MmuINT0040235 @ mm10
Intron Retention
Gene
ENSMUSG00000026837 | Col5a1
Description
collagen, type V, alpha 1 [Source:MGI Symbol;Acc:MGI:88457]
Coordinates
chr2:28018441-28019990:+
Coord C1 exon
chr2:28018441-28018548
Coord A exon
chr2:28018549-28019936
Coord C2 exon
chr2:28019937-28019990
Length
1388 bp
Sequences
Splice sites
5' ss Seq
CAGGTATAT
5' ss Score
7.88
3' ss Seq
CATTTTCTGCTTCCTTCCAGGGC
3' ss Score
11.15
Exon sequences
Seq C1 exon
GGCCATCCAGGCCTGATTGGACTCATCGGCCCTCCGGGAGAGCAAGGTGAAAAGGGTGACCGTGGACTCCCAGGCCCCCAGGGTTCATCTGGTCCTAAAGGAGATCAG
Seq A exon
GTATATATAGTAACTGGATCCATGGAGCAAATTCTAGTTTCCCAAGGAGGCTGGGAGGATGCCCTCATTGCCATGGAATCTCAAGTCTTGCTTTGCAGATGGGGACAGTGGGGCTTGGACTTAGCTAGGTCTGGGAGGCACAGTTAGAACACACCCCAACCCAGACCTCAAGTGGAGGTGGGAGCTCTCTCCTCGCTGCTCCGAGGATCCTCAGAATTTGTGGGGGGGTCTTAGCAGTCAGATCCTTCCTTCCAACTCCATGCAAAAGCCTCTAGGCAGAAGATAGTGGCGAGCCAACAGCCATGTTTACTTGTGAGGAGGGGTGGAGCAATGGCCACTAACATCCTTGCCCCCACCTTACCGCAGATGCCCACATCTGACCCCAGACTTACCCCAGAACCCACTGTAGCTGGTTAGCTTGCAATCACGGTGAGCCATGGCAGAGGAAACCCTGGCTGTGTCTTGATTTGAGGAGACTCCCAAATTCAAGAGGCAGTCTGTGTGTGGCACTGGAGAGATCCCCATTCACTGCAGTGGGAATTCCTACACAGTCCCCACAGTATGACAGCACTCACATCTGGGGATCTTTGCCTACCCAGCCTACATCTGTCTTTAAAGACAGCAGGATGTGGGGTGTCGGGAGCCTCTGGGGGCTGAGAAAACAGTAGACATCAATCTTTAGGTCATAGTGGAAGTGCATGGCATGAGAGGATGGGGCTCCTTGGAGCCCCGCCTCAGCCACTGCACGTTTTTCTGACTGTCCCGTGTCCCCAGGCTTCAGACTTGTCTGGCTCTCTTTGTGAATGTATATTCACTTCTGTGAGCCACAAACTATGTCCTTGGCCAGGGGGCAGGAGGAGGCATCTCCAGGGCGCAGGCTTGGGAAGCATGGGACCCATCAGGGACCCTGAGGTCCAGGCCCAGGACAGGAGAGGGACTTTGTTCCCTGTGAGGCTGGGCTGTCTACTGTGGCTGGAAAACACGTTCATATTTCTCTGTCCACGGTGGTAAGGCCTAACATTATGAGCTGAGATATGTGGCCAAGCTGGGCAGGAGGTTGGAGCAGACTTTTATTAGTTCCAGTAGTGTATGGTAGGGGTGATGTCTTAATGTACAGATCCTTCCAGCCTGGGCAGGGAGCTGACCCTGGGGACTTCAGCCTGTGGCTGTTTTGGTCGATCAGTTCAATCCATTGAGGAGATGTGGTGGCTCTCACCGTGATGTAAGCTCCACCCAGAGTGGTTGACTACAGCTGCCAGCCAGGATTCATGGTTCCTGGAAAGGGGACTATGCGGGATTCCGGAATCATGGCAGGGTCAAGGCGGTCACTTCCCTCAATTCCACCTCCATCTAAAAGCTGATAACCTGCATTTTCTGCTTCCTTCCAG
Seq C2 exon
GGCATCACAGGTCCTTCTGGCCCACTTGGGCCTCCTGGTCCTCCTGGCTTGCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026837:ENSMUST00000028280:58
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.901 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(3.7=8.3),PF0139113=Collagen=FE(50.0=100),PF0139113=Collagen=PU(7.9=13.9)
A:
NA
C2:
PF0139113=Collagen=PD(14.3=55.6),PF0139113=Collagen=FE(27.0=100)
Other Inclusion Isoforms:
NA
Other Skipping 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