MmuINT0039688 @ mm9
Intron Retention
Gene
ENSMUSG00000045672 | Col27a1
Description
collagen, type XXVII, alpha 1 [Source:MGI Symbol;Acc:MGI:2672118]
Coordinates
chr4:62942278-62943727:+
Coord C1 exon
chr4:62942278-62942331
Coord A exon
chr4:62942332-62943682
Coord C2 exon
chr4:62943683-62943727
Length
1351 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAGA
5' ss Score
10.06
3' ss Seq
GCCCCTCCCCCCAACTCTAGGGA
3' ss Score
10.34
Exon sequences
Seq C1 exon
GGTAAGCCTGGAGCCCGAGGCCTGCCTGGACCTCCTGGGCAGCTGGGGCCTGAG
Seq A exon
GTAAGATAGCCCTGTCCCCTCCTGTCCCTCTTTGTCTTCTCTAGCCTATCCCAGCACCTAGCTGGCTCTGTCCAGGGTACCAAAGCCATGATTGAGGGCAGGACCACTTGAGATTCATCACCAGAGAATCTATCTGTTCTCTTACAACCCTGCCTGTGACTCTTCTCTGACCTGGTGGGGCAAGCGACTTTCCTTCCACACATAGCACAGTATCAGTCTCAAAATGAGAGGATAGGAAATGTTGGACCCCTTTCATAAGTGGAGATCCAGGGAAGGAAATGACTGCCAGGCCCCGTGTTAGCAGGCAGGACCTTTACTAGAGCCTAGATGTTCATCAGCCCGGAGTCTATGCTCAGATCCTGTGCTAGTCTCACGGATGCTCCTGGGACCACTAGAGCATCATGGAAATGCCATGCCTTACCAGGCTGGCATGTCAGCAGAGTTCACCTGCATCTAGTCAAGAGGAGCAGGCCTCAGACCTATTGGGCCTCCCACAGGAAGCCTGGCTTTTGCTTGCACATGCAGCCCTGAACCTTGTGCATTGCGGTGCACAGCCGTGGGAGAATGAGCAACCACAAGCAGGCCTTTGCTGATGCGAGTCTTTCTCTGAGCTGGGTGTGGGTCTGGCAGAGTCCCAGTGCTGGCTCTTCAAGTCACTGCGTGGGGCTGCTTTCCTGGAAGCTGCAGATGCTTGCTGCAGGGGTTGCTTAAAGGGGCTTGTGGTCAGGCCCCGGATGCCAGAAGGATCAAGCTGGAGACTGTTGTGTCCTTCGGAGGGCTGGAGAGTCATGGCCAGGAACGGGAATGGAAGGAAGCGAGGGGAGAGACGGTTGCAGCAGAGGCCTCTCTGCCTGTGCTTACATAGCTGCCCAGGAAAACCCTTACTGAGCCAGGCTCTGGGCTTATGGGGCCACTCACTCCTTTATACATTCACCAGGACACTGTGCCTTCCTGAGTGCTGTGTGCAGGGCGGTGTGGCATCGTTAAGGCAAGATGTCACCCGACCTCTAGGACTCAGCTGAAGCCTATCATCAAGGATTCAGTGTGGGGAAACGTCTGCTATGGCGTAGACAACAGAGCTCAGAACCAAATCTGTCTCTGAGCTGGAGCCTGAGATCCCAGTCTTGAACAGCTTAGACACTGGGATTTGTGGTATGACCCTTAGGTGGGGACTGATGGACAACTCCCAAACCTTGAGACCGGGTTGTGAACTCTGCAAGGGCTCCATCCCCCTGCAAGGACTCTACACACTGTATGCTCTCCCTCCTTACAGCAGGAGCTCTCCCAGGATCCCAAGTTAACTTTCCCCTTTGTCTTTCTTCTTTTCTTATGCCCCTCCCCCCAACTCTAG
Seq C2 exon
GGAGATGAAGGACCCATGGGGCCACCAGGAGTCCCAGGCTTGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000045672-Col27a1:NM_025685:21
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(17.9=100)
A:
NA
C2:
PF0139113=Collagen=FE(14.7=100),PF0139113=Collagen=PU(12.5=73.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
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
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: