MmuINT0152232 @ mm10
Intron Retention
Gene
ENSMUSG00000029699 | Ssc4d
Description
scavenger receptor cysteine rich family, 4 domains [Source:MGI Symbol;Acc:MGI:1924709]
Coordinates
chr5:135961889-135963234:-
Coord C1 exon
chr5:135962923-135963234
Coord A exon
chr5:135961967-135962922
Coord C2 exon
chr5:135961889-135961966
Length
956 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAAG
5' ss Score
6.66
3' ss Seq
TTATGCCCCTGCTGAGCCAGGCC
3' ss Score
0.4
Exon sequences
Seq C1 exon
GCGGAAGGCTGAGGCTGGTCGGGGGCCCGAGCCCGTGCCGCGGCCGCGTGGAGGTGCTGTACGCCGGGGGTTGGGGCACCGTGTGCGACGATGACTGGGACTTCGCGGACGCGCGGGTGGCCTGTCGCGAGGCGGGTTGCGGGCCCGCGCTAGGCGCCACGGGCCTTGGTCATTTTGGCTATGGCCGAGGCCCTGTGCTGCTAGACAACGTAGGCTGCACCGGTACTGAGGCCCGCCTCAGCGACTGCTTCCATCTGGGCTGGGGACAGCACAACTGCGGCCACCACGAAGACGCCGGAGCGCTTTGTGCAG
Seq A exon
GTGAAGCTGTGGCAAGAGAGGAGGTGGAGCCGGAGTGGTGGGCGGGGCCCGACCCATAGGAGGTGCGGGCAGGGTTTATATGGAGGAAAGGTGGAGCCGTGCAAGCTGGGCGAGGACCCATGAACGCATGCGCTCACGTCTATGGGCGGGCCTGAATCAGGAGAGGGGTGGGTATCCTGTAGGGGCGGGACAAGATGTGGTTGAGCTGGGCGATGCGTGGGCCATGACGGTCCTGTGGGCGGAGCCTCTTTTAGCTCACAGTCGGGAGTGGGGCCGAGTCTGAGGAGGCCTGGGTGGGGTCGTGCGCAGGAGCTCCCTGCTGTGGGAGCGAGCGGAAGCTGCGTAGCTTTCTGGCTGGCCTAGGACTGGGAAGGCGAAAGTGAAGCAGGGCACAGGGTTTGTGGGCGGGGCCTGATAGCAGGAGCTGCGGTGGAGGAATGGGCGTGGCGCTCTCTGCTGCACTGCAGCGGAAGTATTGCACATAGCAGGGGGTGGGGGTGGGGTGGGGGGGGTGGATGCTCCTGCACTCTCGCTGTTGAGCCTTAGGGGTGTAACCGGAAGGGCGATTTGTCTGCAGGGGGTGACTAGGGCGCGGTCAAGGGAGCACTCGTGCTGTGCTATCCAATTTATAGTCTCTGCTGCTAGTGATTGGTAGGAAGCAGGAGTGGCTGACGGCTTTCCCAAAACTAGCCTTTGACTTTTCAGAGATACCAATGAAAACAGGTGTGTACAAAGTCTGGCAGGACACTGTCAATCCCTTGTTCCCGTATCTCCACCTTTACTTGATGCCTAGACCTAGGGGGTCCTCCAGTCTCCTACCTTAGGTTGGCAGGTCTTTGAGGTTCTTTCTGTCTTTCTGTACAACTTGGGAAGGTTGGGAGAATTGATCTGGTTCTAGGGAGCATATGTTCCCCACCATGACAACCATCTCTTTTTTTATGCCCCTGCTGAGCCAG
Seq C2 exon
GCCCAGAGGAACTGGGACTCCAAGTCCAGCAGGCTGGTTCTGAGACCACCCGAATGCCCAGTCCTCGGCCCAGAGATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000029699:ENSMUST00000111152:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.019 A=NA C2=0.750
Domain overlap (PFAM):
C1:
PF0053013=SRCR=WD(100=93.3)
A:
NA
C2:
NO
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAAGGCTGAGGCTGGTCGG
R:
GTCTCAGAACCAGCCTGCTG
Band lengths:
355-1311
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