MmuINT0039456 @ mm9
Intron Retention
Gene
ENSMUSG00000016356 | Col20a1
Description
collagen, type XX, alpha 1 [Source:MGI Symbol;Acc:MGI:1920618]
Coordinates
chr2:180735919-180737072:+
Coord C1 exon
chr2:180735919-180736048
Coord A exon
chr2:180736049-180737033
Coord C2 exon
chr2:180737034-180737072
Length
985 bp
Sequences
Splice sites
5' ss Seq
CAGGTTAGT
5' ss Score
8.02
3' ss Seq
GACCCTTCATGTCCTCTCAGCAG
3' ss Score
5.55
Exon sequences
Seq C1 exon
ATCTCTGTACCAGGCACCAGGAGCCATGCCGTGCTTCGTGATCTGATGTCTGCCACGAAGTACAGGGTCCTGGTCTCAGCTGTCTACAGAGCAGGGGAGAGCATGGCAGTGTCTGCCACATACCGCACAG
Seq A exon
GTTAGTGGTCACCAATGCTGCAGCTCTTTCTAAATACCAAGCCCAAGCCAGACTCAAGGTCCAGCTAGATGCTAGGCCCAGTCAGGCTTTAGAACTGGTCATACTCCAGAGTAGGCCAGATACTAGATCCAGTGAGACCCCAGATTCAGTGAGGCACCAGAACCAGTGACATCCCGGAGCTAGTGAGACCTCATACCCAGGGAAACCCCAGGTACAACACAGAATGTAGAGATGCCATGGACAGCAGGGTACCTAAAGCAAATAGAGCAAGCTGGATCAGAGTGACTGGGAAATGTCTAGAGAGTATGGAGAGTTCTGCCCAGAAAAGACCTGCTCTTGATGCCACAGGACATGGCAGGTAGGTCTCTAGTGGCCTGGTATCCTCCAACCCACAAGGCCAAGCTTAGCTGTGAACAATTACCTAGGAGCCACAGCTGCTGAAGTCAAAGGGCCTTCAGAGGCTGCCACACCTACTACCTCAGCTGTAGTGCCTCCTTTGGGGTCATCCACTTATAATCTAAATGCCTATCACAATCAGTCCCTCACTGCTCAGTGGATGACCACCGGGCCTGGAGCCCTGACTGTGATGTCATCTGCCTTGTACTGGCTACAGGGCCAGCCTGTACCCTTTCTTACCTCCTCCAGACCTGTGCTGCTTCCAGTCATCTCCCTGACCCTACCATCTGGTGCCTACAGTTCATTTGGAGCCCATAACGTGTTTAGGCAGAGTCCCCAGTGGAACCTTGGTTTTGGCCTGGGGTGTACAGGGTAGGCAGGAGCATCTGCCCACTTAGTGTGATCCCAGGATGGCAGTGAGGAATGGAGACTGCAGGGTTGGTGTGACAAAGGGAGTCAAGGGGAGCAGGCGCCTACCTCAGCATAGGTCCACCTGTGCTCACCAGAGGCCTGACATTGCCGTGAAGTGGTCCTTCTGGTAGTTGGGCTAGCTTTGCTGTGACTCACCAGACCCTTCATGTCCTCTCAG
Seq C2 exon
CAGCCTGCCCAGCCCTGCACCCGGACAGTTCCCTCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000016356-Col20a1:NM_028518:18
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.053 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0004116=fn3=PD(43.2=79.5)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
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: