MmuINT0041957 @ mm10
Intron Retention
Gene
ENSMUSG00000016481 | Cr1l
Description
complement component (3b/4b) receptor 1-like [Source:MGI Symbol;Acc:MGI:88513]
Coordinates
chr1:195129830-195131561:-
Coord C1 exon
chr1:195131188-195131561
Coord A exon
chr1:195130010-195131187
Coord C2 exon
chr1:195129830-195130009
Length
1178 bp
Sequences
Splice sites
5' ss Seq
TGGGTGAGC
5' ss Score
7.23
3' ss Seq
TGCTGTGTCTCATTCAACAGGTC
3' ss Score
10.95
Exon sequences
Seq C1 exon
TGTTTTCTTTGGAGTCGAAGGTTCCTGCAAGTGGAAAACTTCCTGGAGCTGACCTACTAGGTATTGAACCAGTTTCTGCATTGCTGAATCAATCTCCCAAGGGTAATTCCACAGAAATCCCAGGGGCTTGGAGTAAACAAGACCGCGCCTAGCCCAGCTAGAGGAAGTTTTATTCCGGAACCCAGCGCCATTTCTGGGTGGGACTGCTTTCTACACCATTTGCCGTAAAACGTTGTTTGAGAACGGTGTGAGGGGAATGGAGGTCTCTTCTCGGAGTTCAGAGCCTCTGGATCCGGTGTGGCTCCTTGTAGCCTTCGGCCGGGGAGGAGTCAAGCTAGAAGTTTTGCTGCTGTTCTTGCTGCCATTTACTTTGG
Seq A exon
GTGAGCTGCGGGGAGGCCTGGGGAAGCACGGACACACGGTTCACCGGGAACCCGCGGTAAATAGGCTCTGCGCAGACTCCAACGCTGGTCTGGGCTGCCTGTGAGTGCTCAGCGCCCCTTTCCCATGGGTGAGCGTGGGGCGCCCTCTACCCAGATCTTGGGTCGTACGCAGCCGGCAGGAACGCGTGGTCTCCCAGCTGCTTGTCTTTATTAGCTGTACGCTGTGCTTTTCTGTGCTGAATGTAGTGAGAGAAACGGTGTGGGGAGCAGGGGGTTGCAGGAATATTGAGAGATGCAATTTCTAATCCTAGAATTTGGTTATGAGGAAAGTTAATATTTTTGTGTTTCCTTATCTGTGAAATGGAGATATTGATGTCTTTCGTGGTATTGGTATTTAATAGGTGCCATCAAATATCTAACCCAATTTCAGCTCCTTAATTTATTTCTATCTTGAGACATTCCCTATGCACTTTCTCCGAAGGCCTAGACAAACAGGCCCAGGGATACAGTTTTCACACAGTGAGACTGTGTACTTTATCTCCCACCCCAAATCCTCATTAACTCCCTTGAGCTTCCACTTTAAGGAAGGTCCTTCCACTCCCACTCCAAGGTAAGATTTGAAAAGCTAGCAAGCCTCAAGGTGCAATGAAATATTTGCAAGTAGAAAAGACTGTAGAATTTACATATTAAATTTTACTGATGGTTAAGAACAAAATAGAGTGCCCATTTTACCCACCATGAAAGTTCTAATTTCCCTTTCCTTTCTCCTTAATCAGAACTTTCTAAGAGAAAGACTTCCTTGAAGTCTTTTGCATTGTTTGTTTTTTATTGTATTTCCAAAGTTAAATGAAAATGATTTTTTTCCAACATATAGTTATTGGTTACATATTATTTGACTCTCTCTGCCACATAATTAATGCTGCTAAGACTTAAAAGAAAATAACTGAGTCTAGAAGTTAAATCAAAATATGTATTGGAAAGTACATTAACAAAATGAAATGCAGTTTCATTTTTTAAATTATATTATTTTTTCCCCGTTGACCATAGTACTGATCCATTCCTGAGTGCCAGAGAGGAGGATCATGCATGGTCCATTGTAGCTAGCTGGAGAACTGAGAGTATGAGGGATGATGCAAGTTCTTTTATCCAATGTAATGTTGCTGTGTCTCATTCAACAG
Seq C2 exon
GTCACTGCCCAGCCCCATCACAGCTTCCTTCTGCCAAACCTATAAATCTAACTGATGAATCCATGTTTCCCATTGGAACATATTTGTTGTATGAATGTCTCCCAGGATATATCAAGAGGCAGTTCTCTATCACCTGCAAACAAGACTCAACCTGGACGAGTGCTGAAGATAAGTGTATAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000016481:ENSMUST00000075451:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.025 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0008415=Sushi=WD(100=93.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
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:
TGGGTGGGACTGCTTTCTACA
R:
ATCTTCAGCACTCGTCCAGGT
Band lengths:
350-1528
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