MmuINT0032014 @ mm10
Intron Retention
Gene
ENSMUSG00000025461 | Cd163l1
Description
CD163 molecule-like 1 [Source:MGI Symbol;Acc:MGI:2443796]
Coordinates
chr7:140228504-140229058:+
Coord C1 exon
chr7:140228504-140228818
Coord A exon
chr7:140228819-140229034
Coord C2 exon
chr7:140229035-140229058
Length
216 bp
Sequences
Splice sites
5' ss Seq
CGGGTGAGT
5' ss Score
9.89
3' ss Seq
GTTTCATATTTCTCTTGCAGGTG
3' ss Score
12.26
Exon sequences
Seq C1 exon
AGAACAGTGTTCTGCGTGTGCTTGGGGGTGAGGATGGCTGTTCCGGGCGTGTGGAGCTCTGGCACGCAGGCTCATGGGGCACAGTGTGTGACGACTCCTGGGACCTGGTGGATGCCGAGGTTGTGTGCCGGCAACTGGGCTGCGGCCAGGCCTTGGCTGCTTTAGGAGAGGCTTCCTTTGGCCCTGGTGTGGGGCCTGTGTGGCTGGATGAGGTCGAGTGCCTTGGCAGTGAGGTGACCCTGGAGGCCTGCCAGGCTGAGCCCTGGGGACATGGAGACTGCACGCACAAGGAGGATGCAGGTGTTCGCTGTGCGG
Seq A exon
GTGAGTTGGCGGCAGGGAGAAGCAGGGACAGGGCTGCTACATTGATTTCTTCAGCTGTCCTTTATGCTCAGGCTCATATATAGGCACTGGGCCCTGAGATGTCAGGTTCCACTGGGAGCTCCTGACGACCCTACGTGACCCACGCTAAGCTGGCACCTTTCAGGTGTGGGCACATCTGTTCTGCTGAGGCCTTCCCGTTTCATATTTCTCTTGCAG
Seq C2 exon
GTGTCTCCACGACCACTGCATTGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000025461:ENSMUST00000209637:10
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=0.000
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
Cow
(bosTau6)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGTGTGGAGCTCTGGCAC
R:
ACAATGCAGTGGTCGTGGAGA
Band lengths:
292-508
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