MmuINT0055789 @ mm10
Intron Retention
Gene
ENSMUSG00000063600 | Egfem1
Description
EGF-like and EMI domain containing 1 [Source:MGI Symbol;Acc:MGI:1922990]
Coordinates
chr3:29690061-29691209:+
Coord C1 exon
chr3:29690061-29690195
Coord A exon
chr3:29690196-29690392
Coord C2 exon
chr3:29690393-29691209
Length
197 bp
Sequences
Splice sites
5' ss Seq
AAGGTACAA
5' ss Score
6.82
3' ss Seq
TTCTTGGCCTCTGCTCTCAGAAT
3' ss Score
8.33
Exon sequences
Seq C1 exon
GCTGTCCCAGGGGAGCCTATGGAGCTAGCTGTTCTTTGGAATGTCAGTGTGTGGAAGAGAACACCCTGGAATGCAGTGCCAAAAATGGTAGTTGCACCTGCAAATCTGGTTACCAAGGCAACAGATGCCAGGAAG
Seq A exon
GTACAATCCGATGATGGATTTTTATGTTTCTTGAATAAAAATCATCAGCCTTTGTTCAGCACTATTTGGTCATTAATTAGTTAGTCCACACCAGTGGATGATGGGGAGGCTTTATTGATCTCCTGTTGGAGGTGAGGAAACCGAGGCATGAGTGCAATACAATTATTTAACCTTGTCTTCTTGGCCTCTGCTCTCAG
Seq C2 exon
AATTGCCCTTGCCAGCCTGAGCAGAGGAAGAAGATGGCACATCTTTAAATTATATCTGGAAACAATTACAGCTCAATAACATTGACTCATCAATCAAAGACACGCTCTCCTCCAGCATGAAGGACATTCCTTTTTCTGTCTAAAACTCAATCATCCAAACAAATTTATTTATGGTTTCTTAATACCAAGAACTTAAGGATGGATACCCGTACTGTCACTTTTCAAGTACCTAGATATCACGTAATTTTAGATAAATCTCCAAGCAGAAAACTATGGTCCCAGTAGTAAGAAACACGTAGAGATACATGTGCAGCTGTGTGTGGAATTTGGGGAAATGGTATTTCAACCTGTCAGCAAGCCATCCCTGGCTTGTAAAGCCCTTGAGTACTTGTTTATGGTTTTGGTGTCTTGTTACCATGTCACTGACTTCTTTTGATGCCATTTCTTAAGAAGGCAGTGAGCAGCTTTCCTGGAGTTCCTTTTGTTGACTATAGCATGCCTTGTCTTCTAATCTAGCACATTCACCCATTACTGTGTGTTACTATCGACTGCCTGTTCTCTTGCTTGAATCCAAGGCCCATGTAGGCAGTATATTTGTTTGTTTCTTCCTGTATTTCCTCACTCATGCAATAAAGACAGTCATCAGTAAATCTCTTCTTAAATCAATAAACGTGTGGGGGTTCATTTTTACTGTTTACATACTTTTCATGAAGTACTTGGTATTCTTATTCAGGAAAAAAATTGTCATAGTCTTTTTTGCTCTTTAGTGAAAACAATGCACACATATAACAAATAAAAGAATCAGAACCAGTGATAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000063600:ENSMUST00000119598:14
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 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
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAGGGGAGCCTATGGAGCTAG
R:
TGGAGGAGAGCGTGTCTTTGA
Band lengths:
242-439
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