MmuINT0038879 @ mm10
Intron Retention
Gene
ENSMUSG00000024330 | Col11a2
Description
collagen, type XI, alpha 2 [Source:MGI Symbol;Acc:MGI:88447]
Coordinates
chr17:34039437-34042309:+
Coord C1 exon
chr17:34039437-34039736
Coord A exon
chr17:34039737-34042159
Coord C2 exon
chr17:34042160-34042309
Length
2423 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGA
5' ss Score
10.77
3' ss Seq
ACTAACCCTGCCCCTCCCAGGTG
3' ss Score
8.67
Exon sequences
Seq C1 exon
GCTGGGGTCTCTGAGCTGCCAGGGTGGCCAGGGGCACACAGTAGCGGCCACCGAAGAGCAAGCAGCACTGACAAGAAGAGGTGCCCCCACAACGGCACCTTGCTGCATGGAGCTGGGCCACTGAAAGCTGCTGACATCCCGGGGTCCTGGTTCCGAGGCTCAGCTGGCTTCTGTCTGCTGTCAGCACCAGGACTGCCTGGGATCTGGCATTCTGAGCCATGGAGCGGTGCAGCCGCTGCCACCGCCTCCTTCTGTTCCTACCTCTGGTGCTGGGTCTGAGCGCTGCCCCGGGATGGGCAG
Seq A exon
GTAAGAGGAGTCCTGCCTGGGTGTCAGTCAGTTGGAGGTTGTAGCATCTGCTTGGAAGGGACCTCTGATGCCTGGAGTAGGAGCATCTGAGCCTTAAGAAAGGGATTTTGGGCACCAGGATTTAGATGAAGGGCATGACACTTTTGGTTCCTTGGAGCCACTATAGGACTGTCTCCCTCTCTGAAATGACTGGCAGAGGGCAGGTGACGCCGGCCAACAGGAGCCACCGTCCAGAGGCTGAGTAGGCTGGATTCTTGGTTTGGATCCTTAGAAGAACTTGAGATGGCCAAAGCCAGTTTTGTCCAGGCTTTGCTGATGTCAGGGTAGTGAATACCAGGACTGATGGGTAGAGGAAATGGGGTGAACGTCTGTAGGTTGGAGCCTAGAAGGCTAGAGAAGAAAGCTACCTCCACTGTCCCGTCTTCTTTGGGTCCCCCAACCCCTCCCTGTGCCCTGGATGCTGCCACGCGGCTGGCTCTAGGGAGCCTGGGGGCTGGCTGCCAACAGGACGGCCGCTGGACAGGCCAGGATCAGGTGTCTGAGGCCAGAGCCAACTCTTTGCATTCCTGCCCCTCCCCTCTAGCCAGCAGGACTCCCGTGGGACCTTGGTGTCCACTGGCCCCATCTTTCCCCTTTTTACCTCCTAGAAGGGAAAGCCTCCTAGAAAAGAGGATTTGATAACTGGATCTAAGCAGAAAGGAACCAGTTCCTCTCTCCTGGAATACGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGATTTTTGTATAGATATCCATTATTCATGTTTTCTCTGCTCAAGAGAGAAAATTGGCAGGATGACCGTGTAAAGGATCTAGGTTAGACTAAAGAAAGAGCAGATGAATGAAGTACACAGTGTTTACAGAGTTGAGGCAGGGGGATGACCAAGATAACTGTCTCCATTTGGGAACTGAGTGGAGGTGGGGGGAGGGACTCCAGGGAGATGGTTAGCTAAGAACTCCTGAGGGTATAGGACAGGGCATTTGGGGGCTCAAGGGGATAGGTGGAGTGGCAGTGGGTCTGAGACAGTGGGGTTAGTATGTGGCTTGAGGTGGGTGGGCTGTGAGCATGGCGTGGAACTGTCCTCCATCAGGATTTGGCGGAGGGTGGGGACCTCTCAGGTCTCCTTTGCCCGGGGTCTCTGTGAGTCTCTGTGTCTCTGTCTCCCTCACCGTACTCTCTCAAAGCTGCCCTTGTGTGTCAGTGTTTGCAAAGCTGCTACACTTTGGGGCCAGGCTCCTCAGGGGCGGGGGGAAGGTCGCGGTTTCCTCAGCTCCTGGACTCAAAGGGCCTTTTCTCTCCTGCCTGCCCCACCTCATCCACCCCACCAGGCTCTGCTCTCCTGACTGCCCTGGCCTCTGCCCCGCCCCACACTTCTACCAACACTTTTGCAAGCACTCTCTGTGGGAGTTCTCTGCTGTGGAGATGGTGTGGGAAGTGTGGGAGCAAACTTTCTCGTTCCATCATCGAGTTTGGGCCCGGGAAGCTGAAACCTAAGGAGACCTGGCTGATGGCCTGAGACTTGAATCTTGGGATTCAGGTGGTGGGGGATGGCAGGGCAGGACTGAGGTTCCAGGTGTCCGGAGCTTGCCTGGGCTTTGGGCAAGAACTCTGATAGCATTTACAGATGTGTGGCTTGGGGCCCTGGACCTGCTCCTGGTCTGTGTGGCAGCTTCAGTTTCCCCTTCCCCCTCTTCGAACCCATTCGCCAAGTCTGAGGGCACAGGCTTCTGGGCCACCTTATTCTTATATGCCCTTCCTTAGCACAGGCAGAGTTGCCCCTGCCCCCACCTCAACCCAGTCTCTGTGGCAACTGGAAGACCTCTCTTCTACAGCTGCCTCTCGGCCTCCCCTGTGCCCAGGATGATCGATTGCCCAGATGTTGTTTGTGCTAGAGACCAAGCAGATGCCAGGAAGCCAAAGACTGGGAGATAAGGAAAGAGAGGAAGAGGGAGAAAGAGGGAGAGAAAAGGGTGAACAGTGTGTCAGAGAGATGGGAAAACTGAAAAGAGGGTGTGGGAGGGTCCAGCAGGTGCACAGGCGGGGGAGCAGGGGGCAGAGGGCAGGAGAGATGGATGGAGCAGGGAGTCAGAGTGTGAGCCTAGCAGACTCACAGCAGAAAGACAGAGACAGCGAGTCTGAGACACAGATGCTGACAGAGGGAGGCAGAGAGAGTGTGGAGTTGCATGCCAGCCGGCTAGGTGCACCTCCCCTCTGTATCACTTTGCTTCCTATATGGAAATATAGGTCCCTTTAGGAGAATGTCAGGGAGACTGAGATCTGGGTGTTCCCTGGTTAGACCCCCCCTTGAGACATGTTCTCACTCCTAACTAACCCTGCCCCTCCCAG
Seq C2 exon
GTGCTCCCTCTGTGGATGTGCTTCGTGCCCTGAGGTTCCCCTCCCTTCCCGATGGTGTTCGGAGATCAAAAGGGGTCTGTCCGGGTGATGTGGCTTACCGTGTGGCACGGCCTGCCCAGCTCAGCGCACCCACGCGCCAGCTCTTCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000024330:ENSMUST00000087497:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion 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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
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