MmuINT0039171 @ mm9
Intron Retention
Gene
ENSMUSG00000040690 | Col16a1
Description
collagen, type XVI, alpha 1 [Source:MGI Symbol;Acc:MGI:1095396]
Coordinates
chr4:129754464-129756524:+
Coord C1 exon
chr4:129754464-129754496
Coord A exon
chr4:129754497-129756407
Coord C2 exon
chr4:129756408-129756524
Length
1911 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGA
5' ss Score
10.57
3' ss Seq
CTTTCCGTTTTCCCCATCAGAGC
3' ss Score
10.24
Exon sequences
Seq C1 exon
GGATCCTTACCCATCGAGAAACACCTCCTCAAG
Seq A exon
GTAAGAGGGCCGCTGGCAGGTGTCACCAACGGGATTCTCACAGCAGGCGCTCAGCTGCCTGCCACCTAACAGCAGCAGGTTGAGCCTGCTGGCACCCTGCGTTGGGGGAAGGACCTCCTAAGCAGCTGTCTGAGAGGGCTTGGCTGGGCCTCTGGCTTTGGAACCACCCTCTAGGCAGCATTTATTGAGTGAATGCTTAAAGGAAGGCTGCAAATCCCCCCACCTGCAGCGCTCCTGGTGACAGAACCCAGCCTGAAGTCAGCTCGCATCAGTTGCCAAAGAAGCACCCTAGCACCTGGGTCCGCAAAAGCCACCATGGCATCACACAGAGTGTGACAGTGAAGTGATATGGGGAGTGGGTGGGTGTCAGTTTAAAAAGACTTCAGCAGGGGGAGGGACTTTAAAAAAAAAAAGCAGCTGTGGAGGAGAGTTGGCCTGCGGTCCTGCCAAAGGGCTGTCTGGTCTGACTGACCAAGTTCTCTGGAGCCTCAGGCTTCCTACAGTCTCCTCTCCCCCCTGTTTATTCACCTTTAGAAGTGACATGGGCTGGGTCATTCCTGCAGGCTCACTTCAAGCTCCTGCACCCCTCTCTAGGAGTGCGGCAGCCTCAGGACACCCTTCCCCATGAAGCCTCCTCTAGCTTCTCTCTTGGGCACAGGCTGGTCAGTGTCGTGGACATTATGCCACCCCAGGGAGCTCTGGTCAGGGCACAGTATAAGGGCTGCCTGCCCTGCCCCTCTGAACCGTGGATGTTTCCAGAAGCAGCTTGCACCAGCCCTGAGCTGCAGCACAGTGAGGTTACAGCAAGGAGACCACCCACCCCCTTCTCTCCTGGTCTCAGGGGAGCCTGAGTCCCCCAGGCCCTGCCCTCCAGGCAGTGATGGTGTGACTCCAACCCCAGATGGGTCACACTTCTAACATCTCACTTGCTGGCTTTGTAATCAAGGGCTCCACAAAAAGTCTGACACAGGAACTGAACTCAGCCTGTAAGAGAAGTCAGACGGCAGCCAGGGGAGCTGGCCGGGAGACAGTGGTCACTGTGTCCGCAGCCCAGAGAAAGTGCTGACTCCAGACAGTCAGGCAGGGACCAATCCGGGCTTACCTGGACAAATCACACTGCCTCTTTTGAATATCGGCTTTCTTATCTCTACAATGCTCATAACATAAGCAGCCTCTCTGTGCCCTGGGACTGAATGTGCCAAGGCCCATTATAACCCGTGGCCTTATGGCTGCTGTGCAAATGGCCGTTGGTATTGATGTTACTAGGAATAGTGAAAGTGAGCGTGGGGCTCCTGCCTCGGACCCCAGCACCACGCCTGCAACAGAGAAGCTCCAGGCTCCCAAGGGCTCTATCATCTCTCAGAGTCTGTGACCAAACAAGGGCAGTGCCTGATCCAGAGAAAGCCTTTCCTATAAGGACAGACAGTTCAGACCCAGGGACCTGTGGAGCCTGTGACAGTTGTTGAGCTGCAGGCCCTCCCCAGGAACATCCATCGAGGGCCTCCTCCTGCGGCTGTCTCCTGGCATCCCCAGGCAGAGGTGCTGGCACCAGGAGCCAGCTTTTTCATCCTGGATCCTTGGGGCTTGTCCTCGCGGCGGGTGCAGGTTGCAGGAACAGGCGGGACAGATGGTCCCTCCGCGGGTCCCTCCGCCTCCTCCCACACTCCTGTCTGGAAAGCGCTCTGGCTTGGCCCTACCTGAGCCTCTTCCTGGAGGAGACTCAGAGCCAATTGCTGTGATCGGGTCCCCTGAGGACAGAGCGGAGCTGCTGCAGGGATGTGGCTGGGGAAGGAGAGTGTGAGGGTGAAGGACTGCTGGGCAGGGTGCCCGGGCCCTGCATTCTGTGAGGGCATCCCCTAGGCTGCCCATCTCTGACCTGGGTCCTTCTGTCCTTTCCGTTTTCCCCATCAG
Seq C2 exon
AGCATCTGTGGTGACTGTGCCCAGGGCCAGACGGCTCATCCAGCCTTCCTTCTGGAGAAAGGAGAAAAGGGGGACCAGGGCATCCCTGGCGTGCCAGGTTTTGACAACTGTGCCAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000040690-Col16a1:NM_028266:44
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.462 A=NA C2=0.730
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(2.6=18.2)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
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: