MmuINT0039145 @ mm9
Intron Retention
Gene
ENSMUSG00000040690 | Col16a1
Description
collagen, type XVI, alpha 1 [Source:MGI Symbol;Acc:MGI:1095396]
Coordinates
chr4:129736976-129737512:+
Coord C1 exon
chr4:129736976-129737014
Coord A exon
chr4:129737015-129737467
Coord C2 exon
chr4:129737468-129737512
Length
453 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGGC
5' ss Score
10.08
3' ss Seq
TTTAACCCTTCCGATTACAGGGC
3' ss Score
9.45
Exon sequences
Seq C1 exon
GGAGATCCAGGTGGCCCACCAGGCCCTAAGGGAGAAAAG
Seq A exon
GTAGGCACAGGGGTGTCATGGACATGGGGTGGGGTGTGATCATGCAGTGCGCGTGCCAGGAGGTGACCAGGCGATGGGCTGAGAGCGGCTCAGTTCAGCCAGGCTGTATGGGGTGGGTGGGGGGTTGTCTCTACTCCACTACTAGCTGGGGTGGGAGCCTTGGCCATGGTGAGCAGCCAGTTACTGGAACTGGAGTGGTCAGTCTGTCTATCTATCTGTCTGTCTGTCTGTCTGTAACCTCCTCCTTGTACTAGGGAAGGATACTCAGAGCCCTTGTCACCTCTTATCTTTTTTCAGAGCTAGGCACACAGGTAGACAGGCAATAGGAAAAAAGGGTTTATCCAGCCAGTGGTCCACACTGAGATGGGAGGCTCAGCTGAGGGTCAGAATGAAGGGGCAAACAGGCAAAGGTCACATCAGTGGGAGCCTCCCCTTTAACCCTTCCGATTACAG
Seq C2 exon
GGCAGCTCTGGAATACCAGGAAAGGAAGGCCCAGGAGGGAAGCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000040690-Col16a1:NM_028266:20
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=PD(7.4=38.5),PF0139113=Collagen=FE(21.4=100)
A:
NA
C2:
PF0139113=Collagen=FE(25.0=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
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: