MmuINT1032234 @ mm10
Intron Retention
Gene
ENSMUSG00000029699 | Ssc4d
Description
scavenger receptor cysteine rich family, 4 domains [Source:MGI Symbol;Acc:MGI:1924709]
Coordinates
chr5:135967738-135968259:-
Coord C1 exon
chr5:135968224-135968259
Coord A exon
chr5:135968044-135968223
Coord C2 exon
chr5:135967738-135968043
Length
180 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGT
5' ss Score
10.28
3' ss Seq
TTTTTTTTTTTTTTTTACAGAAC
3' ss Score
12.01
Exon sequences
Seq C1 exon
CCAGTGCCCTCCAGCCCACTCCGCTGCCCTTTCCAG
Seq A exon
GTAGGTCCTGCCTCTTCCCCTCATCCTCATGGATATTCCCAAGCTGGCATGGCCCAGCTGCACCAGTATAATAGAAGGCTCCCGTGGCATCCCGTCTCCCGTGGCATTCCGGAATTCGGGCTCCCGATTCCCCACTGCACCAGCTTGTCTCCATTTTTTTTTTTTTTTTTTTTTTTACAG
Seq C2 exon
AACTGAGGCTGGTAGGGGGCCCGAGCCGCTGCCGAGGGCGCCTCGAGGTCATGCATAGCGGCTCCTGGGGCAGCGTTTGCGACGATGACTGGGACGTTGTAGATGCTAACGTGGTGTGTCGTCAGCTGGGCTGTGGCCTGGCATTGCCGGTGCCACGGCCCCTCGCCTTTGGCCAGGGCAGAGGGCCCATTTTCCTGGATAATGTGGAGTGCCGCGGGCAGGAAGCGTCTCTGAGCGAGTGTGGCAGCAGGGGCTGGGGTGTCCACAACTGCTTTCACTATGAAGATGTGGCAGTCCTGTGTGATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000029699:ENSMUST00000111152:3
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:
PF0053013=SRCR=WD(100=100.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTGCCCTCCAGCCCACTC
R:
CGGCACTCCACATTATCCAGG
Band lengths:
247-427
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- 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