MmuINT0039326 @ mm10
Intron Retention
Gene
ENSMUSG00000026141 | Col19a1
Description
collagen, type XIX, alpha 1 [Source:MGI Symbol;Acc:MGI:1095415]
Coordinates
chr1:24301400-24303500:-
Coord C1 exon
chr1:24303456-24303500
Coord A exon
chr1:24301451-24303455
Coord C2 exon
chr1:24301400-24301450
Length
2005 bp
Sequences
Splice sites
5' ss Seq
CCTGTGAGT
5' ss Score
7.21
3' ss Seq
TGTCTCATTTTTTTCCTAAGGGT
3' ss Score
9.12
Exon sequences
Seq C1 exon
GGTAGTGAGGGACCCCCTGGGAAACCTGGACCTCCTGGACCCCCT
Seq A exon
GTGAGTTGTTTGAGGTTTTAATTCTGTGTACTTATGACTCATACGTAGGTTACCTAGATGCTTGCAAAACAAAATATTCAGTTGAGTGTGTGCTTTTGTGACTGCTTGTGTGTGAGCATGTGTGCCTGTATACATGCCTGTGCGTGTATGTGTGTGTGTGTGTGTGTGTGTATACGTGTGTAAATGACATGCAATGCAGCATTAGGTGGGCCTAACCCGTCTCTATTTCAGCTCAGCTGCAGTCTGCAGTGTTTAGAGTTGTTTGTATAGTGTGAACTTCTTTTCCATGGAATCCGGACGCCTGACTCTCTACTTCCATCAACGGATGGAGAAACATTTGACTACACAGATGATAAAGCTCCACAGATATTAAAAGGCCTTTAAGAAGACATCTTTCCAACCACGCAATTTGCTTTTTCAAAGATGTTGTTTATGTTCACCCCATAAGCAGTGTCTGAGACGGGAAGACATTCTACTTCCAGGGCACGCAGTGAGAAAAATGCCCCAGGGCTCTGGAGGTCTTCTGCCCTAGTCAGCCACACAGACTTCCAGGGAGGCTGTGCAGAGCAGCGCGGCCTCTCTCTGTAGCAAGTCTGCCCTCTTGTGGAGCCATGTTCGAATAGCAGCAGAGCTGGGGCTCACACGTGTTATTTCCTGCATTACCTCGTAGGAACTTAAAAATCCAAACTTAGCAGAGAAAGGGTGAAGTCTCACAGTAGCTTTCTGAAAACTAAAGAGTATGTTATGAGTCTGGGTATAGTTGCATGCTTTACACACAAATTAACTGCGTTGGCCTCCGCTTTCTTAAACACATTCTGCATCGGATTCTTCCTTCACATAGAAGCAAGCCAGACAACTCACAGAGTTCAGATTCTAAAAATGTCATCTCCTCAATGGGGGTAAAAAGCAAAATATATCATGAGACCGTTAAAGAAACCTGTGCTTTTCTATAAGGCTTAAGAAATCTGCCTCTTGTCTCTAGATTTTTTTTTTTAAGCCAGATTATACATCTTCTCTTGGAAAACATTCTTACATCTATTCGAGGCCAAGTATACTGAAATATAGCCCATGTTCAGTTATTGCCAAAAGAGTGAAGAATCAATAAAAGGATAAACAGACAGAGCATCCTCTTCTGTCACCACTGATTTGAAGATGCGTGGAAACAGTGCTCGCTGGGCACGGCTACCTCTACTGTTATCCTCAAGCAGTAATGAAATAAAGACTTCCTCATTTTTACAGCTGAGGTATAGAAAAAATAACAAAAAAAAAATGAAAACACACTTGGATTTTTTTTCTTAGAGTCTGTTATCCTTTCTAGGTGTTTCCAAACTGAATGTTTCGTGTGCATTTTTGCAAACATGGACGAGAGTTTTCAAGCTACACAATGAGTGCAGTTTCATGCTCTATATTTATGCATCAAAGTTTTAGTTTTGTTGTTTTGTTTGTTTGTTTGTTTGTTTTGAGCAAGTTCTTGTTCCCTGGTTATTAAAGACATCTTGGTAGAAGCATCCACACAGGGTGTTATGAGTGACGTTATCCTCCCATTCACCTTAAGTTTCTGTCTGGCTTGAAGAGACTGTGAGGAAACGTCACTTTGCAGTTGGCAAGCTGTTCCCTAGTCACAGCTACATCAGTCCGACGGCATGGCTGCCTGCAGGTCAGCAGGCTGAGAACACAGTAAATTGGCTATTCAGACACTGAATTTTAATGAGCAGATAGTATTTTTTCAACCAATTGCATTAGAACCTCATGTGCCACACCTGAACACGACTCACACTCCAACCGGAAGCATCCAAGTGTTCCAGACATAAGTCAGGCTCCTTTGTCCAGTTTTCCCCACTGTTTTAAAATATTGAAACACTGTGGTATTTGGTTTATGGTATTAAATTCACCTTAAATATAGAGTAGGGGGAAATTTAAGTAAAAGTTAATATAGAAAGAATACCATCTGATAAAATGACCAAAGTTCCAAGTGCTAACTTCTGTGTCTCATTTTTTTCCTAAG
Seq C2 exon
GGTGTCCCGCTCAATGAGGGAAACGGCATGAGCAGTTTATATAAAATCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026141:ENSMUST00000115244:37
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=FE(20.9=100)
A:
NA
C2:
PF0139113=Collagen=PD(13.4=52.9)
Main Inclusion Isoform:
NA
Other Inclusion 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:
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