MmuINT0115065 @ mm9
Intron Retention
Gene
ENSMUSG00000021223 | Papln
Description
papilin, proteoglycan-like sulfated glycoprotein [Source:MGI Symbol;Acc:MGI:2386139]
Coordinates
chr12:85116293-85117511:+
Coord C1 exon
chr12:85116293-85116419
Coord A exon
chr12:85116420-85117303
Coord C2 exon
chr12:85117304-85117511
Length
884 bp
Sequences
Splice sites
5' ss Seq
GCGGTGAGG
5' ss Score
7.93
3' ss Seq
CCACCTTCTTTTTTGGTCAGCTG
3' ss Score
6.06
Exon sequences
Seq C1 exon
GTCACCAGTCCCGCCTGGTATTCTGCACTATTGACAACGAGGCCTATCCAGACCACATGTGCCAACACCAGCCTCGGCCCACCCACCGACGTTCATGCAACACTCAACCTTGTCCGAAGACCAAGCG
Seq A exon
GTGAGGCCTTGCCAGCCCCTTCCACCTTTGGTGGTGCCCAGGAACTTGGGTGGGAAGGGAGGGGAAGCCCTAAACAAAGCTGCTTTAGGCACAGGCTGAAGGTTGGAGGGGGGCGGGGGCAGGGCTCCTCACATCAGGTGGCAGCTGTCACTGAGGGAGGCGGTGAATGGGCCTGAGCAGGAGACCCAGGACAGTTCTCTCCATTCACGGGTTTCCTCACAGTATTCAAAATGCCTGGGAACAAGAGGCTTTGGGGACAGTGTCAGAGGTCCCTGTCTAAGGCAACAGGGGACTCGAGCAGATGGCTAGGGGAGAGCGAGGCAGGAATCTGGCCAAAGGGCCAGTAGACTTTGGCAAACACCTTTGTTCGTGCACAAAGGATCTCTTTCCTGCACCGGCCGGGAGCGTGGCGCTATGCTGGGGTCCAGCATATGTGTGGGAACAGGTAATCGGTGGGCCAGGGGGTTCCTGCCGGGCTGGTGTTGCTCTCCCTACCCTCCCGGCCTCCTGGTGAGATGGTGATGGTCTTGGCTTTGCATGGTGTGTTTGGAGCTTCCCTTTCCTTTGGTCCTTGTACCCCTCGCCCCCAGCCAGGCAGGGCTTCTCCACATACAGGGAGATCACCTCACACAGGATGGCAACCCATGGAGTCTGGCTATGATGCCAGCACCCAGTGAGAAAGAGAAAGGGAGAGTTGGGCGCAGCCGGGTTATAGAGACCCTTCAGGGGCCAGTGAGCCATAGGGGATGCCTAGGAGGCCTGGCTGGTGGTCTTTCTACAGAGCTCTTGGGGAGGGTGGAGACAGGCCCTCGATGTACTCTGAGTTGGGGAGCTGCAGCCTCCTGGGCTAGTCTTAACTGTCCCCCACCTTCTTTTTTGGTCAG
Seq C2 exon
CTGGAAGGTAGGCCCATGGACGCCCTGCTCGGTCTCCTGCGGGGGTGGAGTCCAGTCTCGCTCTGTCTACTGCATATCCTCAGATGGGACTGGTGGCCAGGAAGCTGCTGAGGAGACCCAGTGTGCTGGCCTAGTTGGGAAACCCCCTACCACACAGGCTTGCAACCTGCAGCACTGTGCAGTCTGGAGCGTGGAGCCCTGGGGAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000021223-Papln:NM_130887:11
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.151 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0009014=TSP_1=WD(100=82.9),PF0009014=TSP_1=PU(13.0=10.0)
Main Inclusion Isoform:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCCGCCTGGTATTCTGCACTA
R:
CTCTCCCCAGGGCTCCAC
Band lengths:
326-1210
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: