MmuINT0152224 @ mm10
Intron Retention
Gene
ENSMUSG00000029699 | Ssc4d
Description
scavenger receptor cysteine rich family, 4 domains [Source:MGI Symbol;Acc:MGI:1924709]
Coordinates
chr5:135960223-135961966:-
Coord C1 exon
chr5:135961889-135961966
Coord A exon
chr5:135961209-135961888
Coord C2 exon
chr5:135960223-135961208
Length
680 bp
Sequences
Splice sites
5' ss Seq
ATGGTAGGT
5' ss Score
8.6
3' ss Seq
AGGCCTTATCTCCAACACAGGGC
3' ss Score
5.35
Exon sequences
Seq C1 exon
GCCCAGAGGAACTGGGACTCCAAGTCCAGCAGGCTGGTTCTGAGACCACCCGAATGCCCAGTCCTCGGCCCAGAGATG
Seq A exon
GTAGGTGTTTACTGCCACTGAAAATGAGGTTGGAACTTTAGGGATAAGATGGACCTGGAGTGATAAAACACTACAGCAACCTAGAGATTTCTCCACTTGGGATCAAACAAACTGAAGAAATGAGAGAATGCAGAATTAGGCATGGTGGCCTATGGCTTTCATTCCAGCATTCTGGAGACTTGGGTCAGAAGGACAGTAACTTCAAGGCCTGCCTGAACAACATACAAGGGCTCATGGAAAAACAAACAACAAATTAGCCCAGGGAATGTAGGTGTGGAAGTGGGGACAGTAAACTTTGAGGGTCAGGATAAGACATGGTCATAGTTTGCAAACAGCCTGTGGCTAAGGGGCTGAGACTGTCTGTTGAGGGTCTCACTACATAGCTCTGGCTGACCATTGCTGTGTCGAACAGGCTAGGCTTGAACTCACAGAGATCTGCTTGCCTCTGCCTTCTTAGTGTTGGGATCAGAGGTGTGTGCCAACTTGTCCAGCATTATTTATTGGTGTCTGTGTACCCGTGTATATGCATGATATGTTCACACATGTGAAGGCAAAACAGTATGAAGGAATGTGAAGGTCAGAGGACAACCTGTGGTGGCAAGTGCCCTCAACTGTAGAGCCATCTCTTGGGTCCCATGATCCCATGGGCTCTTCTGACCCAGGCCTTATCTCCAACACAG
Seq C2 exon
GGCACCTCCGTCTGGCTAGTGGAACACACCGATGTGAGGGGCGCGTAGAACTCTTCCTAGGACAACGGTGGGGCACTGTTTGTGATGATGCCTGGGACCTACGGGCAGCCATTGTCCTGTGCCGTCAGCTGGGATGTGGCCAGGCTCTCGCAGCCCCGGGAGAGGCCCACTTTGGCCCAGGCCGAGGCCCAATCCTCTTGGACAATGTCAAATGCCGAGGAGATGAGAGCACCTTGCTACTGTGCTCTCATATCCGCTGGGATGTCCACAACTGTGACCACAGCGAGGATGCCAGTGTCTTGTGCCAGCCATTGTGACCCAGATGGCTCTGTACTCCATACCATATCAAAGGAGCCTATGAGGAACTGCCTGTCCTTTCCCAGGATGCCTTCCTATGATAGCTCGGGTTCCTGGTACCCCTTTCTCCCCGTGCATGGGAGAGATGCAGTACCTGCCCGAGTCCTCTTACTGTGTGTCCCGAGACTGTTATCACCTGCGGAAGGCCCAATACAGTGAACATAGCAATGTTTTGCTCAGCCAAATCAGAAAATGTGAGAGAATAACCCACTTCTCTTTGGGGGAACTCATATAGTACCCCCAATCCTTCCCTTCTGCACCCACATCCATGAGGCTTGGGCTGTCTGTAAATGCCTTCAAACCCTTACCGTGACCTCTCTTGGTCTCCTGCTAAAAGTGGGGAGACAAAGGGGTTGGGGTGCTCTTTTCTATAGACTGGCAGGGGACTGCAGAAGAACCAGGCCATCACCTTCCCTGCTGGGTGAGGACCTGGACTCAGATGGTGCTCCGCTGAACAAGGGGGCTGCAGGGGCCAAAACAGGGACCAGAGGAGCCCTTCCTGCAGCTTCTCTGATTTCCACTGCCCCCCCCCCCCCAGCACAGAGCCTCCATTTTGCAGTAACAAAGAACCCTGGAGGCCCATAGCCACTGTCCTTAGGTGCCAAGTCAATAAAGCATTATCTCCCCCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000029699:ENSMUST00000111152:10
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.750 A=NA C2=0.020
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
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGGTTCTGAGACCACCCGAAT
R:
CACAAGACACTGGCATCCTCG
Band lengths:
348-1028
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