MmuINT0006617 @ mm10
Intron Retention
Gene
ENSMUSG00000035279 | Ssc5d
Description
scavenger receptor cysteine rich family, 5 domains [Source:MGI Symbol;Acc:MGI:3606211]
Coordinates
chr7:4930002-4933452:+
Coord C1 exon
chr7:4930002-4930163
Coord A exon
chr7:4930164-4933134
Coord C2 exon
chr7:4933135-4933452
Length
2971 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGT
5' ss Score
10.1
3' ss Seq
TTTTTTTTTTCCTATTCCAGGGT
3' ss Score
11.3
Exon sequences
Seq C1 exon
GCATGCCTCTCGGTGCTGTGCAGCCTACAGTTCCTGCAGTGGACAGCAACAGCACAGCACACAGGCTTCTGTCTACCTCCGTGGGTCAGATGCCAGGCCCAGCAGGCCCTTGGCCTCCTTCTGCTTCTCCTACTGCCCCTCCAGAGCCTGGGCCCGAAGCTG
Seq A exon
GTGAGTCCCTCTCTGCCCTAGCTCTAAGACTGTCTCCATGAAACCTGCTTACAAAAAAAAAAGGTAGAAAAGAAGAGCCCAAACCCCTGCTCAGATCAGTACTTGATTAATGCTCTGCTGATAGCCTAAAATCCAGGGTTGCTTGTAAGAGTTCTCCCTTCTGTAGCTGGCCCTGACCTGGAGAGGAGGGTGGGCACGAGAGCCCACTGCCTAACGTCTGGGTTCTGTGGTGGGACTGTTACAGTGTCCTCTGGCTAGCCACTGACTGCTCTTCCAGAGGACCTGAGTTCAATCCCCAGCACCCACATGGTGGCTCACAACCATCCGTAATGGAATCTGATAGTGTACTCATATTAGAAAAAAAAAAGGAATTGTTCTGAGTCAGGCGGTGGTGGCACACACCTTTAATACCAGCACTCTGGAGGCAAAGCAGAGGCAGCTTGGGCTACAGAGTGAGTTCCAGGACAGCCCGGCCTACACAGAGAAACCCTGTCTCAACAAACAAACAAACAAACAAACAAACAAACAAACAAACAATCAGGGCTCAATTGGGTAAGTGCTTAACTTGCAAGCACAAGGATGTGAATTCAGATCCCCAGTAGCCAAATTAAAAAAAACCTAGGTACAGCAGTGGATATGTCTAACTCCAGCACAGGGTGGGAGAGATCCTTGGGGCCTGCTAGCCAGTCAGTCTGGCCAAATCAGTGAGCCTCAAGCTCAGCGAGAGACCCTGTCTCAAAACAACAACAACAACAACAACAACAACAACAACAAACCAAGCTAGAGAATGATGTCAACCTCTGGCTTCCACATGAATGCACACACACGTACATTCACACAAACACAAGTTGTCTCTCAGGACCAGAGGATGGTCCAGTAGGTAAAGGCCACCGAGCCTGATGGCCTGAGTTGATCCCTAGGACTCACACTGTGCAAGGAGATCCCTGACTCTTAAATTTTTCCTCTGACCTTCACATACATGTGGTGGCATACACACACCCTTGTGCATACATACATACACACATAAATAAGTAAATAAATAAATGTAATATTTAAAAACTCCAAAAAATAAGATAAAATAACCCCCTTGGTGCAGTGGGCACGGTACTCCTGCAATTCCAGCAGATGAGAGGCTGAGGCAGGAGGATTATGAATTTGAGCCCAGCCTGGGCTGCACTGTGCATTTCAAAGTGCATTGCAGAGGTCACTACCATGTCCTGTTTACCTGTCGCTACACTAAGGAGCGCCTTTGAATTATTGTGACTAGCACAGCGCAGTGTATGTATACAGCAAGTGACTAGCATAGCACAAGTGTATGTATACAGCAAGTGCATGTATACAGCAAGTGCATGTATACAGCAAGTGTATGTATACAGCAAGTGTATGTATGTATACAGCAAGTGTATGTATGTATACAGCAAGTGCATGTATACAGCAAGTGCATGTATACAGCAAGTGTATGTATACAGCAAGTGTATGCTAACAGACACTTTCAAGTTTTTAGAATCATGTCTATCATGGTACATATCGGTTAGAGTGTAGTGGTACCCGTTCTGTGCTCCTGATTGGTCTCACAATCGCACCACTGGCTGTTGACATCTTTATTTACCAGTTGGATGCAACTGGGGGCCGGGTCCTTCATTGCCTTATGTGCAGATACTTGTGTAAGCAGTTTGAGGGACCAAAATTAATATTATAACACAAGCAGCATTAAGCCAAACTCACTTCATTTCCCCCCTTTCATCTAATTAACAGGGCTCTTTTATCTCAGACATAAATTGAGTACAACTATAAAAATTATGTAAATTACAAAGTATGATGTACAAGTGACATCTGATTCATCATATTTGTCAGTTAGATAAAGTATTCCACCATCTAGCTAAACTCAAAGAGTTTATACTTTTATATCTGAATTATGTTCTGATATTAGCTTGCATTACCATCTGAAAACCATCCTTTCAAATATATATCATCTCTCTCAATGCTAAACAACTTGTGTTTGATTATGAGACTATAACTAGTCTCATAATCCAAGAAAGAAAATCCAAGAAAGAAAGAAATATAACCTGAATATACAGGAAGCACAAAAACATAGCTTCCAAAAACTTAAACAAATTGTGGAGACAGCTGCCTGCCTGGACAGCCCCTAACTTCTTATAACAGATGTCAGAGCATCTGTCTTCCGCTTTCTGGCCCAGAACCATCTGACAGACCTTGAAATAAAGCAGGAATATGAGGGGCTAGCTTACCCTGCCTTGGCAGAGCTTAGCAGTTGACTAGCCCACATCTGTTTGTCCTCTTTGGACAGTATTTTGTCTGCAGATGAATAGGGCAGTTTTTGCTTAGTGGTTACCTTGCCATTACTGGAGCAACTCCATGTGGAGGTGTTGATGCTCAATTTCTTCTTTGAACCATGAAGAGGGTACTGTCAGGAGCAGGCATGTCTCTAGTCAGAATTTCTAATAATAATGAAATGATTAAATGTTAACAGATACATTCAAGTTCTTAAAATCACGTTTCTCTCCGTGCATGCATGTGTGCACACATGCCACAGTACACATAGTGGGAGAACTCTTTTTCTGCCATGTAGATGTCCCACAGGTCAGACTTCTGGTGTCAGGCTTGAGGGCAGGCGCCTTCACCCACTGAGCCATCTCGCCAGCCCCCTTTCAATGTATTTTGGGTGTATCCCTAGGAGTGGGATTTCTATATCATATGGTAATTCTACATTAGCTTTCTGAGGAGCCAGCCAGCTCTGCTTGGCTCTGTGTCCAGTGCAGGAGAGATCTCGATCAGTGCCTGCTACCTGAGCTGAAGGGTTATGAGGAGAAGCAGAGCTGAGGGAGCTGATGGGCATTTAGAAAGGAAGGCAGAAGGCAGGTAGATGAAGGCTCAGAGTGCTAGCTGGGCTCTTTGACCCTGACTCTTGCTTCTTCTTCTTCTTCTTCTTTTTTTTTTTTTCCTATTCCAG
Seq C2 exon
GGTCCCCCCAGTTGCGCCTGGTGGCTGGACCCAGCAGGTGCTCTGGCCGGCTGGAGGTATGGCATGACGGACGCTGGGGGACAGTATGTGATGACAGCTGGGACATGAGAGACTCAGCTGTGGTCTGCCGGGAGCTGGGCTGTGGGAGGCCTCGGCAACCAGACCCCGCAGCAGGCCGCTTTGGCTGGGGTGCAGGCCCCATCTGGCTGGATGACGTAGGTTGTATGGGGACGGAGGCTTCACTGTCAGAATGCCCTGCTGCTTCCTGGGGGAAACACAATTGCGCCCACAATGAGGATGTCGGGGTTACCTGCACTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000035279:ENSMUST00000057612:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.873 A=NA C2=0.280
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0053013=SRCR=WD(100=92.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
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