MmuINT0115085 @ mm10
Intron Retention
Gene
ENSMUSG00000021223 | Papln
Description
papilin, proteoglycan-like sulfated glycoprotein [Source:MGI Symbol;Acc:MGI:2386139]
Coordinates
chr12:83773108-83773947:+
Coord C1 exon
chr12:83773108-83773238
Coord A exon
chr12:83773239-83773823
Coord C2 exon
chr12:83773824-83773947
Length
585 bp
Sequences
Splice sites
5' ss Seq
CGAGTGAGT
5' ss Score
8.49
3' ss Seq
CCCCCCCCCCTTCCCCGCAGGTG
3' ss Score
14.41
Exon sequences
Seq C1 exon
CCCCTAATAAGTGTGAGCTGAACTGCATTCCCAAGGGGCAGAACTTCTACTACAAACACAAGGACGCCGTGGTGGATGGGACACCCTGTGAGCCTGGCCAGCGGGACATCTGTGTGGACGGAGTCTGCCGA
Seq A exon
GTGAGTGCTGCCCCCTCCCAGCTGGCTGGGGGACTATTATGGGTGATGTCTTCCAGCATCAGTGGGACCAAGTGGCTGTCAGGAGTTTGGTGGCTTAAGTCCTAGTTCCCAGAATGCAATGCAGTCATCACGGATATTCTCTGACGACCTCAGCTTTGTCCTTGAGAACACTAACCTCATCAAAGAAACTCTCTGGATGTCTAAAGCTGCCCTCAACCAAACCCAACCAAATGGGAAGGGGTGGCTGTAGAAGCCATGGGCTAGACATTCTCTACCCATCTCGTGCTTCCTTCTCCTCTGGGTCAGCTTCAGACTCGGGCAGGCTCTCCTCATGAGCATGAGACAAGATGGCAGCCCCAGGCCTCTACTACACCAGTCTGCCAGCATCTGAGTTCATAGCAGCCTGGTCTCAGCTCTCTGTCCTGTCAGCCTAAGGGAGGCAGGGAGTGGTTAGTGGCAGCTGGGACGGGTCTGAGCCATTCCGTGCCCTGCTGCCCTGCCTCGGGGCATTTGGAATCCTGAGCCTGCCTCTCCTGTTCTATCCCACCTTGCTTACTTTCTACCTCCCCCCCCCCTTCCCCGCAG
Seq C2 exon
GTGGTTGGCTGTGATCACAAGCTAGACTCAATCAAGCAGGAGGACAAGTGTCTGCAGTGTGGGGGTGATGGCTCATCCTGCTACCCGGTCACAGGAACCTTTGATGGCAATGATCTCAGCAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000021223:ENSMUST00000121733:6
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=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF059869=ADAM_spacer1=PU(12.1=33.3)
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:
CCCCTAATAAGTGTGAGCTGAACT
R:
TCTGCTGAGATCATTGCCATCA
Band lengths:
254-839
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