MmuINT0038923 @ mm9
Intron Retention
Gene
ENSMUSG00000024330 | Col11a2
Description
collagen, type XI, alpha 2 [Source:MGI Symbol;Acc:MGI:88447]
Coordinates
chr17:34181764-34183447:+
Coord C1 exon
chr17:34181764-34181955
Coord A exon
chr17:34181956-34183384
Coord C2 exon
chr17:34183385-34183447
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-Col11a2:NM_009926:5
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.701 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
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
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:
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
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: