MmuINT0038818 @ mm10
Intron Retention
Gene
ENSMUSG00000027966 | Col11a1
Description
collagen, type XI, alpha 1 [Source:MGI Symbol;Acc:MGI:88446]
Coordinates
chr3:114105390-114108334:+
Coord C1 exon
chr3:114105390-114105446
Coord A exon
chr3:114105447-114108280
Coord C2 exon
chr3:114108281-114108334
Length
2834 bp
Sequences
Splice sites
5' ss Seq
GTGGTATGT
5' ss Score
7.64
3' ss Seq
TGTTTTGCTTCTATCCTCAGGGG
3' ss Score
10.56
Exon sequences
Seq C1 exon
ATTGCTCTGAGAGGCCCTCCTGGCCCAATGGGTCTTACTGGAAGACCAGGTCCTGTG
Seq A exon
GTATGTTACATAAATTATATGTTAAAAGTTTCCTATTGATATGTTTTCCCACATCATCTTCCAGACTCTGTTCATTTCTCAGGCTAGAAACCAATTGTTTATGACTGATACTGACTCATTTAAAGAGTTTTAGTTTAATTTTTCATAATTCTGATCATAAGATTTTAGGGAGGCTATCATCAAATTAAAGGAAAATTAAACAAATGTAATAAAATCACATAACTGTTACTTAAACCATCATTATAGTTTATTTGAATTCTATTTAATTATCAAAATGCAATTTTACATTAAATTCTTGAAAGTTAATTATATACTTGAGTTCTTACTAAATTGCCTGTGAAATCTTTGATAATTATTGTGCAATTTTTACACTCCATTTTATTGAAAATAATTTTTATACAAATTATTTTGATTAGTTTCCTTTTTTGTGCCTCCACCGAATGTTTTCTTTCTTATTATATTTTCATCATTTAAAACAATTCTTAAATTTAGTCATATTTTATTCATATTGTTCTCTTCCTGTAAGTTGGAAAGAAAGAAGGTAAAGTATCTTTGCCCACAGATGATAAAATTGTACACGTAAATGACCCAGAGAATTCCCATCAGAGGAAACTCTTACAGTTGATCAACATTTTCAGACAAGTAGTTCGTTATAAAAGTAATTCATAAAAAAACAGTTTGCCTGCAATACACAAATGAGAAAGGACTGAGAGAGAAAGCAGGGAAACAAAACCTTTCATGATAGCCTCAAATAATATAAAAGATCTTAAGAAAGCAATAAAAGATTTGTATGATAAAACATCAAGTCTTTGAAGAAAGAAATTTTAGAAGATGTCAGAAGATGCAAAGATCCCCATTGCTCATGTCTGGAGGATTAACATAATAACAATGGTTAGCCTATCTGAAGCAATATGCAGTTAAATTCAATTCCTATCAAAATTCCAATATAATTCTTTACAGATGTTAAAAAGGTAGTTTTCAGCTCATATGGAAACCCAAAGAGACACAAAAACATGATAACGAAAATAGTCCTGAATAATAAAAGAATTTCTGGGAGGCTCACCTTCCCTAATTTTAAGTAGTACTATAGTAATAAAAATAAGCTTGGTTAATTAATCCCTGATAATACGTTAATAACTGGTACCGCAAAGAAAGTAGATAAACTGATAAATGCATTAGTATAATACAGTAAAAATTAAAAAGTTCGCCTGCCATTTTAAATGTATATTTCTTTTAAGCCTTAAATTTTCATCTTATATACATATGTATGTATATAATTTTGATATATACTCCTGTGTGAAATGTTCAGGTAACGTAGTCAATAGGACTTTAATTATATACAGTTTTGAACAGGTTATCAAAAGTTCTTATTGTTGTGCTTTTCAAACTACTAGAAAAATATATTAAGTCACAAAAGAAATAAATTTTATTCACATGTTGGTGATAGAAATAAAGTATAGACACATGAGAGGAATACAGAAATATTTTACAAAATTTTAGGATAGAAAGAGGGTAGAAATAATATCCTGTACATCTTCCTTCCCGTCAATTATGTGATAATTTTGATTATATGTGGAAAGATGTAACTACAATCTACAGAGCAAGTGATGCATACGTACAATGAATCCCAGCCAATAAACCAAAAAACAACCCGACCACTCTATAATTGTATTCAGTTCCCCGATTAATAATTTAATTTAATGCCTTGCCCTCATTTTATTATAGGCAATTAGTTGCAAAAGCTATTTATTAGAAGCTTGGAGGTAATCATCATAGTTTTGAAAATTTACAAATACGTTCAACATTGACTTCTTTCTTGCGAGACAGAGTAGGAGTTATTTTACTTTGTTGCCACAAGGAGGCGCGAGAAAGCTTCTTTCTGATTTATCAAGTTTTGATTTTGTTTTTTGTTTTTGTTATTGTTGTTGTAACTTAGTTTAAAGGAAGGTATACTGATTAAAAAAAAAAAGAGAGTACCTGTTAACACACGAAGCAATTTATTACAACCATATTAACTTAATATTATAAACTTTTTGATAATATGGATGCATATTCCATAACTCCTTTTTTTTTTTTTTTTTTTTTTCTTTTTTGAGACAGGGTTTCTCTGTATAGCCCTGGCTGTCCTGGAACTCACTTTATAGACCAGGCTGGCCTCTCGAACTCAGAAATCTGCCTCTACCTCCCAACCATATCTCCTTTCTAAAGTAATTAATTTTCTCTTGCAGTTAATCTACTTGGCCTCATTGTACTGTTTAAATTATATAAACAGTTGTAAGCTATATTTATTGTAATGATTTATATTTATAGAAAAATCAAAACAATCTGAGGGAAATGCTTTGATATTATTTTACAATAATAATAATGGTACCAATAACACCATCCTAAAACAGTTTACTACTAGAAAATGCACTACCTGAGAATTATATGTTCATAAAGAGTTGGTTTTGCACAACCTTTACTGTGTGAATTAACTCAGTGTATGCCTGACTCTGTTTAAATTCACTGCCCTAGTAGTAACTCACAATGTAGTGGTTTCTCTGGTCTTGTTTACCAGACAATGTTTGTTACAGCAAAAATTTAAAAGAAAAATTCAGGGTGATTTCAATGTTGGCTTCTGTTCATTTGCAAGTGTAATATAGATCTTTATATATGGTTCATATATCAGGATGCACTTGACTGTCTAGAAGTGCTATACTTTAGACACAGGACTTAAATAGCTCATTGCATGAGAAGTATCAAACTGATTAAGAAAATGTTTATTTATTTTGAGTGAATTAAAGAGCATTGGTGACTTAACATTAATTGGTCGTCTGTTTTGCTTCTATCCTCAG
Seq C2 exon
GGGGGTCCTGGTTCAGCTGGAGCCAAAGGTGAGAGTGGGGATCCAGGTCCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000027966:ENSMUST00000092155:14
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PU(25.8=84.2)
A:
NA
C2:
PF0139113=Collagen=PD(39.4=86.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
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