MmuINT0115072 @ mm9
Intron Retention
Gene
ENSMUSG00000021223 | Papln
Description
papilin, proteoglycan-like sulfated glycoprotein [Source:MGI Symbol;Acc:MGI:2386139]
Coordinates
chr12:85121500-85123245:+
Coord C1 exon
chr12:85121500-85121638
Coord A exon
chr12:85121639-85122770
Coord C2 exon
chr12:85122771-85123245
Length
1132 bp
Sequences
Splice sites
5' ss Seq
ATGGTGAGC
5' ss Score
8.27
3' ss Seq
CTTCCATCCCCAACCCACAGCTT
3' ss Score
8.1
Exon sequences
Seq C1 exon
AACCCCAAGATCCACCAACCCCAGGCCCATGAAGGCGAGCCCAGTGAGTGTCGAAGCTCTAGGTTTGGATGTTGCTATGACAATGTGGCTTCTGCAGCGGGTCCGCTGGGGGAAGGCTGTGTGGGCCAGCCCAGCTATG
Seq A exon
GTGAGCCAGTGCCCCTTCTCATCCTTATCTCACTGGATCCTCATCCCCAACCCATGGCCATACCTCACTGACTCAGGTTTCCCAGTACGTGAGCACACACCTGATACCAGGCCAGAGGGACGGCCCTGCATCTAAGATGTTTACAGATGGATGTCCCTGCATCTAAGATGTTCACATAGGGCTGGGAGGATTAGAAGTGGAACTCTCGGTGCTGGAGATGTGGCTCAGTTGGTAGAGTGCTTACCTAGCATGCACCAAGGCCTGGGTTCAACCTTCGGTGATACATAAACCAGATATGGTGGTACAGGTTTATAATCCCAGCACTTGAGAGGTAGAGGGGCAGGATGATCAGAAATTCAAGGTCATTTTTGGCTATATACTATGTTCAAGGCCAACCTGAAATTTATAAGATTATGTCACAAGAGAGAGAGAGAGAAAGAAAGGAAGAAAGAAAAGAAAGAGAGAAAGAGAAAGAAAAATGGGGATCTTAAATAAAACAAGGTCCATCCTGTGTCTGGAATGAGTTTCCTCCCAAAGGAAGGGCAGGACAAAGTAGACAGTGTGCTGTAGGGCTTGCCTGTGCCTGAGATGGGGCGGATGTTACAGGGAGTAGCGGCTGAGTTTTAGAGAGAAGGTCGGGGCTGAAGCATGGGATGGCAGATGGGTGGTGCTTCCGGGCTCTGTCATGGGAATATTCATCTAAAGTCTGACAGCCTGGTGGGCTCTGCAGAAGGGTGGGGAACAGGACAGGCAGCCAAGGCCACTTGGAACATGAAGAGATGGAGCAGGCTGTTTAGGCTGACCAGCTGTCCTGCCGCATATGTTCATAGCCCCTCAGGGGCAGCCACAATGAACTCCCGGTTGGTTTGTGTGCGCACCACACCATGAGGATCAGGCTGGAAGGGACATTAGCTTGCTCAGGGAGCCCTGGTCTTTTCTTCCTGGGGACTCTAGTTTTGTATGGGTGGAGGCTGCTGTCTAGGACAGACCCTGGAAGTGTCCTGGGCTCCTAAGGGAGGTCAGGGGTCCTGGCAAGAGTGGGGCTGTGCTCTTTAAAGCAGGACAAGTATGCTCCTTAAGGCGAAAGTGAGTAGTGCTCTCACCGGTGACATCTTCCATCCCCAACCCACAG
Seq C2 exon
CTTACCCAGTGCGGTGTCTGCTGCCCAGTGCTCAAGGGTCATGTGGAGACTGGGCCGCCCGTTGGTACTTTGTGGCATCGGTGGGCCGGTGTAACCGCTTTTGGTATGGCGGCTGTCATGGCAACGCCAATAACTTTGCATCGGAGCAGGAGTGCATGAACACCTGCCGGGGACAGCATGGGCCCCGCCGTCCTGAGGCAGGAGCCGCTGGGCATCGTGCCCATGTGGATGGTGGTCAACGTGGTCCTGGAGGCCAGCAGGAACCTGACTGGCACAGGGCAGGAGCCACAATCCCGAGACTGCCCTCCCCTTCTGGAAGCCCTTGGCGGAGAGAACAAGAGCCTGCGCCAGGGGAGCCACCCCACATCCCAGCCTATGGAAACCGGCCTGGAGGCCAGGAAATCCGGCCCAGAGTTCCTGGACTGGACAGAGAGGCTAGGCCAGCAGTGCCGCCTACACATAGCCCCTCCTACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000021223-Papln:NM_130887:18
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.277 A=NA C2=0.692
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0001418=Kunitz_BPTI=WD(100=33.3),PF0768612=V-set=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:
CCCAGTGAGTGTCGAAGCTCT
R:
ACGTTGACCACCATCCACATG
Band lengths:
342-1474
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: