MmuINT0152229 @ mm10
Intron Retention
Gene
ENSMUSG00000029699 | Ssc4d
Description
scavenger receptor cysteine rich family, 4 domains [Source:MGI Symbol;Acc:MGI:1924709]
Coordinates
chr5:135964619-135965885:-
Coord C1 exon
chr5:135965571-135965885
Coord A exon
chr5:135964697-135965570
Coord C2 exon
chr5:135964619-135964696
Length
874 bp
Sequences
Splice sites
5' ss Seq
CAGGTGCCA
5' ss Score
3.75
3' ss Seq
TGTCTTCTCTCCTGCTCTAGTTC
3' ss Score
9.78
Exon sequences
Seq C1 exon
GTGAGGGCAGTGTGCGTCTGGTGGGCGGCGCCAGCCCGTGTCAAGGCCGAGTGGAGATTCTGCATGGTGGCGTCTGGGGCACTGTATGCGACGATGACTGGGGGCTGCAGGATGCTGCTGTTGTGTGCCGCCAGCTGGGCTGTGGGGTCGCCTTGGCCGCCACCACTAATGCCTTTTTCGGCTATGGTACCGGGCATATCCTGCTGGACAATGTTCACTGCGAAGGTGGCGAGCCCCGCCTGGCAGCCTGCCAGAGCCTAGGCTGGGGCGTGCACAACTGCGGACACCACGAGGATGCTGGGGTGCTCTGTGCAG
Seq A exon
GTGCCAGGGGCAGCGGGGGCGGTGCCAGGCTACGGGGCGGGGTCTTCGGAAGGAGTAAAGGTGGGAGGAGAACTGGAAGAAACTAATGGCTGAGTGGGAAAAGGGGTTGGCTATCTTTCCAGAAAGGCTTTGAAATTACCTGTACTATTCAGGCCCGCTCTGGGGAAGCAATTTGGATAACTCATTCGCACATTCTCAGTAGCTCTTATTCCTCCATTATTAGGACTGCTTCCAGAATTTTCTAGCAATTTCCAGGTATTCTTCATGGATGATTTCAGAATAAAGCAATAATATTCTAGAATGCTCCCTCAAAGATTACTTTCAAAGAACCTAACTGCAGAACCATGCCTAGCTATCTGTAACCCTGAGAATCTAATAATAGACTGCCCCCCCATATGGACCCTCTCCAATTTGGGAGGTGTTTTCAGCAAATTAAAGGTCAGCATTGGAGCAGAGTTATGTAGCTTATTTGATGGGGTGCTTTCCTAACATGCAAGAAGCCCTGGGTTTAATTTCCAGCCCCACACAAACCAGGCCTGCTGGTACATACTTACAGCTCTACTACTCCCTCAGCTACATAAAACCCTGAAGAAAAACAAAAACAAAAACAAGCCAGGCAGTGGTGGCACACGCCTTTAATCCCAGCACTTGGGAGGCAGAGGCAGGCAGATTTCTGAGTTCGAGGCCAGCCTGGTTAACAGAGTGAGTTCCAGGACAGCCAGGGCTACACAGAGAAACCCTGTCTCAAAAAACCAAAATAAATAAATAAATAAATAAAGGACTGCTGTCAAAGCTGGCCAGGGCTCATTGAATGCCAGTCCTGGATGTAAAGCTGGTCCAATGACTGACCCTTCTGTCTTCTCTCCTGCTCTAG
Seq C2 exon
TTCTAAGCCCTCCGACTTCCACAGCTCTGCCTCCGTCTGTCACAAAAGAAGACTGGGCACGGCACACTGGGCCAGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000029699:ENSMUST00000111152:6
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=0.694
Domain overlap (PFAM):
C1:
PF0053013=SRCR=WD(100=92.5)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion 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:
GTGTCAAGGCCGAGTGGAGAT
R:
TGCCGTGCCCAGTCTTCTTTT
Band lengths:
342-1216
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