MmuINT0093730 @ mm9
Intron Retention
Gene
ENSMUSG00000024940 | Ltbp3
Description
latent transforming growth factor beta binding protein 3 [Source:MGI Symbol;Acc:MGI:1101355]
Coordinates
chr19:5753929-5755674:+
Coord C1 exon
chr19:5753929-5754048
Coord A exon
chr19:5754049-5755545
Coord C2 exon
chr19:5755546-5755674
Length
1497 bp
Sequences
Splice sites
5' ss Seq
AAGGTATGA
5' ss Score
9.11
3' ss Seq
GGTCTCCTTGCCTCTCCTAGATA
3' ss Score
7.35
Exon sequences
Seq C1 exon
ACATTGATGAATGTGACTTCCCTGCGGCCTGCATCGGGGGTGACTGCATCAATACCAATGGTTCCTACAGATGTCTCTGTCCCCAGGGTCATCGGTTGGTGGGCGGTAGGAAGTGCCAAG
Seq A exon
GTATGAGAAGTTGGCCAGGGATTCTGAAAGGAGAGGCAGGGCAGTGTGATCTATTTGACACACTGTAGCTCTTCTCTACCTATTTGACACACTGTAGTTCTTCTCTATTTGACACACTGTAGCTCTTCTCTATTTGACACACTGTAGCTCTTCTCTATCTATTTGACACACTGTAGCTTTTCTGTAGTCTTTGTATCCATCCATTCCCCATCAATCCATCTAACCCATTCACCAATGTATTTGTTCTCTAACAAGGGTCGCCCTGCTGGCTGCAGTGTTTCTATGTCGCTTATTTTTCCTTTTTTATTTTTTATTTATTTTTGTTTTTTTGATACAGGGTTTCTCTGTATAGCCCTGGCTGTCCTGGAAGTCACTTTGTAGACCAGGCTGACCTTGAACTCAGAAATCCGCCTGCCTCTGCCTCCCGAGTGCTGGGATTAAAGGCGTGTGCCACCACTGCCTGGCTGAAAAATCCTTTTTGTGCATGTATGTTTGCCTGAATCATGTCTGAACTACATTTATACATCCCTGTGGAGGCCAGAAGAGGGCATTGGAGCTACAGATGGTTGTGAGTGGACATGTGGGTGCTGGGTCATCTGGAAGAGCAGCCAGTGTTCACAAGGGCAGAGCCATCTCTCCAGCCCCTCTGGTCAGCCTCTTACAGATATGATAGTCTGACCTATCAACCAACTGACCTCTATGTACCTTCACTGTCATGTGATACCTGCACAGCCCTGTTTGCCAAGTGGTGTACTAGGTATTTCAGCAATGAACTGGGCCTTCTACATTGGAGGGGGACATGAAAATGAGCCTCAGGTTCAGGGTGAGGGTACCCAGAAGCTAATTAAAGGGAGATGACTGTAGAGTGGAGATTAAAAACATAAGGAGCCTTTTAGCAGGGGCTCTGGGGAGGGAAGGGATCCCTCTGAGTGGGAAGGGGTCTCTCTGGGTAGGAAGGGGTCTCTAAGTGGGGCTCTGGGTGGGAAGGGTCTCTCAGCAGAGGCTCTGGGTGGGAAGAATCTCTCTGCAGTGTCATGAACAGCAGTTGCAATGTACTCAGTGTGTCTTTTAGAGGGGTAGGGACAACTCTACCTTAAGCAAAAATTTGGGAGGAGTGAAAGAGTGCAGAGCCAAGTTTGATGGCACGTACCTGCCATCCCAGCTGCATAGGAGGCTGAGGCAGGAGGATATCAAGCAACTGACTATCCGTCGAGGAATAGCAAGGGAAAGGGAGCGGGAGATGAGCAGGAAGGTCTCCATGTCAGCTGAGGGTCAGGAGCTCATTCCAGTGACCCAGGCTGACAGCAGTGTCACAAACCTACCCACACAGACAGACAAACAGGCCCAAGGGGACTTCTATTGTATGCCCTTTGAAACCAAAGCAGAAACTCAGGTTCTGAGCCTGTGTAAGGTGTTTGGGCACACCCCAGGGAAAGGGGGCTGTGTTTCTCCGCAGCGGAGGTTGTTCTTGCTTCCTGGTCTCCTTGCCTCTCCTAG
Seq C2 exon
ATATAGATGAGTGCAGCCAGGACCCAGGCCTGTGCCTGCCCCACGGGGCCTGCGAGAACCTCCAGGGCTCCTATGTCTGTGTCTGTGATGAGGGTTTCACACTCACCCAGGACCAGCATGGGTGTGAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000024940-Ltbp3:NM_008520:19
Average complexity
IR-C
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
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTGATGAATGTGACTTCCCTGCG
R:
CCTCACACCCATGCTGGTC
Band lengths:
246-1743
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: