MmuINT0039420 @ mm9
Intron Retention
Gene
ENSMUSG00000029661 | Col1a2
Description
collagen, type I, alpha 2 [Source:MGI Symbol;Acc:MGI:88468]
Coordinates
chr6:4477055-4478413:+
Coord C1 exon
chr6:4477055-4477153
Coord A exon
chr6:4477154-4478305
Coord C2 exon
chr6:4478306-4478413
Length
1152 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAAA
5' ss Score
8.38
3' ss Seq
TCACATGGTTTTCATTCCAGGGT
3' ss Score
8.36
Exon sequences
Seq C1 exon
GGAGAACGTGGTACCCCGGGTGAGAGTGGAGCTGCTGGCCCTTCTGGTCCTATTGGAAGCCGAGGTCCCAGTGGAGCCCCAGGGCCTGATGGAAACAAG
Seq A exon
GTAAAATTATTATTTATAGATTGATGGAATGGGCCCATGTGCTCCAGAATAAAGAGATATAATAGAAGAATGACCATTTTTGAAAGTTTTTATTTATTTCCAATTGTGTAATTTCTACCTCAGTTACAAGCAATATGATTCCTGTGAATATAATTATTCCAAAAGGTAATTTAAAGAAGAAAAAAATCTTTGTCTAGAAGCCAAGAATGAATTCGTATGGTTTATCCCTTTCCTGATTACACTGTTCATGTTTTGTTGAAATCTCGGACTACCCTTTACATTTCTAGGAAGTAGTTTTTGTTGTATCAACATCCAACCCCATACAGTCAAATTTCTAGAAGTAGTCTAGATTTTAATAGTCAAACTTATAGTGATTTAAATTAACTAAATATTACATTTACCCCAAAGGCACATGTCGAAAAGTTTGTATTCCAAAGTAGATTTCTAGTTTAGGGGGAAAAAAAAGATAAGATTGCACATCTCTGAAAATCAAGCAACTTTATATGACTCTCAATTCAGGCCTTCAAGGGGAACAAATGTAAAGACTAGATTCAAAAAGTTATTTCATTCTGCAGAAGATGATATTAGAGGGGGGATGAAAACAACATAAGAGAGGAAAGAAGAAAGGAATATGATGACATTCAGTGGGGCTTTTAAGGGGGTCTATTCATCTCAGTGGCTAGCCAACAGGCTTTCCGTGCAGAGAATTATGAGGCTTATTATAAAAATGGAAGCTACATTCTCCACTCTTATGGAGACAATCATCTCCCAAGTTGATGGGGTCTCTTTCTATGTCACTTGCCTGGGCTAAGAGACTTATCATTGAAAAGGTTTGTGGGCAAACATTTTTCAATCTCTCCATTCCATTGTTCCACCTTCTTCTTGTCCATGCTTGTCTTCCTTAAGAGGACAAGATACAGGTTGTAGAAGAATAGCAGGCACCCACTCTCTGTCCTCTTCTTTTTAGCCATCGTGTCATTAATAGCAGGCCCCCAGTTCCATCCTTCTGCCTTTCAATGATGCTCCTTTGTGTCTCTATGCAGCCAAGAATGCCATCTACTAAGTGTTTAAATTGGAATTCTTCAAGAGTTTCAGTCTTGGCTTTCTTCTTTTGCTACTGAAATAATTGATTTCACATGGTTTTCATTCCAG
Seq C2 exon
GGTGAAGCTGGTGCAGTCGGTGCTCCAGGCAGTGCTGGTGCCTCTGGGCCTGGTGGGCTTCCAGGAGAGAGGGGTGCTGCTGGCATACCTGGGGGCAAAGGAGAAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000029661-Col1a2:NM_007743:31
Average complexity
IR-S
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=FE(44.4=100),PF0139113=Collagen=PU(35.6=78.8)
A:
NA
C2:
PF0139113=Collagen=PD(23.6=47.2),PF0139113=Collagen=FE(47.9=100),PF0139113=Collagen=PU(42.0=80.6)
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:
GAGAACGTGGTACCCCGGG
R:
CTTTTCTCCTTTGCCCCCAGG
Band lengths:
206-1358
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: