RnoINT0034828 @ rn6
Intron Retention
Gene
ENSRNOG00000026604 | Cercam
Description
cerebral endothelial cell adhesion molecule [Source:RGD Symbol;Acc:1304778]
Coordinates
chr3:8442682-8444739:+
Coord C1 exon
chr3:8442682-8442885
Coord A exon
chr3:8442886-8443763
Coord C2 exon
chr3:8443764-8444739
Length
878 bp
Sequences
Splice sites
5' ss Seq
AAAGTGAGA
5' ss Score
4.23
3' ss Seq
CTTCTTCTCCCACTTCACAGTGA
3' ss Score
8.58
Exon sequences
Seq C1 exon
CTACCTTGGCCGGAAGCAGGTGAACCCTGAGGAGGAGGTGGCTGTGGAGGGGCTGCCTGGTCTCGTGGTGGCCGGGTACTCTTACTGGACACTCGCATACACCTTAAGCCTGGCGGGCGCTCGCAAACTGTTGGCCTCTCAGCCTCTGCACAGAATGCTACCAGTGGATGAGTTCCTGCCTGTCATGTTTGATCGTCACCCAAA
Seq A exon
GTGAGACCTGGGTTAGATAGGGCAGGGTCAACCTAGCCAGGAGCCCAAAGCAAAACCCCTTACTGGGCAGATGTTCAATGTTCACCCACATGGTGTCGGTCACCCAAGAGTTGCCCAGGGGCCAGGCTCAGCTAGATGTGGGCACTGTGTTCTCCATGTCCATGTGGGCTTTAGTTTAACTAAACTAAAGTTAGTTTGTTTATTGTACACTGTCTCTGTCTTCAGACACACCAGAAAAGGGCACCAGATGCTCATTACAGATGGTTGTGAGCCACCATGTGGTTGCTGGAAATTGAACTCAGGACCTCTGGAAGAGCAGTCAGTGCTCTTAACCTCTGAGCCATCTCTCCAGCCCATTTTTTAAAATTAGATATATTTCTTTACTTGCATTTCAAATGTTATTCCCCTTCCCGGTTTCCTGTCCATAAGCCCCCATTCCCTCCCTTCCCCTCCCCGCAGCCCATGGGTTTTATTTTTAGATTTATTTTAAATTTTTAATTACATGTGTCTGTGTATATATTTGCATGTGAGTGCAGGTGTCCAAAGAGGCCAGCAGAGGGCATCAGATCCCTTAGAACCGAAGTCACAGGCAGTAGAGAGCCACTTGATGTGGGTGCAGGAACCCTGAACTAGTAGTGACTGTTCCTACAGGCCTAGACATCTCCTCAGCCCCTGTCCCTGTGGTTTTGAACTCCATGACGTCCCTGTACTGAGCCTGCTTGTTCTCATCATGGGATATTAAAAATGTCACTTCCCAAGTAGCTGTGGGGACTAGTGGGCCAGTCAGAGGAACTGCAGATAGCCAAGGCCCCAGCTCCAGGTGGGAGTCAGGGAGAGGCTGTGTGAGTTCACTTAAGACTTCTTCTCCCACTTCACAG
Seq C2 exon
TGACCAGTACAAAGCACACTTCTGGCCTCGGGATCTCCAAGCCTTCTCAGCCAGGCCTCTGCTTGCTTCTCCCACCCACTATGCGGGAGACACCGAGTGGCTCAGTGACACGGAGACATCCTCCCCTTGGGATGACGACAGTGGCCGCCTCATTAGCTGGACTGGCTCTCAAAAGACCCTTCGTGGCCCCTACCTGCACCTGGCTGGCAGCAGTGGACATAGCCTCCACCCTCACCCTAGGGATGAACTGTAGGTGAGGCTGAACCTAGAAGAGAACCAGCCCATGGCCCCGACTTTTCTTCTCAGCTCTCTTCTCCTTCCTCCTGCTTCTCCCCTATCCTCAACCCACCTCTTCTCTCTCATTCTCTCTGATTTCTCTAGCTTTGTCTCCTTTTTGTTTTTGTGTCTGTCTCTCTACCTGTCTGTCTGTCTCTACAGCTGTTGACATCTTTGTCTGACTTTCCTTTTCCCTCCCTTGGCTCCTTGGCCCCTAGCCCAGGAGGTTCCAGCAGGAACTCCAAAGGAGCAATGAGAGCGGAGAGGAAGAGTTGACAGAGCCATCGGAAACCTGACTGCTAGCTTGGGCTCAGCCAGTCTTCTACCCTCTGGACCCATTCCAGGGTGGGAGAACCACTCATAGACAGAGTCCGTTCCTGAAGGTCACATTGAAGAGACTAAGACCCCAAGGCTCTTGACTCTGCATATAAATTTAGAGCCCAGTTAGCTCAAGGACAGGGGGGCCTCAGCCTTGGGGGTTTCAAGTTGGACAGAACCCAGAACCCTGGCCTCTCTGAGGACTCAGCTACTTTGCCTCCATCTACCTCCGCCTCGGCTCCCTCCCCGCTTCCCATCTAGGGCTCATTAGCACCTCTTTCCTGGCTGGTGGAAAGTGCAGGAAGATGGGAGGCATACCTGGTGCTCAACACACAGTAGGCCTTCAATAAAAGCTGTCTGCATTAGCACTTTATTTTTTACT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000026604:ENSRNOT00000060969:12
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.190
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
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGGATGAGTTCCTGCCTGTCA
R:
CTGAGAAGAAAAGTCGGGGCC
Band lengths:
346-1224
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]