MmuINT0034979 @ mm10
Intron Retention
Gene
ENSMUSG00000039787 | Cercam
Description
cerebral endothelial cell adhesion molecule [Source:MGI Symbol;Acc:MGI:2139134]
Coordinates
chr2:29876161-29878136:+
Coord C1 exon
chr2:29876161-29876267
Coord A exon
chr2:29876268-29878003
Coord C2 exon
chr2:29878004-29878136
Length
1736 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGG
5' ss Score
10.07
3' ss Seq
TGTATGCTTGTGTCTTGTAGGAC
3' ss Score
9.23
Exon sequences
Seq C1 exon
GTCTTTGTCATCAGCCTGGCCCGCAGACCCCAGCGCCGGGCTCGAATGCTGAGCTCTCTCTGGGAGATGGAGATATCTGCCCAGGTGGTAGATGCTGTAGATGGCAG
Seq A exon
GTGAGGCTCCCAGGGATGCGGCTTGGGATCGTGACACCCATCTTGAGATCCTAGGAGTGGACAAGCAGACCAGTAGAATGAGCTTCCTAAAGATCCAGGAGGTAGCCACATGGGGCCTGAGTCCTGCTGTCTCAGGAATGCCAGAGCAGGCCAATGAGGACAAGATGTCCTCCCTCAGCCCACCTGAGGGAGAAAGGTGCAGTGCAGAGGCCCCCCAGGGCCTGGGTTGAGGGCTCTCACATGGCAGCTGTATAAACTCTGGGAAACTGTCCTATCTCTCTGCTAAGGGGTAGGCAGCCTCAGGGATGTTCTTCATGCTAGAGTTAGGTCCCTGAGGGGCTGGAGCGTGGAACATGGGTAAAGTCTAGCTGTGTTCCACAGGGATTCAGTGGCCAAGCTACAATTGCTGCCACGGTCACATGCCTCAGATGCCAGCTGCTGTTTGCTTCAAACCCTAGGTCCCTTTTGTTCAGATATATACAAATATATATACATATATATATATTTCAATAGATAGGTAAATAGATAAATAGACAGATACACATACACACATACACACACACACACACACACACACACACACACACACACACATATATATATATAATTTCCCCATCATTCTTTTGGGGTTTATTTAGAAAAATTTCAAGTTTATTTGTGTGTGTGTGTTTTGCATATATGAGGGCGCATACATGTAGAGATCAGAGAGCATGTTTTGGGAGTCATTCTCTCCTTTCACTGTGGGATCTGGGGATTGAATTCACATTTTCAGGATTTCTAGTCAAACACTGTGTCTTACTGAGCCACTGCTATCCTTCTGGACCTTGGTTTGTTTTTCTTTGTTTGAGACAGGTTCTCATGTAGCTAAGTTTGGCCTAGAACTCCTGATCATTCTGCTCCCAAGAGCTAGGCTGCTTTGTTCTGTCTGTCTGTCTGCCTGCCTGCTTGCTTCTTTTCTTTCCCCCTTCTCTCTCAATATAGGGTCTCACAAAACTCTAGCTGGCCTGGAACTCACTATGTAGACTGGGCTTGGCCTCAAACTCACAAAGACGCCTCTCTGCCTCTGCCTCTGCCTCTGCCTCTGCCTCTGCCTCTGCCTCTGCCTCTGCCTCTGCCTCTGCCTCTGCCTCTGCCTCTGCCTCTGCCTCTGCCTCTGCCTCTCCCTCTCTGCCCCTCTGCCCCTCTGCCCCTCTGCCCCTCTGCCCCTCTGCCCCTCTGCCCCTCTGCCCCTCTGCCCCTCTGCCCCTCTGCCCCTCTGCCCCTCTGCCCCTCTGCCCCTCTGCCCCTCTGCCCCTCTGCCCCTCTGCCCCTCTGCTCCTCTGCCCCTCTGCCCCTCTGCCCCTCTGCCCCTCTGCCCCTCTGCCTCTGCCCCTCTGCCCCTCTGCCTCTGCCCCTCTGCCCCTCTGCCTCTGCCTCCCAAGAGCTTGGCTTGTAGGCCTGCACCATTACACCTGGTCGCCCTGCAGGTGTCTTCCCTTTACTGGGCCTTGATGCAGAAAGGATTAACTACTTAGACTGCATGTCTTCCCCATCAAGCAGAGTCCGTAAGCCCATCTTCCTGAGGCTTTCTTAAGGAGACTAGAGTTCTCTCAGCCCAGGCCACGTGAAGGAGCTACAAATCTGGATCCTCCTTTAATCCAGGCTCCTGTGTGATTCTCTCCAATGTATATAGGTGAGGCCCCTCTGGCTGCATCTCTGGTTAGCGCTTGTTACCCATGTATGCTTGTGTCTTGTAG
Seq C2 exon
GACACTCAACAGCAGTATCCTCAAACATCTCGGTGTGGACCTGCTCCCTGGCTACCAAGACCCCTATTCAGGCCACACACTGACCAAGGGTGAGGTGGGCTGCTTCCTCAGCCACTACTCCATCTGGGAAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000039787:ENSMUST00000047521:8
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:
PF0175512=Glyco_transf_25=FE(18.9=100)
A:
NA
C2:
PF0175512=Glyco_transf_25=FE(23.8=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:
GTCTTTGTCATCAGCCTGGCC
R:
CTTCCCAGATGGAGTAGTGGC
Band lengths:
238-1974
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