MmuINT0006607 @ mm10
Intron Retention
Gene
ENSMUSG00000035279 | Ssc5d
Description
scavenger receptor cysteine rich family, 5 domains [Source:MGI Symbol;Acc:MGI:3606211]
Coordinates
chr7:4936263-4937222:+
Coord C1 exon
chr7:4936263-4936826
Coord A exon
chr7:4936827-4936907
Coord C2 exon
chr7:4936908-4937222
Length
81 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGT
5' ss Score
10.67
3' ss Seq
GAGCCTCCCACCTCCCCCAGGTC
3' ss Score
8.62
Exon sequences
Seq C1 exon
GGACCCCCGGCCTGGATACCATCTCAGACCCTTTCAGTTGGAGCTGGCTCCCTGGGCTGGGTAGAGATCAGGATGCCTGGCTCCCAGGAGAGCTAACCACCAAACCTTCTGCCAGTCTCACCTCCAGTGTGCCACAGAAACCCACAAAGGTTCCAGGGAAAGCTCCCAAGAGTACCAAGAAGTGGGTGACTAAAAATGCAAGGAGACCAACCACTCAGCCCCCTGGGATGCCAACCACCAAACATTCCAGGGCCCCAGGCACCCCAACCTCCCTACATCCAACAGCACGTACCTCTGAGTTACCAAAGAGACTGACCACTGAGGCTCCCCACAGGCAGACCTCACATACCACTGTAAGGCTGACCCCTAGGGTCCCCTGGGAGTGGACCTCAGAGCCTGTGGTGTCACAGTCCACTCAAGGTCCCCAAGAAGTGACCTCTGAGGCCACCACAACGGAAAACCCTCAGACCTCTTTGGAGCCATCGGGTGAGAACACCGAAGGCTCTCTGGAATCATCCCAAGATCCAGCTACCACCCCAACTGCTGGAGTCCCTGTGCCATCAG
Seq A exon
GTGAGTAGTAGAGAGTTAAAAGGGTGGGGACAGGGAGGTGGCCCTGTACCTCCTAACCTGAGAGCCTCCCACCTCCCCCAG
Seq C2 exon
GTCCCTTCCGGGTTCGTCTGGCTGATGGGCCCAACAGGTGTGCTGGCCGGCTAGAGGTGTGGCATGCTGGACTCTGGGGAACAGTCTGTGATGACAGCTGGGACATCCGGGATGCCACAGTGGCCTGCTGGGAGCTGGGTTGCGGAAAGGTCCGGCCCCGAGTAGGCAAAACTCACTATGGCCCTGGCACTGGGCCCATCTGGTTGGATGACATGGGCTGTAAAGGAAGTGAGATGTCACTGAGTGACTGCCCCTCGGGGGCATGGGGGAAGCACAACTGTGACCACGAAGAAGACGTGGTGCTCACCTGCACTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000035279:ENSMUST00000057612:10
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.894 A=NA C2=0.170
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0053013=SRCR=WD(100=92.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTTGGAGCCATCGGGTGAGAA
R:
CAGACTGTTCCCCAGAGTCCA
Band lengths:
180-261
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