MmuINT0034970 @ mm10
Intron Retention
Gene
ENSMUSG00000039787 | Cercam
Description
cerebral endothelial cell adhesion molecule [Source:MGI Symbol;Acc:MGI:2139134]
Coordinates
chr2:29869494-29871133:+
Coord C1 exon
chr2:29869494-29869725
Coord A exon
chr2:29869726-29871022
Coord C2 exon
chr2:29871023-29871133
Length
1297 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGA
5' ss Score
7.54
3' ss Seq
ATTCTGTGTTGTGCTCACAGGTG
3' ss Score
9.93
Exon sequences
Seq C1 exon
TGTGGTGGGAAACCCGGGGCCCTCCACAGCCACCGAGTCCCGCCATGCACGTTGCGCGGCTCCTACCTCTGCTGCTCCTGTTGGGGCAGCAGCTCCGGGCTGCCAGTGTCACAGAGCCGACGCTACCCACCGTGGTCCTTGCCATCCTGGCCCGCAATGCTGAACACTCTCTGCCCCACTACCTGGGTGCGCTGGAGCGCCTGGACTACCCCCGGGCCAGGCTGGCCCTCTG
Seq A exon
GTGAGAGATCCAGGGGTGGGTGCATATGGGCATCAAGCCCCAGGACCCAGGAAGGCTTTTGACCTGGAGGCCTCATTACTTCTGCCCAGACACAACCCGAACAAGCTCCTCCCTCCCAGACAGCCCTTCAACAGTATTCCTAGACCCCGCGGGGCAAGAATAGACCTCTGAGGCCAGGGTTCAGCCCAGGGACACTCACCCCTCCTTTGGGCTCCCTACATGTCTCGGGCGTCCCCGGCTTCCCGGGTTTCCCCTGGGTTTCAGTTAGGCCTGTCCTTTCTGACCTAGCCCTTGGGGCTCGGCAGTACATCGCAGTAAAGACCTGTGGTCTGCCTGATGTGCGGTAGAACAGACTGAACCTCTGGAATCCCCTGGGGCCCAGCATAGAAAGGATCAGTCAGACTGGAGGTTTCTAGAGAGCAGGTGGAGGGAACCCTCAGCTCCAGGCGGCATGCTCGGGTGCCCTTCTGAGTGGTACTGCTAAGCTTCTCTGGGTAGAGAGAGGGGCTGGCTGGTTCTGATAGCCAAGGGTGTGGTCTCATGGGACGCTGGGATCAGAGGTTGCAGTACCCTGTCTAAAAAAGTCAAAACAGGGAGGAGCCTGAGCAGAGGCTGGAGATAGAGTACTCCTCACAGCACACCAAAGTTGGGCTGGGGTGGAGCTGTGGCCTGGGGAGGCTGCCCACAGCCACCACACTTGGGGAGTTAGTTAGTTCCCACCCCTGTAAGACTTGACACGTAGTTCTGGGGAATTGGCTTAAAGGAACAGCATCGCCTAAAACCTGGGCTCTTGGCTAAGCCTTCCACCTCCATTACTAGAGCCCCCTCCCCAGCAGAGGGAAAGCTGTGCTCCATGGTAACAGAACTTGGATCACCACTAACACTTCTCAGGGGTTGTCGGAGCATGGTGTGAGCCTAATTACAGCTGGGGGGAGTTAGGTAAGGAGAGAAAGGCAATGACTGTTTTGTCTGATTCTGAGCTGGAAAAGGCCTGATGTGTGGAGCCATGAAGAGGGACGGAAGTGAAGGGACGTGGCAGGTGCAATCTTTAAGCTCAAGGGACTTTTCAAGTGCACTCAGGCCGAGGATGGCTCAGGGGTCAGGGGCTTGCTTGATGTGTACAAGTCTCTGGGTTCAATTCCCACAGTACAATGCACAAAATTAGAAGGACAGACGTGAAGCACAGAGAGGCATGGACCTTGCCTGAGGCTACACAGGACATCCTCCAGCACCTCCACTGGAGCGCACAACTCTGCCCCATCGCTCTCAGGACAGTCATTCTGTGTTGTGCTCACAG
Seq C2 exon
GTGTGCCACAGATCACAACATGGACAACACCACAGGGATGCTCCGGGAATGGCTGGCTGCTGTGGGTCGGGACTATGCGACTGTCGTCTGGAAGCCTGAGGAGGAGGCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000039787:ENSMUST00000047521:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.109
Domain overlap (PFAM):
C1:
PF137041=Glyco_tranf_2_4=PU(21.5=41.3)
A:
NA
C2:
PF137041=Glyco_tranf_2_4=FE(30.6=100)
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:
CCTCCACAGCCACCGAGTC
R:
CTCCTCCTCAGGCTTCCAGAC
Band lengths:
318-1615
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