MmuINT0039135 @ mm9
Intron Retention
Gene
ENSMUSG00000040690 | Col16a1
Description
collagen, type XVI, alpha 1 [Source:MGI Symbol;Acc:MGI:1095396]
Coordinates
chr4:129733234-129734213:+
Coord C1 exon
chr4:129733234-129733269
Coord A exon
chr4:129733270-129734186
Coord C2 exon
chr4:129734187-129734213
Length
917 bp
Sequences
Splice sites
5' ss Seq
AATGTGAGT
5' ss Score
7.8
3' ss Seq
TCCTTCTTCTGTTCCCTTAGGTC
3' ss Score
12.12
Exon sequences
Seq C1 exon
TGCCCACCCTGTGCCCACAGTGCCCGGGAGAGCAAT
Seq A exon
GTGAGTCAATGAAGGAGCCAGTCTGGGAGTGGGTGTTGCCTGGAGTGGACTGGAGCTTCCTGGTAGAGGACAAGGGGGGCTTTGTTCAATTTCCCATCACTCCCCTGCCTGATTCCCAGAGCTAGGCTTGTCCCCACCCCTAAGCCCACCAAGCCAGGGCTGCCTTGAAGGCAGCACTGGCCCTGACGTCTCAATGGAGTGTTGTGATCTAGGGTGGTGGCCTGAGTAGGGGATGGGGTCGGGGGAGAACAGGACTCAAGACCTTGGTTGCTGATTTCAGCTGTGCCTCCAGGCCTCAGACCCACTTTGATCACAAGGTACCATATGCCACCTTGGAGACGTAGAGCAGGGCCGGAACAGCCCAGTGTCTCACAGCTCAGAGCCTGAACATTCTCCTCTCCTCCTCCTCCAAAGCTAGCCTAGCCCAGCTTTCCCACTGGGAGTTGGAAGGACAGGGTTTGGGGCTCATGTGAGCTGTCTGGTACCTATTGTGCCCCTTCCATAGGCATCGAGAGTTACTGTGTTTTTAGCATTCATTCACAAAGGGCATGGATCTCCTAATTCTCGGGGGGGGGGGGTTAGAAGTACCCACACTTCTTCCAGCCAGCCTGTCTCTTTTTCTACCCAGTCTCCCATAAAATCCCAAATGCACTGGGGTTGCCATGGCAACTGAGTGACCATGTTAGCCTAACAATTTGAGGTGGGGCTGGCCAAAAGCAGGCAGGTTGGAGAAAGTAGACCCCTAGGTTGGCTTTATAGCCTTGAAAAGTAGTGTCAGCATGCTGATTGGCCTAGGAGGCAGACCTGGCGTTGGACTTTGGTCATGTTGTGGTGAACCCAACTGACTTCCTTGCTCTCTCTGGACCGCGGGTTGTTCCCTGAAGTTTAATATTCTTGTCCTTCTTCTGTTCCCTTAG
Seq C2 exon
GTCACACTTGGTCCCTCTGGCCTCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000040690-Col16a1:NM_028266:11
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=PU(0.1=0.0)
A:
NA
C2:
PF0139113=Collagen=FE(21.6=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
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: