MmuINT0152228 @ mm10
Intron Retention
Gene
ENSMUSG00000029699 | Ssc4d
Description
scavenger receptor cysteine rich family, 4 domains [Source:MGI Symbol;Acc:MGI:1924709]
Coordinates
chr5:135965571-135966152:-
Coord C1 exon
chr5:135966075-135966152
Coord A exon
chr5:135965886-135966074
Coord C2 exon
chr5:135965571-135965885
Length
189 bp
Sequences
Splice sites
5' ss Seq
AAGGTATGT
5' ss Score
9.79
3' ss Seq
TCTCCATCCACCATCACCAGGTG
3' ss Score
7.58
Exon sequences
Seq C1 exon
AATTCTTGCACACACAGCCCCCAACAAGGAAGGTGTTAACCAGTATGGCACCCGCTACAGCCCTCCAAAATGGAAAAG
Seq A exon
GTATGTCATACGGTAGTGTGAGGCTTGGCCAAGCGGGTGGGCTGGCTATTTTACCCCTGCTGTGGGGTTCTGGACCTGCATGCCAGGTTGCTGTCCCTGGGAGACCTGGTGCATTGATTAAGTAGATGAAAATGGTTCCTTCCCTGTAAAATGTTACTTGCCCCACCCATCTCCATCCACCATCACCAG
Seq C2 exon
GTGAGGGCAGTGTGCGTCTGGTGGGCGGCGCCAGCCCGTGTCAAGGCCGAGTGGAGATTCTGCATGGTGGCGTCTGGGGCACTGTATGCGACGATGACTGGGGGCTGCAGGATGCTGCTGTTGTGTGCCGCCAGCTGGGCTGTGGGGTCGCCTTGGCCGCCACCACTAATGCCTTTTTCGGCTATGGTACCGGGCATATCCTGCTGGACAATGTTCACTGCGAAGGTGGCGAGCCCCGCCTGGCAGCCTGCCAGAGCCTAGGCTGGGGCGTGCACAACTGCGGACACCACGAGGATGCTGGGGTGCTCTGTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000029699:ENSMUST00000111152:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.212 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0053013=SRCR=WD(100=92.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TAACCAGTATGGCACCCGCTA
R:
GATATGCCCGGTACCATAGCC
Band lengths:
242-431
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