MmuINT0115067 @ mm9
Intron Retention
Gene
ENSMUSG00000021223 | Papln
Description
papilin, proteoglycan-like sulfated glycoprotein [Source:MGI Symbol;Acc:MGI:2386139]
Coordinates
chr12:85117970-85118445:+
Coord C1 exon
chr12:85117970-85118152
Coord A exon
chr12:85118153-85118303
Coord C2 exon
chr12:85118304-85118445
Length
151 bp
Sequences
Splice sites
5' ss Seq
CTAGTAAGT
5' ss Score
8.78
3' ss Seq
CTCCCACCCTGGGCCTTCAGTGC
3' ss Score
5.95
Exon sequences
Seq C1 exon
TGCTCAGTTACATGCGGGACTGGCATCAGGAAGAGGAGTGTCACCTGCCGAGGGGACGAGGGGTCTCCGGTCCATGCTGCAGCGTGCTTGTTGAAGGACCAGCCAACCCTCACGGAGCCCTGTGTACAAGAGGCCTGCCCTGTGTTCCGTGGCCAGGCCTGGCATGTTGGCTCATGGAGTCTA
Seq A exon
GTAAGTGCCCTACCCTTCCCAATGCCTTCTGTCCAGGTCTGGTCCCCAGGTCCTGGAGGTGACTTTGAAGAGTGTGGTCCCCTCCTTCTCCACGGATGTCCTTGGCCTCAGTGTCTCTCTCTCTCTTTCCACTCCCACCCTGGGCCTTCAG
Seq C2 exon
TGCTCTAAAAGCTGTGGTTCCGGCATTCGGAGAAGGCAGGTTGTTTGTACCATCGGGCCGCCTGGTCGTTGTGTGGACCTGCAGTCGTCCAAGCCTGCCGAGATGGAAGCCTGCAACAGACAGCCCTGCCATCTTCCTCAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000021223-Papln:NM_130887:13
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.167
Domain overlap (PFAM):
C1:
PF0009014=TSP_1=PD(83.3=73.8),PF0009014=TSP_1=PU(12.0=9.8)
A:
NA
C2:
PF0009014=TSP_1=PD(84.0=87.5)
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:
TGGCATCAGGAAGAGGAGTGT
R:
CTGCAGGTCCACACAACGAC
Band lengths:
247-398
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: