MmuINT0039727 @ mm9
Intron Retention
Gene
ENSMUSG00000045672 | Col27a1
Description
collagen, type XXVII, alpha 1 [Source:MGI Symbol;Acc:MGI:2672118]
Coordinates
chr4:62988864-62989737:+
Coord C1 exon
chr4:62988864-62988929
Coord A exon
chr4:62988930-62989568
Coord C2 exon
chr4:62989569-62989737
Length
639 bp
Sequences
Splice sites
5' ss Seq
GAGGTACTG
5' ss Score
7.67
3' ss Seq
GCCCTGTTTCTCCATAGCAGGGG
3' ss Score
6.94
Exon sequences
Seq C1 exon
CAGCAAGATGACCTTGGAGCAGCTTTCCAGACATGGATGGATGCTCAAGGAGCCGTCAGATCGGAG
Seq A exon
GTACTGGTAGGATCTCTTCTCACATGACCTCTGGTCCTAGGAGAAAGAGAAAGGTCAAAGAGGTCGATGCTGTGCCCGTGGCTGGCACCAAGAGCCTCAGAGTCCTTCTCTTAGTGATAATCTCCATCTGACATCAGGACTCTGAGTCTAGTGTGTGCTGGCCTGAGTCAGGAGGGGATGCTCATCTGGTCCATAGCTCACAGAATGTTCCCATGGTTACCCAGCGATTGCACAGAAGCAAGTGAGCCCCGGGGCGCTGCTGAGACCTGGCCTGTGGTCAGCTTTGCTCCACAGCCTCATCTCAAGCTGAGATGGGTCTTGGGTGTTCCTTACTCCACCCAGTATCAGAGCCCACTTTGCCTCCTTGTATCCTTCTCATGATGGGGAGATCACTCCCCTAGTTCAGACCTCCAACCCTCCTACCTATGCTGGGTTTCATAGGCCAGGGGCAAGAAATCAGCCCCTGTCCCTGTTACATTATGTCCCTGACTCTCCCTCCCCTTATTTGTTATAAGGCAGAGTTGCCAGTCTAAGCTGGCCGTGGTCACCAGACAGTGAAGATTTTTAAAGCAATGTATCTGGGACCTTGGGCAAGGCCCAAGCACTTAACGGGCCAATGGCCCTGTTTCTCCATAGCAG
Seq C2 exon
GGGTACAGCTATCCGGACCAGCTGGCGCTAGACCAGGGAGGGGAGATCTTCAAAACCTTACACTACCTCAGCAACCTCATCCAGAGCATTAAGACACCCTTGGGCACCAAGGAGAACCCAGCCCGGGTCTGCCGGGACCTCATGGACTGTGAGCAGAGGATGGCGGATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000045672-Col27a1:NM_025685:57
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.500 A=NA C2=0.070
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0141013=COLFI=PU(38.6=47.4)
Main Inclusion Isoform:
NA
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:
CAAGATGACCTTGGAGCAGCT
R:
CATCCGCCATCCTCTGCTCA
Band lengths:
232-871
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: