MmuINT0038923 @ mm10
Intron Retention
Gene
ENSMUSG00000024330 | Col11a2
Description
collagen, type XI, alpha 2 [Source:MGI Symbol;Acc:MGI:88447]
Coordinates
chr17:34044819-34046502:+
Coord C1 exon
chr17:34044819-34045010
Coord A exon
chr17:34045011-34046439
Coord C2 exon
chr17:34046440-34046502
Length
1429 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGG
5' ss Score
10.07
3' ss Seq
CCCCCTCCCCTTGGGGCTAGTAC
3' ss Score
5.93
Exon sequences
Seq C1 exon
GGCGATGTTCAGGAGCTCCTCGTTGTCCCAGGCGTCCAAGCTGCCTATCAGTCTTGTGGGCAGAAGGATCTGGAATGTGAGAGAGAACAGAGGGACGGCCCTCAGACTCAGAAGCCTCACAGAGCCCAGAGATCTCCAAAGAAGGAACCAGCAAGACTTCATAAGCCACAGAGCCAGGAGCCCCAGAAGCAG
Seq A exon
GTGAGGGGGTTGGGCAAACAGAAACTGCAGCCTGTGGGGAGGGCACTGGGCTTCTCCAGGACTGTCCCCCATAGCAGTCCATCCTCACTGGTCCATTCTCCACCCCGTCCTCTTGTTAGTCTGCAGCTGTACTTCCCCACTCCCATCATGCCCTCTTCCCAGTCCTCAGTCATCAGCCTTTTTATTTTCATTTAAAAATAAAAAGGATAATAAGAAGAATCCCTGGTGGGAGCTGCATGCTCCTACCCGTGTGAGAACTTCTTCCTATCTGCCTCGGGTTTTCCATCTCTTTCTTGAATTAAGAGATTGGGAGATAGTAGGGGGACAGGTGAGCCTGAGGAGGAGGGGACAGGTGACTGGAGCTGAGCCGTGGTACCAAGGAGGGGGGGGTGGTAAGGAGGGACTAGGGGTAGAGGGAATCTCAGGGAACAGAGTGTCTGTGGCTCACCAAGTGCCTCAGGGATACAGTGGGAAGAGGGACGGAAGTGTGGGTTGGAGGGCCTGGGAGTTCAGGTGACAGATGTGTTCTTGGGATAGTATGAAGACTGAAGGGTCAATCTCTTAATCATGTCTGCTTCCATCCACATGGAACCCATTTCCTCTTTTCTCTTCTCCCCCCCCACCCCCTCTCTCCCTTGCTGTCACCTCTCCTCTGTTTACAACCCTCATTCTCCAACTCTGCACCCCCTTTCCCAACCTCTGCACCATCACCTTATGCCCCCCAATCTCCCATCCTGTCTGTCCCCCTCCCTGCTCCCAGCCCACTGAGTCTCTCTACTATGACTACGAACCCCCCTATTACGATGTGATGACTACGGGGACAGCCCCTGATTATCAGGTAACCTCGAGGGTCCCCTTCACCTCTCTCCCTATCAGTGTCCTCTGTGTTAAACCCCCATTGTACCCCAGCTTCTGGGGTGGACACTAGATTATGGAGGGTCACTTGCTCACTGCCTGCACCCGTATTTCTCCACTGCAGCGTCCTCAGAGCTCCAACCACAGGGCTCCCCCTTCCCCTAGGGGGCGTCGGACCCCTCCCAGAAAGTCTAACCCTCCTGCCAAGAGGTCAGCAGCCAGGCAGGCGCCCCAATCACCAGCCCGGAGGCCCTCTCCAGCTGGAGGCTCTGGCAAAGCCCTCGGCCAGCCTCCCCCCTCCCGACACCCAGCTCGACGGGCAGCTTCCCCCACTGCCAGGGCTTCCCCCAGGACCAGAGGCAGCGGTTATCGGCAGGTAGAACGGGGCATCCAGATCTTTGCCCCCAATTTATAGACACTGAAGATTGATTCTCCTCAAAGGGGATGCAAGATCTGTGATTTCCCCCACCCCGATCCCAGATCCTGCCTGTGGTGAGGACAGGTGGCAGCTTTGCTTTCTTCTCTGCTACTCTCTCACCTCCCCCCACTCCTTTCCCCCTCCCCTTGGGGCTAG
Seq C2 exon
TACCCCACCCCAGGTGAAGAGGAAGGAGTCCTGGAGTCCAGTCCCTTGCCATTCCTTGAAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000024330:ENSMUST00000087497:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.703 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0221019=Laminin_G_2=PD(7.3=14.1)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCGATGTTCAGGAGCTCCTC
R:
CTCTTCAAGGAATGGCAAGGGA
Band lengths:
254-1683
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- 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