MmuINT0039343 @ mm10
Intron Retention
Gene
ENSMUSG00000026141 | Col19a1
Description
collagen, type XIX, alpha 1 [Source:MGI Symbol;Acc:MGI:1095415]
Coordinates
chr1:24526385-24530008:-
Coord C1 exon
chr1:24529928-24530008
Coord A exon
chr1:24526511-24529927
Coord C2 exon
chr1:24526385-24526510
Length
3417 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGGT
5' ss Score
10.29
3' ss Seq
ATTCTCTTTGGGGATTTTAGTGT
3' ss Score
4.16
Exon sequences
Seq C1 exon
ATCGAACTTCACCAACTTAGAATCTACTGCAATGCAAACTTCCTAGCTGAAGAATCATGTTGCAACTTATCACCTACTAAG
Seq A exon
GTAGGTTAATTTCCTTGCCATGTGAAACACAAGCAGTGAGATATATTTCAATTGGCATTCGTCATCTGTAGGTTCTATGTGTAGGACTTTGTGAAGCATCTCAGTTGAAACTGGGTGAGTAATTTATTCTCCGTATGGAGCCATTCTTAGAACCAGCTCAACACTTCAACCACAGGGTTGCACACTGAAATTTGATGGTGATTTGTGCTCAGGTTGGTCTCAGTGTAAGAAGAACCAGTCTTTTTGTTTGTTTTTTTCTGAGACAGGGTTTCTCTGTATAGCTCTGGCTGTCCTGGAACTCTCTCTGTAGACCAGGCTGCCCTTGAACTCAGAAATCCGCCTGCCTCTGCCTCCCAAGTGCTGGGATTAAAGGCGTGCACCACCACTGCCCGGCGAGAACCAGTCTTAATGTACACCTTCCTGCCACCCACTGTACCTGTTGCCTTGTCTCATCTGAGGCCCCAGCTGATTGGAGGTGCTGTCCTGGGCATCTTTTCTCCTTCAAACCACTGCACAGGAGGAGTGTTCCATTTCTTGATTTGTCAGCTACAAAATGAAAGGCTTTCAATAGGGAAAAATTATTTTTTAAAAACCCTCCTCAAAATAACATATGAAAACCAAAAGTCCAATATTCAATGAATTGTTTCTTTGGATCTTAATTTCTCCAAATTTTTACACTTCCTAAGAAATCTATATGAAATTTTTAATCAGTGATTTTTTTTTCAATTTAAAAACCCTTGTAACTTCTTTCGTGTGGTGTGTGTACTAGAGTGAAATCTAGCCAAATAACTCAGAGTCTTTCAAATATTATGCCTTGCTTATATAACTTGGCTATATAAAGCATATCTCAAACCCAATTTACGGATCTCATTCCAAGTAAAGTGAAAGTCTGCCAAATATCTTTCTTTAAATACCTAAAAAGATAGCTCAAATGCCAGTCTACAGACCTGAAATACTGAGGTTTCCTGAACCTATACCTTTAATCATTTTTCTTATTTCAAAAGTGTATTGTAAATCATTATGAATGTGTTATATTGGAGTTCTTAAAATAACTATTTTCTTTCACTTAAAAGTAATGTAATGATGTTTTTATACTTATAAGTTTTATATTCTTCTTCATTATTCATTGCCTTATGTTAATAGATTACTATGAAAACAGGTTAGAATAGAAATGGATGAAGAATTGGATGAAGTAACAAGTCTGACATGACTTCACACAATAGTTTAGTTCACAGTGCTAACCTTAAATTTTAATAAAAAGATAAATAACAATCTTTACAAGTATTATTTGAAAATCAGGTTTACAGTTGAAAATAAGTTAAGAATTTAGTCCAAGTATGTAAAAATAACCAAACGATATTTTTTATGTTGATGATCATTTGTGATGATCACATCACCATCCATTCTGAAATTAAAAGTAACTAGAACTCTGATACATTTTTACAAGCAGGAATACATAAATAAGATAATCCTAAAAGCCATTAAATACAGTGGATGAAGATTTGAAACCAACTGTCTTGTATGCTTTTTAGTTTTGAAAACTGTCTTAAAGGGGGCTAGAGAGATGTCTCAGTGTTTAAGAGTGCTTGTTGTATAGCCATGGTGAGCTGAGTTCTTGCTCATCTCTTAGCCCTGATACTATAGTGGGTGGGCAAAGACAAAACACCCCTGAGGCTTGCAGGCTGCTACCCTCTTCTAAGACTACAAGTGTGTGTTTCAGGGAGAGACCCTACTGCAAAGAATAAGGTAGAATATGATAAAGGAGGACAACTAACCCCCCATTGACTTCTGTGGGAGCACACAGGTACACATACCTACACACATATATGCACACCACATACACATAAACTATACACATATTGACACCCACAATAAGTATATTCATAAACATATAAATGTCTAAATCCAAAAATGGCATTATATCTGTGCATTTATAGCTACATATTAATATTAAACCGCACATGCTATTTTCATGTTAATATTTTATGGAGTACTTCAAAGCTGAAATTTATTCCAGACTATCTATAGACATGTTCCACTTCTAATAAAGTCAGATTTTCAGTCTCTGAAACAATCAAATGTCACATGACTGAGGGTATAAAGTAAAAAGTGCATAGGAAATAATAAATCATTCAGGAGAAATGAACTGTGTAGCAATCTTGTTTCATTTGAATATAATTCTAGGTTATTAAATTGAAATTTTATTAAGATACCAAATGATTATTAAATATAGAGGCGATTAACATGGAATCTCTCGTTTCAAATATGAGAATATGGTCACAGTGTGTCTGGGTGTGAAGTTTATTGTGGGTCTTATTGTTACTACAAATATTAGAGTGATACCTATTATTCAAGAGTCATTTATGAATTCTATTTGAGAAAATGCAGGAAGGGAATAAACATCAGATATGAAGATGAAAATAATACCTACCGTGGGCTCACACCACAGTAGCAAGCCATTGACTTTTTATTTGCATAACTTGAATGCAGTTTTCCACTCATGTATAATTTGCATCCAGTGAGTTTTTCCATCTGTTGCTTCATCTTCACTGAAGCTTCAAATAAAGAGTTAGCCATGGGGAACAGCGTGGTATGAGTTGTCAGAACAAGAAGATAAATTGGAATTCCCTTTAGAATCAACATGTGATACTTCCTCTATATTTAAAAATATTTATTATATCTCTGTGTGTTGATATGCTTGTATGAGTGCAGGTATAGAAGAGATCATCAGAGGTTAGAGTAACAGCTGGAGGAGGTCTCCAGATGTAGGGCCTGAGAACAGGACTTGTGTTCTCCACAAATTAGCCCTGGCTTTTAACTGCTGTCTCTCCAGTCTCCTGCATGAAATTAGAGGGGGAAGATTCTGCCTATTTATAGCCGTGTTCAGCATGTTCTAAACTCACCAGGTTCAGAATCCTCCACTTTTACGTCTTTAAAGAACACTGGACTAGAATAGACTATATTGTAATTAGCCGTCTTAGAGTATAAAATAAATTCATTTCCAGCTTGACTTACACTTACCACCAGCTTGCTGCAGTGCCTATATTTTACCAACCAAATTTATATGCTTTTAAACTTTTGTTTGCCATATACTATTCACATTTTGCTTGTGTGAAGTATTTTATTGGAAGAATGTACTATTATTGATATATAATATCACTATACTTATCATAAGGCCACCTAATGTGGCTTTAAAATTTCTCAATAATCACTTTTCATATGCTCTTTGTGTGTAGTCAACATGGTTAAGTACACTGCAGGCTTAGTGATAGAGTAAAAAATGTAATAAACTTTTATAAATGGTTGGCAATCTTGGTTACTAAGAAGGAAGGATGGCAGGCATCCAGACATCTCAGCTTGATGGGAGCTAACTGCAAGAACTGACGTCATTCTCTAAATTCTCTTTGGGGATTTTAG
Seq C2 exon
TGTCCAGAGCAAGACGACTTTGGAAGTACTACTTCATCCTGGGGGACCTCTAACACTGGTAAAATGTCTTCATATCTGCCAGGAAAGCAGGAACTTAAAGACACATGCCAGTGTATTCCAAACAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026141:ENSMUST00000115244:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.667
Domain overlap (PFAM):
C1:
PF133851=Laminin_G_3=PD(7.1=40.7)
A:
NA
C2:
PF0139113=Collagen=PU(0.1=0.0)
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:
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
- 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