MmuINT0039448 @ mm9
Intron Retention
Gene
ENSMUSG00000016356 | Col20a1
Description
collagen, type XX, alpha 1 [Source:MGI Symbol;Acc:MGI:1920618]
Coordinates
chr2:180731971-180733204:+
Coord C1 exon
chr2:180731971-180732100
Coord A exon
chr2:180732101-180733058
Coord C2 exon
chr2:180733059-180733204
Length
958 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAAA
5' ss Score
8.59
3' ss Seq
TGATGATCATCCCTTCCTAGCAC
3' ss Score
5.14
Exon sequences
Seq C1 exon
GTGGTGGTGGAGGGGCCTGTCTCATCCATGGAGCTTGGAAACCTGACCTCCAGCACAGAATACTTGGTCTCTGTGCTTCCTGTCTATGAGAGTGGGGTTGGCAAGAGCCTGCAAGGCCGGGCAACCACAG
Seq A exon
GTAAAAGGGTGGCCTTTGTGTAGTCCTGCCCTTTGGGGATAGTACCAGCAGGGCATGACTACAGGCAGCTCTGGGTCAGAAGTGTTCCCACAAGCCACAAGAGGCTTGGGATCTAGACTCTGATCCTGTATCACACCATGGCTCAATACTGCTGCTGCCATGATGTCCTAAGGCTCCCATCCTGTCTGGTGACAACACATGGTCAAGACCACTGTCTCTCAGCCTGCTGCTGGACCTATAATGATTTCTGGTTAACAACTCCATTGAGATAGGGCTCATGCGCCCACACTTACCCACTTACAGGGGACAATAGATAGCTGTTAGTGTATCCAGGGCTTTGCCAGTTGTGGTAGCACACACCTTTAATCCCAGCATTGGAGGGGCAGGTGAATCTCTGTGAGTTCCAAGACAACTAGAGATAGATAGAGAAACCATGTCTCAAAAGACAGAAACCTAAACAAACAAACAAACAAACAAACAAACAAGGACAGTATATTAAGGGCTATTTGCACTAAGACTATCATAGATCATACTCATTTCCCAACAAAAACTGCACATTTCATTAACACCTTCACCCAGCCCTTGCAACCTCTGCTCTGCTCTATGCCTCTGGATCTGCCTCTTCCAGTTATTCACAGAGACACCTTGGTGAAGTATGTGAGGTTTTGTGTGTGTGATCCTGGATACAACATCCCTTATCACCTTTGTAGCAAATTGCCTTAGGCTAGCAGGGTGATCTGGCTCCCCCAGGACTGTGAGCCGAAAACACAGCCCACTGACATTTGAGACACGTGACTTAGAGTCCTGTACTCTGGATGGTGGTTGCCTACCCGGCCATCTGTACAACCCTACCTACTCAAAGTCTTGTCACTGGAAAAAGGGCTTTGTTGTCCATGTATATGAGTTCTGCATGTGCCACAATTCCCCTGAGATTCTCCTGATGATCATCCCTTCCTAG
Seq C2 exon
CACCCCTGCCTCCACCTGGGCCACTGACCCTAGCTGCAGTGACACCCAGAACTCTCCACGTCACCTGGCCGCCCTCTGCTGGGGTCACTCAGTACTTGGTGCAGTACTTGCTGGCTACCTCCACTGGGGAGGAGCAAAAGAGAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000016356-Col20a1:NM_028518:10
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.268 A=NA C2=0.390
Domain overlap (PFAM):
C1:
PF0004116=fn3=PD(43.8=79.5)
A:
NA
C2:
PF0004116=fn3=PU(57.0=91.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTGGAGGGGCCTGTCTCATC
R:
CTCTCTCTTTTGCTCCTCCCC
Band lengths:
270-1228
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: