MmuINT0039539 @ mm10
Intron Retention
Gene
ENSMUSG00000079022 | Col22a1
Description
collagen, type XXII, alpha 1 [Source:MGI Symbol;Acc:MGI:1916950]
Coordinates
chr15:71804114-71806281:-
Coord C1 exon
chr15:71806215-71806281
Coord A exon
chr15:71804297-71806214
Coord C2 exon
chr15:71804114-71804296
Length
1918 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGT
5' ss Score
10.47
3' ss Seq
CTCTTCTTCCCATTCCATAGCTA
3' ss Score
8.3
Exon sequences
Seq C1 exon
GGGGAGTCTCCATCCATGGACACCTTACGGCGCCTCATTCAGGAAGAGCTTGGGAAGCAGCTAGAAG
Seq A exon
GTGAGTAGCTGGACTTGATTGCAGCTGCCAGGGTAAGATCCCCAGTGAGCTGGGACAGGTGCGCGTGGAGCAGCAAGCTTGAGAAGTAACTTGAGGGCCCAGCTTTACCCTCCAGATCCTCTCTCAGCTTCTTCCTGGTCACCTCTAGTGACAATGACTCTAGTGAATGATGACACCAGATACCACCATCTGCTGGGTGGTGATCACCTGCACTTTCTGTGTATTCAACCATGTGCATGATTAATCATTGTTCTAGGAAAGTGTGCAGGGGGCCTCATTGAACTCCAGAGGAAGAGCTAAGTCGGGAGACAGATGAGATGACTGCAGTTTACCCTCAGAAGACATCTGTAATTTCTTTCTGGCACATAGGGCACTGAAAGAGAACAGTTGGCACTGCTTCAGATAGCTCTAAGACAGAGTATGGAATGGGAAGCAAGAATGGTGACAGCTTTAACAGCTGTACAGGGGTTCTTGTCTTGGGAGGGCTCTCAGAGCTTGAGCATGCCCAATGACAGCCTAGTAGTGGCCATGAGAGACAGCATGGTTATTGGGAGGATACTGGAGAGCAGGGAGGCTGGGCTACTGAAATATAAGTCTGGGATTTACAGCCTCATTGTCTGTATATTATATTACCATAGTCTGGATAGCAGTCATTCTTCCCATTTCCCCTGTGATAAAAGCTTAGAAAAAAAATGCTCACAAACCTGTGATATGAAAGAGTTAGACCCTAAAGGTGTATCCATTCCCATGTCCCATGTCCCAGTATTGTGTGTCTCACACATTCAGACTACACTGAATACGAGGATGTAGAAGCAAGGTGCCCCTCTACTCTGCCCCTCTGGAATCTAGGTAAATGTGTATGGGCCGTGGATGAGGAAGGGAAGGGAAGGCAGGGATGGACTAGAAATGTTGTAAGCCCCACTGGACCAGGCAAGTCTGAGAACTTGTGTGTGAGAGTTCCAAGTTCTACCGCTTGAATGTTAGACTTGTCAGTGATGGACTGGCTTCTGCCCTAGCGGAGTGTCAACCACTCGTTTTTTAAGGCGGTCTGGGAACATCTGCTGGAATGAGTCCATTTCAAGCAACCTTTGAGGAGGAAATATTGACAAATTCCAGCAAAGATAAGAAAATCAAAGACTCAGACAAGGTCAGCAAATTTCCAAGGTCACTTAGGTAGCATCCACAGACTCCTGGGCCTTGTGAAGGTGCAATGGCAAAGGGAGCCAATGAGGCAGTCAGAAATCCCACCTCTTCTTTACTCTTACCAACCAAAATGTTAGTGTTTATCCGTCACTCCACCCACTGGCTAGGCATTTCTATCCAGTGCTCTCTGACTATACAAATATAAGTGGCTCTTGGTAGCCAGTAGGTAAGCACTGGATCCAGTGTCCAGCATCCAGCATGAAAGTGAGCCCACCCACAGTTGGAGCTCTGGGTTTTAAATAGATTCTGTAGTGCTTGTATCACAGATGTGCAAGCATCTCCAATTAACAGCTTATTTGGATCTTTGGTTGTTGATGGAACTTGATTCAAAAGATAGAAGTCACTAAATAGCTTTTTGTAAGCCACTTAAACATCCCAGGCCTCAGTTTCTCCAACTGGCAGTTACAGCCACTTCTATTACTGCTGCTGCCATCACAAACAGCAGTGCTGCTGTTCCTGCATTGCTAATACTACTATTACTTAATCTCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGTAGGCATCCACACAGTTAGAAATATTTGTACAGGAGCTGTTCCTTGTCTTCATCTCCAGTTGGTTTTGCCTGCAATTCTAGCTTGCAGTAAGCTGCCAGTATGTCCCTCAGCCCATCCTCACTCCATTCCTCAGGATCTTCTCTCTTCTTCCCATTCCATAG
Seq C2 exon
CTAAACTTGCCTACCTCCTAGCCCAGATGCCTCCAGCACACATGAAGTCCTCTCAAGGCAGACCCGGACCTCCTGGACCCCCTGGAAAAGATGGGCTGCCAGGTCGGACAGGCCCCATGGGTGAGCCAGGCCGTCCTGGCCAAGGTGGTCTGGAAGGACCCTCTGGACCAATGGGCCCCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000079022:ENSMUST00000159993:61
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=PD(8.3=21.7)
A:
NA
C2:
PF0139113=Collagen=PU(75.0=72.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping 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:
CATCCATGGACACCTTACGGC
R:
CTTTGGGGCCCATTGGTC
Band lengths:
240-2158
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