MmuINT0152225 @ mm10
Intron Retention
Gene
ENSMUSG00000029699 | Ssc4d
Description
scavenger receptor cysteine rich family, 4 domains [Source:MGI Symbol;Acc:MGI:1924709]
Coordinates
chr5:135968224-135970426:-
Coord C1 exon
chr5:135970182-135970426
Coord A exon
chr5:135968260-135970181
Coord C2 exon
chr5:135968224-135968259
Length
1922 bp
Sequences
Splice sites
5' ss Seq
TGGGTAAGT
5' ss Score
10.24
3' ss Seq
TCCTTCCCTATCTGTTTCAGCCA
3' ss Score
8.78
Exon sequences
Seq C1 exon
CTGGCCCAGGCAGCTGGAAGTAAACACGCAGGACCTTGAGTCACAGATGTTCCAGCTGTGACTTCTCCTCAGATTCTTGATGGGACCGTCGGAAAGGCCATCCATTGGCTGGACACCCAAGGAAGCAGAGATGCAAATTGGCCCCCAGCCTGATGGATGGAGCAGGGGATGGAAGCCTGGGGACAGGGGTGCTGTCCCCCTGCCCCTCTCCCCAGCACTGTCCTTCCTCCTTCTGTTCCCACTGG
Seq A exon
GTAAGTGTTCCCAGCCACTCCCTGCCACATCTCTCTAGCTCTGTTTTCCCCGATAGCCAGCTATGGTGGGAGTCCGGGCATGGTGGTACATGTTTGTAATCCCAGTACTTGGGAAGTGGAAGCAGAAGGGTCAGAAGACCAAAGGTCATCCTCAGCTACACATCTGTTCCCAGGCTAGCCTGGGCTACATGAGACCCTGTCTTAGAACAACAAAAATGAGCCAGGAGTAGTGATGTGAGCCTTTAATCTCTCTTTTTTTTTTTTTTTGATTTTTCGAGACAGGGTTTCTCTGTATAGCCCTGGCTATCCTGGAGCTCACTTTGTAGACCAGGCTGGCCTCGAACTCAGAAATCCACCTGCCTCTGCCTCCCGAGTGCCGGGATTAAAGGCGTGTGCCACCACGCCCGGCCTGTGAGCCTTTAATCTCAATGCTCAGGAAGTTGGTGGATTTCTGTGGGTGCGAGGCCAGCCTGGTCTACAGTCAGGGATATACAGAGCATCCCTGTTTCAAAACAAACAAACAAACAAACACCCACCCAACAGTAAACAAAACCAGGACAGACAAGATGGCTTGGCAGTGGGAGTGCTGCTTGTCACCGAGACTGGGTACCTTAGCGAGATCCTGGCATCCACACAGTGGAAAGAATGAACCAGCTCCCGAAAGCTGTCCTATGGCCTTAACATGTGCCATAGGGCATGCACATGCCAGCATTCATGCCCATGACACATGAATGTACACACACACATGGTAGGAGCAGCAGGAGGATAAAAGTTCAAGGCCATTTTTATCTACACAGCAAGTTCCAGGTTAGCCTGGGCTCTGAGACTCTCTATCTGAAGAAATAATTAAGATGGGACTGGAGAGGGCTGGAGAGATGGCTCAGAGGTTAAGAGCACTGACTGCTCTTCCAAAGGTCCCAAGTTCAATTCCCAACAACCACATGGTGGCTCACAACCATCTGTAACAAGATCTGACGCCCTCTTCTGGTGTGTCTGAAGACAGCTACAGTGTACTTACATATAATAAATAAATAAATCTTTTTTTTTAAAAAGAAGAAAAAAAAAGGACTGGAGAATGTGGTTCACTGGCTAAGAGCACAGGACTGGCTGCTCTTCCAGAAGACCCAAATTCAATTCTCAGCACCTTCATAGTGGCTCATTTGTAAACATTTGTCACTTCAGTTCTAGAGATCTGATGATGCCCTCTTCTGGCCTCTCTTGGTACTGCATGTGGGGCACAGAAACATAGGCAAAACACTCACACATTAAAATAAAAATAAAATTTAAAAACAACAATACAAAAATGGCCAGTGAGGTACCTTGGCAGATAAAGGCACTTGCTAGAACCATCTACGTTCAATTAATGGCAGTGATCCTTTGACCTCCACACACATACACACATGAATGCAATTTTTAATTTTTAATTCTTCAGTGGTGCCACATGCCTTGTAATCCCAGCACTTACTAAGCAGAGACAGGTGGGTCTCTTGAGTTTGAGACCAGCCTGATCTACAGAGCGAGTTCTAGGACAGCCAGGGCTAAACAAAGAAACCCTGCGGGGGGTGGGGAGAAAAGGAAAAAAAGAAGAAAGAAAATATAAAATAAATAAGTTAATGAATTCTTTTTTTAAAAAATGATATCAAAAGTCTGCTTTGTTGAGAGAGAAACCTCAGGGGCTAAAACTCCTGTAGGTAGCATAGAGTGCTCATGAGATTTTGCTGTTGAATAGACAAATGGGTCAGTGGGCTGTGGAGCACTGGAATAGGGAAGTTGATGGAGTGGTCCCAGAAAGAGGCCTTTGACTAATGAGACTTCCAAGAGCAGGGGAGTTACAGGGAGACCCCTGGGGAAGGGGAAGCTGTACGAAAAGACCAGTCCTCCAGAGCTGGACAGAGACTCATGTCCTTCCCTATCTGTTTCAG
Seq C2 exon
CCAGTGCCCTCCAGCCCACTCCGCTGCCCTTTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000029699:ENSMUST00000111152:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.625 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGGCAGCTGGAAGTAAACACG
R:
TGGAAAGGGCAGCGGAGT
Band lengths:
273-2195
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