MmuINT0039346 @ mm10
Intron Retention
Gene
ENSMUSG00000001506 | Col1a1
Description
collagen, type I, alpha 1 [Source:MGI Symbol;Acc:MGI:88467]
Coordinates
chr11:94936224-94938104:+
Coord C1 exon
chr11:94936224-94936444
Coord A exon
chr11:94936445-94937909
Coord C2 exon
chr11:94937910-94938104
Length
1465 bp
Sequences
Splice sites
5' ss Seq
ACAGTAAGT
5' ss Score
9.49
3' ss Seq
GTCTCTTCCCATTTGCTCAGTCC
3' ss Score
6.62
Exon sequences
Seq C1 exon
TATAAAAGGGGCCCAGGCCAGTCGTCGGAGCAGACGGGAGTTTCTCCTCGGGACGGAGCAGGAGGCACGCGGAGTGAGGCCACGCATGAGCCGAAGCTAACCCCCCACCCCAGCCGCAAAGAGTCTACATGTCTAGGGTCTAGACATGTTCAGCTTTGTGGACCTCCGGCTCCTGCTCCTCTTAGGGGCCACTGCCCTCCTGACGCATGGCCAAGAAGACA
Seq A exon
GTAAGTTCCAAACTCTGGGGAGTTTACTACAGCTTCTTGGTATTGCGTTCTGTATAGAGGGGTCCTAGCAGATAAGACTTAAATGGAGGTGCAGGGCTGCTCCAGAGGCAGGGATGGGACGGTGATGGAGAGGAAACGGGATGAGAGAGGTCACCCTGTTGAGCAGATGAGGGGGAGCAGTTCTCAGAAGTGGAGCCTTGCATGAGATGGCCCAGGAAGAAATTTCAAGCACCCATCTGTAGCACAACAGGAAAAGTGGGAATCTGGACACGGGTTGGGGCAGAGTACGTCGAAAATGAAATAAGGCCTCTGGAATAGAGATTCGGAGCTCAAGATGTAAAAGCTATCAAAAAGGCTGCGGGATGATTCATAAGGAAAGATTGTTTGCCCTCTCTGCAGGCTAGACAGTGTTGCTGGGGCCTCCGGGGTGCTGGGCTCTCGGGGGGGGGGGAGGGGACGCACGGAGAGGGCGGGTTGCTGGATGAGAAAGTTTGGCTAGGACTTGACTGGGCGCGGTCCCTGTGCCTCCTGCTGGCCAGCCGAGAGCACTACGAGTCCTGGTACAGCACTTTACAGCGCACAGGCTGAGAAGGAAAACCTGGGTTATTGCGGACCCTCATCTCCAGACTAGGAAAATAAAAGCAGGGATGGATGGGGTAGCTCTGGTCTTTGAAAGAAGTGACCCAGGCCGAGTAAAAGTCGGTCCGCCCCTGCATTGCTTAGTTTTGCCCGCCACCTAGTGGTTGCCTTGATCAGGTCCTGGAGCGGTGGGCGTGGTTAACTCATCATTACTATTTGTAGACTTGACTTCTTTGGCTAAGGAGATTCCAAAGCACTACTGGCTTTGAAGGACCCGGCTTGTCTAGTTAGCAAGTTTTCAAGATTCCTGGGAGCTGGAAATTGGGATGTATCTAACTTTAGGGATACATTTTACTACACTGGACAGGGCTCCACTGAAATCAGCCCCTCCACATTGTAGCCCCGCCCATTCCGCCCCACCTGCCCCGGGAAAGGAGGTGGGACCAGGGCTGAATTTCCCCTTCTCTCCTCCCACCCCCGCCTCCTGTCTCCGCGCAAACCACGTCCCACGAGCCCCCACCTACTGCGTAGGAGCCCTCCTACTCTCCTTCAGCAGGCTTTTTTATTTCATTTGGTTCCCGCGCGCGTGGGCTGAAGTTGTTTGGAAGAAACCCCAGTCTAGAGCTTTGTTTAAATTCCTGAGAACTGGGACGTTATAGTCCTGGCCAGGCGCCCTGGTGCTGTCACTGAACGTCGCCGATATGGAGCAGACCTGCATTTAAGGATTTGAGGGAAGAATATAGGGAGTGGGGGGAAAGATTCAGGAAGTGGGAAGTCTCCGTGCGCCTCTTAGACAGGGCAAAGAGTGAGTAAGGCTGGGATCCCTGGTGCTCCGGGGTAAGGTCTCTGACCCGCACACATCCTGTGTCTCTTCCCATTTGCTCAG
Seq C2 exon
TCCCTGAAGTCAGCTGCATACACAATGGCCTAAGGGTCCCCAATGGTGAGACGTGGAAACCCGAGGTATGCTTGATCTGTATCTGCCACAATGGCACGGCTGTGTGCGATGACGTGCAATGCAATGAAGAACTGGACTGTCCCAACCCCCAAAGACGGGAGGGCGAGTGCTGTGCTTTCTGCCCGGAAGAATACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000001506:ENSMUST00000001547:1
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=0.030
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0009313=VWC=WD(100=84.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCCAGTCGTCGGAGCAGA
R:
GGGTTGGGACAGTCCAGTTCT
Band lengths:
353-1818
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