MmuINT0039194 @ mm10
Intron Retention
Gene
ENSMUSG00000040690 | Col16a1
Description
collagen, type XVI, alpha 1 [Source:MGI Symbol;Acc:MGI:1095396]
Coordinates
chr4:130095543-130096534:+
Coord C1 exon
chr4:130095543-130095587
Coord A exon
chr4:130095588-130096345
Coord C2 exon
chr4:130096346-130096534
Length
758 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGG
5' ss Score
9.16
3' ss Seq
ACTGTGACCTGTCCCTGTAGGGT
3' ss Score
10.95
Exon sequences
Seq C1 exon
GGACCTCCTGGAAAGCAGGGACTCTATGGACCCCCTGGCCCAAAG
Seq A exon
GTGAGGGGGCACTGACTGGGTTTGAGAAGAGAGATATTCGGGAACTCCAAGCTGCAACTTTAGCCACAAAGGAGGCCTAGGGTGGCCAGTGGGCAGGAAAAAGGGGATGTGACCTCGCCTGGGACTGTCCCATCTATAGCTCTGGGAACGAAAACCTCTTTAATCCCCTAATAATTGCTCACTCCAGGGCCCCTCTGTGTTGGTCTGGGGTAAACAGAAGCCCCCCCTGAACAATGACAGCCCCTGTGCCTAGTCACCATGACACTAGAGTGCAGCAAATTTTAAAGAAGACTGGATATAGTGCTATGAGACCCCAGGCAGTGAGGGAGGAAGGCACAGGGGACAGGAACAGTTTCTACAGAGGACAGTAGAGGGGGACTCATTGGGGTGCTAAGGCTGGAGAGGGGCATTCCAGACAGCAGATTCGAGCAACATGGTAGAACCAGAGTGACAGGTATGACAAGGTACGTCTGTCAAGCCGAGGCTGAGGAAGGTGTGAGGAGGGCATTGTGAATGGTCCTGGGCACTTCCTACTGAGGGAATGTGGGAGCCAGGAGCATTTCCCAGCATTCCCAGGGATGTAAGCACTACCTTCCAGAAGCACTGCTCTGGGAGGTGGAGAGACAGGAGAGTCTGTATCATGGTGACTGTAGCCCAGCCAGAGATGCTGGGGACTTGGGGAAGGGGCAAGCTGCTGACACATTGCGACACAGACTTGGAAACAGTTGGTAATAGTGTACTGTGACCTGTCCCTGTAG
Seq C2 exon
GGTGACCCTGGACCTGCAGGACAGAAGGGCCAAGCAGGAGAAAAGGGAAGATCTGGCATGCCAGGGGGTCCTGGCAAGAGCGGCTCCATGGGACCTATCGGACCACCGGGGCCTGCAGGAGAGAGAGGTCACCCTGGGTCCCCAGGGCCTGCAGGGAACCCTGGATTGCCTGGTTTGCCGGGCTCTATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000040690:ENSMUST00000044565:65
Average complexity
IR
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(17.1=100)
A:
NA
C2:
PF0139113=Collagen=PD(47.6=61.9),PF0139113=Collagen=PU(90.3=88.9)
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:
CTCCTGGAAAGCAGGGACTCT
R:
CATAGAGCCCGGCAAACCAG
Band lengths:
230-988
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