF_CA=WD(100=95.5)
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:
TTGATGAATGTGACTTCCCCGC
R:
CCTCACATCCATGCTGGTCCT
Band lengths:
246-1711
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]