MmuINT0006616 @ mm10
Intron Retention
Gene
ENSMUSG00000035279 | Ssc5d
Description
scavenger receptor cysteine rich family, 5 domains [Source:MGI Symbol;Acc:MGI:3606211]
Coordinates
chr7:4929237-4930163:+
Coord C1 exon
chr7:4929237-4929554
Coord A exon
chr7:4929555-4930001
Coord C2 exon
chr7:4930002-4930163
Length
447 bp
Sequences
Splice sites
5' ss Seq
ATGGTAAGG
5' ss Score
9.33
3' ss Seq
TGTCGTCTTTCCTGCCCCAGGCA
3' ss Score
10.25
Exon sequences
Seq C1 exon
GTCCTGCACCCAGGATACGCCTTGCTGATGGTCCCCACGGCTGTGCTGGCCGCCTGGAGGTGTGGCATGGTGGACGATGGGGGTCGGTGTGTGACGATGCCTGGGATCTTCGCGATGCTGCTGTGGCCTGCAAGGAGCTGGGCTGTGGGGGTGCCCTGGCCGCCCCAGGGGGCGCCTTCTTTGGAGAGGGGACTGGACCCATCATCCTGGATGATCTCAGATGTCGAGGAAATGAGACAGCCTTGCGATTCTGTCCTGCGAGGCCCTGGGGTCAGCACGACTGTCACCACCGGGAGGATGCTGGGGCCGTGTGTGATG
Seq A exon
GTAAGGGTGTATGGGTGATGTCAGTGGGGAAAGATGGGACACTGTGTGTGTGTGGTCACTGGAGTGGATGGGAAAGAAGTGTTGTCCCAGTTCAGCCTTTACTTCCTGTGTGATTTCCCTCTTTCCCTATCTCATATTCTTATGTGAAACCTTATGCCAAATTAACTAGGGGTAACTAGGTCTCCCTAAGGGGCACTGGATATTATTTGGTATTTGGTGGTCATAATGAGGGGGTGAGCCCTACTTCCTTGCTCCTAGTGGAAGCCAATCAATCTTGCCTTGCTAGGTGCCTCCTCTGTTTTCTCACTTCCAAACTCCCTCCATTTCCTGCTCTCTCTACCCTCTTCTTTCTATCCACTTCTTGTTGCGGCTCAGAGTTGTGGAAGCCTTGGGCCTGTGTAGGAGGCAGTCCTGGAGGTGGTGCTAATGTCGTCTTTCCTGCCCCAG
Seq C2 exon
GCATGCCTCTCGGTGCTGTGCAGCCTACAGTTCCTGCAGTGGACAGCAACAGCACAGCACACAGGCTTCTGTCTACCTCCGTGGGTCAGATGCCAGGCCCAGCAGGCCCTTGGCCTCCTTCTGCTTCTCCTACTGCCCCTCCAGAGCCTGGGCCCGAAGCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000035279:ENSMUST00000057612:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.009 A=NA C2=0.873
Domain overlap (PFAM):
C1:
PF0053013=SRCR=WD(100=91.6)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTGACGATGCCTGGGATCTTC
R:
GAGAAGCAGAAGGAGGCCAAG
Band lengths:
357-804
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