MmuINT1022512 @ mm10
Intron Retention
Gene
ENSMUSG00000040488 | Ltbp4
Description
latent transforming growth factor beta binding protein 4 [Source:MGI Symbol;Acc:MGI:1321395]
Coordinates
chr7:27335653-27337692:-
Coord C1 exon
chr7:27337428-27337692
Coord A exon
chr7:27335712-27337427
Coord C2 exon
chr7:27335653-27335711
Length
1716 bp
Sequences
Splice sites
5' ss Seq
CGGGTAAGC
5' ss Score
9.14
3' ss Seq
TCCCACTCTCCTATTTACAGTGT
3' ss Score
8.15
Exon sequences
Seq C1 exon
TTGCACGGTGGAGAAAGTGAGTCGGCCTCTGGCTGAGGCGGGGGTAGGGGGCGGGACCGGGGCCAGGCCGATCCGGACCCACTGGACACACTGCCCTCTTGGAGCCGGACTCTGCACCCGACACGATGCGCCGGCCTGGCCTCGGCGGCCCCTGCCCCCTCTTGCTGCTGCTGCTGCTCCCAGCCGCCACATCTGCTAGCGGCTCCAGTCCCAGCCCCAGCCCCAGCCCCATCGAGAAAGCGGTGGTCCCGAGCCACCAGGCCGG
Seq A exon
GTAAGCCCACTGCAGCGTCTTCTTCCTCGTGCTGTACCCAGTAAGTCTTGTGGTCTCGGAGGAGCAAGACCTTCAGATTTAGGAGGCTACAAAGCAACTGCTTTTGGTAGAAGGATGCTAAGGCCAAAGCCCTTGGATCTGCTGGGAGCCCCTACTTTGCAGTCGTTAGAATTCGAGATGCGCTGAGAAATTGAAGCGGAGGTCCCTCCAGAGGGGTAGGATGGGTAAGGCTCCAGCCAACTCCCGAGTTTATTGGGGAAAGAACCCCAGTTGATACCGGGTAAGACTTCGAGTTTTCTTAGAATAATAGCGATGGGTGGGGCCCTTGAACTAGCCTTCAGCTCCCCAAGTTTCCTGAGTGTTTTTTTTTTTTTAAAGGTGCTGGAAGGTCGTGGTGAGATCTTAAAGAAAAGTTGCCGTGTTCTGGGTTTCTAGGGGGGCTGGATTAATTGGAAAAGACTTCTAGGTTCTTCTAATAGATTAGGAAGACGCATATAGGCTCCTGGCAAGGGGACTGGAGGAAACCTGTGTAGGGGATCCTTGGATTTTCTGACGCTTCTAGTTTTCTGAGATCAGAGCTCCTCCGGATTGAATGAATTACTAATGACTTGGTGGTAAGGTCCAGGGTAGTTTATAAATTTCAGTGTTTATAGGACACCATCGCGTCTGCGGGTGACAGGATCGGAGGAGATGGTCTGCTTAGCATCCCAGTCCTGCTCCTGGCAGCTCTGCGCACCGTTACAAAGGCCGTGGGCTCCGCTCCCGCTCCCGCCTGGGTCTCTGGGAATGCGTTTAGTAACCCGAGCCGCGCCGGGGGCGGGACTGGGAAGGGGTTAACCTGGAGGAAAAGCGGGAGGGATGACGACAGGATTCGAGGGTCTCAGAGGCTCCCCCAGGGCAGCCTGCGCTCCCTCTAAGCCTCACTCATCTAGAATGGATCCGGGCATTGGATTCCCTTTCTCAGTATCTTCCAAAGTTTTTCTCTCTGGGTCTGAACGCGCACCATCATCCCTCACCCCCCCCTCTAACTTGGGGATAATGGACTTGTCTGGGGGGCCCCTGGGTGACGACGCTCTGGCAGTACCGCTGAAGGGTCGCGGCTGAGACCCAGTGGCACTGAGACATATCCGGAAAAGACCCTTTCCTCTCGGACATTGAAGTTCAAGGACCAGGAGACGCTGGTCCCAGGACGTACATCCTAGAAAGGCGGGAACTGGATAAAATTCAGGCCTCGGGATTCCCAATTCTGGACTTCGGTATCCCTACCACCTCAGCACTGTGCTGGACCCGTAGTCTAAGGCGACACCGCAGTGCACAGCCGCCGAGGTCTGTGCATGTAGCGCCACCTACTGTTCGATGTTAGGATGGCGTCTGAGCCTCCACTCTCCTCGAATTAGTGGGCGGAGTTCTAGATCCCAGACAGTCCAGGCTTGTAGATTCGCTTAGAACTCTCCTTTGAAAGTCTCTTGAAATAATTTTAAGCCTGGCGTGATGGCTTATGTATGTAACTTTAGCTTTAGTGGAGAATGAAGCAGGAGGATTGTCGTGAGTTTGAGGGCTACCTGGGCTACACAGTACATTCTAGACCTTGTCTCAAAATAATGATAGTAATGAGTGCTTGGAATTCCCTTGAATCTTGTCTTGGTTTCTCCTCTGTCCTCCACCCCTGCTCTCCTTTGTTCTGAGGCCTGAACAGTCCCACTCTCCTATTTACAG
Seq C2 exon
TGTTGCTGCCTGTCACTGCTGCCTAGACCAGACACCTAAGAGTAGCCGCTGCACCCGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000040488:ENSMUST00000038618:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.362 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTGCACGGTGGAGAAAGTGAG
R:
TGCAGCGGCTACTCTTAGGT
Band lengths:
318-2034
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Ribosome-engaged transcriptomes of neuronal types
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types