MmuINT0034972 @ mm9
Intron Retention
Gene
ENSMUSG00000039787 | Cercam
Description
cerebral endothelial cell adhesion molecule [Source:MGI Symbol;Acc:MGI:2139134]
Coordinates
chr2:29736435-29738360:+
Coord C1 exon
chr2:29736435-29736638
Coord A exon
chr2:29736639-29737215
Coord C2 exon
chr2:29737216-29738360
Length
577 bp
Sequences
Splice sites
5' ss Seq
AAAGTGAGA
5' ss Score
4.23
3' ss Seq
GTTCTTCTCTCACTTCACAGTGA
3' ss Score
9.63
Exon sequences
Seq C1 exon
CTACCTTGGCCGGAAGCAGGTGAACCCTGAGGAGGAAGTGGCTGTGGAGGGGCTGCCTGGTCTCGTGGTGGCCGGGTATTCCTACTGGACACTTGCGTACACCTTGAGCCTGGCAGGCGCTCGCAAACTGTTAGCATCCCAGCCCCTGCATCGCATGCTACCTGTGGATGAATTCCTGCCTGTCATGTTTGATCGCCACCCAAA
Seq A exon
GTGAGACCTTGGTCGGTTAGGGCAGGGTCACCCTAGCCAGGAGCCCAGTGCAAAACCCCTTAGTGGGCAGCTACAGAGAGGGAGATGTTCACCCACACGGTCTAGGTCACCTGAGAGTTGCTAGGGTGTCAGACTCAGCGAGATGTGGACACTGAGCTGTTCATGTCCACGTGGGTTTTATTTTTAGATTTATTTTTAATTTTTAATTACGTGTATCTGTGTGTGTGTATTTGCATGTGAGTGCAGGTGTCCAAAGAGGCCAGAAGAGGGCATCAGATACTCTTAGAGCTGGAGTCCCGAGCAGTAGAGAGCCACTCGATGTGGGTGCAGGAACCCTGCAAAAGCAATGGCTGCTCCTAAAGGCCGAGGCGGCTCCTCGGCTCCTTGGCTCCTGTCCACGTGGTTTTCAACCCCATGATTTCCCTGTACTGAGCCTCAGTGTCCTCATCATGGGATATTAAAAATGCCACTTCTCAAGTAGCTATGAGGACTAGCAGGGAGGTCAGAGGTACTGCAGACAGTCAAGGCCCCAGCTCTGGGTTGGAGTCCACTTAAGAGTTCTTCTCTCACTTCACAG
Seq C2 exon
TGACCAGTACAAAGCATACTTCTGGCCTCGGGACCTCCAAGCCTTCTCAGCTAGGCCTCTGCTTGCCTCCCCCACCCACTATTCGGGAGACGCCGAGTGGCTCAGTGACACAGAGACATCCTCCCCCTGGGACGATGACAGTGGTCGCCTCATTAGCCAGACTGGCTCTCAAAAGGCCCTTCGTGGCCCCCACCTGCACCTGACTGGCAGCAGTGGACACAGCCTCCATCCTCACCACAGGGATGAACTGTAGGTGAAGCTGGACCTAGAAGAGGACCAGTCCACGGCCCGGGCTTCCCTTCTCAGCTCTCTCCTCCTCCCTCCTCCTGCTTCTCTCCCATCCCCAACCCACCTCTTGTCTACTTCTCTCTGATTTCTCTAGCTTTGTCTCTGTCTTGTCTCTGTATCTGCCTCTCTACCTGTCTGTCTCTCTCCATAGCTGTTGACATCTCTACATCTGATTTTCCTTTTCTTTCTCTTGCCCCCTTGACCGCTAGCCCATGAGGTCCAAGTGGGAATCCAAATGAGCGATGAGAGGGGAGAGGAAGAGGTGACAGCCAGCAGAAATCTGACTGTTATTTTGGGCTCAGCTAGTTTTCTGTCCTCTGGACTCATTCCAAGGGAGGAGAAGCACTCAGAGACAGAGTCCACTCCTGAAGGTCTCAGAGTGAAGACACTAAGACCCCCAAGACTTTTTTTTTTTTTTTTTTTTTGTGACAGGGTTTTTCTGTGTAGCCCTGGCTGTCCTGGAACTCACTTTGTACACCAGGCTGGACTTGAACTCAGAAATCCGCCTGCCTCTGCCTCCCAAGTGCTGGGATTAAAGGCGTGCACCACCACTGCCTGGCTACCCCAAGACTCTTGACTCTGCTTGCAAATTTAGAGCCAGTGGGCTCAGGGACAGGGAGGCCTCAGCCTTTGGGGTTTCAAGCTGGCTGGAGCCCAGAGTCCTGCCCTCTGAGGACCCAACTACTTTGCCTCCATCTACCTCCGCCTTGGTGATTCCCTCCCTGCCTCACATCTGGGGCCCATTAGCACCCTCTTTCCTGGTTGGTGGAAAGTGCAAGAAGATGGGAGGCATACCTGGTGCTCAACACGCAGTAGGCCTTCAATAAAAGCCACTTGCATTAGCATTTTATACTTCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000039787-Cercam:NM_207298:11
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.464
Domain overlap (PFAM):
C1:
PF0175512=Glyco_transf_25=PD(31.9=85.5)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Human
(hg38)
No conservation detected
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGTGAACCCTGAGGAGGAAGT
R:
GCTAATGAGGCGACCACTGTC
Band lengths:
343-920
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: