MmuINT0040519 @ mm10
Intron Retention
Gene
ENSMUSG00000025650 | Col7a1
Description
collagen, type VII, alpha 1 [Source:MGI Symbol;Acc:MGI:88462]
Coordinates
chr9:108984018-108984875:+
Coord C1 exon
chr9:108984018-108984212
Coord A exon
chr9:108984213-108984501
Coord C2 exon
chr9:108984502-108984875
Length
289 bp
Sequences
Splice sites
5' ss Seq
CAGGTATGA
5' ss Score
9.46
3' ss Seq
TTCTGATGTGTTCCATGCAGGTG
3' ss Score
9.67
Exon sequences
Seq C1 exon
ATCTCTGCTCCCTACCCTTGGATGAGGGCTCCTGTACTGCCTATACCCTGCGCTGGTACCATCGAGCTGTGCCTGGTGGCACAGCCTGTCATCCCTTTGTCTATGGTGGCTGCGGAGGGAATGCCAATCGTTTTGGAACCCGTGAGGCGTGTGAGCGCCGCTGCCCACCCCAAGGGGTCCACAGCCAGAAAACAG
Seq A exon
GTATGAGCATTTAGCTCTCAGTGAAGGCTGCATCTACACCTGTTAGTGCTTGGCCAAGACATTCCCTGAGTCTGGAGGACCTGGAGCAGATTCCAGATCCCATAACTGGCTACATATCCCCAGCCGAGGAGCCGGCATGGTCCCTCTCCATAGTCCTTTTTGCTAAGGGTCCCTCTTGAGTCAGAGCACACACCCCATCCCTCCTGGAGGCTTTGGTATGTTTCTGTGCAGACTTCACGTTGGGGAAGAACCTCAGAGGGCTGAATGTTTTCTGATGTGTTCCATGCAG
Seq C2 exon
GTGCTGCCTAGGACTGAGGCCCGGATGATGCGCTTGGTGGCCAGCAGTCCCTGGAGGTGGCAGGGTCTCAGCCGGGTCCTGCTGTGCTCCATTTGGTGCTAGAGTTGTGTGTGCACGTGAGCATGTATATTGTGTGTGCACATGAGCATGTCCACTATTTCAGTGACTTGGTCCTGTGGGTCTAAGTGGGGGGGGACCCCCATGGACAAATCCCCATTGTGGCGCCCGCTTTCCTGGCAGATGACTCACTGTTGGGGGTGGCTGTGGGCAGTGAATGGATGTGACTGGTGTCCAACCTGCCCCTTGACCCGAGGCTGTGATACCATGGTGCTGATGGGAGGGGACGGGGCATTAAAGCTGCTGTTTTAAAAGGC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000025650:ENSMUST00000112070:118
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.106 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0001418=Kunitz_BPTI=WD(100=83.3)
A:
NA
C2:
NO
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:
CCTTGGATGAGGGCTCCTGTA
R:
GCACACACAACTCTAGCACCA
Band lengths:
294-583
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