RnoINT0042650 @ rn6
Intron Retention
Gene
ENSRNOG00000007057 | Csmd2
Description
CUB and Sushi multiple domains 2 [Source:RGD Symbol;Acc:1565728]
Coordinates
chr5:146671165-146672549:+
Coord C1 exon
chr5:146671165-146671342
Coord A exon
chr5:146671343-146672403
Coord C2 exon
chr5:146672404-146672549
Length
1061 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGG
5' ss Score
9.68
3' ss Seq
GCTTTCTTTCCTGTGTGCAGGGA
3' ss Score
9.41
Exon sequences
Seq C1 exon
TCCCCTGTGGTGGGAACATCACCTCTTTCAATGGCACCGTGTACTCACCTGGATACCCCAGTCCCTATTCCAGCTCCCAGGACTGTGTCTGGCAGATCACTGTCCCCATTGGCCATGGCGTCCACCTCAACCTCAGCCTGCTCCAGATAGAGCCCTTTGGAGACTACATCACTGTCTG
Seq A exon
GTAAGGTCATGTCAACAGCAAAGCAAAATGGGGCTCAGCTTCAGGCCACCAACTCTATCACAGGCGGGGATTGACAGGTCAGAGGTCCTCAACCTGAAGGTGCCAGTAGGGGCGTGGTTGGGGATGGTGTGGCTATGCAGGCTTTCCTTCATATTTCCAGAATTTACTCAGCACTCCACTTACACCTAACTAAGCTGACCAGACCACGGGAAAGGCTTGGCATGACGTTATGTAAAGCTCCTCTTCTCATCATGTGCGGAGCCAGTGCTGCCCCACAGAGCATTCTGAATTGACGGTGGCATTTTATGCCCTTGCCATTCAACATGGCAACCACCAGACTGGTTTTTAAATTGTGTCTAATCTTAATGAATCTAAATGTAAGTAGGCATGTACTGTTAATGGTTACTGAATCAAGCAACTCAGCCGCCTAGTTACAGAGCTCTATAGACAGCGGCCTGAGTCCATTTTAAAAAGGAAATGCAGATTCTCGACTGCTAAGGGCAATTTCCTTGACAACATTCCCCAATGACTGAATCTGTGGACAAAGATACATAACATTTTAAAACTCCTTTGTTTGGACGTCAGTGGCATTCTGAAAAGTATCATGGGGTAGTGGAATAATTTTTCTCAAAACCCTGAATGATTTCTAATCCATGGATAGGAGCAGAAAGGAAGGACTAGATAAGGTTCCAGGCAAGAAGTCATTTACCCCAAAGAGGGTGTGTCTTTGTTTGGGTAGCAAAGGGCTGTCAGAGAGCAGCAAGAGAGTTCTGCCACAGTTCCCTTAACCAAGAAGGTCTGTGGTTATACCAGCAGCCCTGCCCCAGGGACCTCTGTTGCCCCAGAAGCCCACCCAACACGGGGTGAGTAGGACTGATGAAGAATCAGATAAATAAAGGTTCCATCAACTCTATTGGAAGACCTCACAGAGAGATACTAGAGAGAGTTTCCTAAAGCCACAGCCACCCACTACAGGTCTCTCTCAGGGCCACTGATGGCTCTGGGAAGAGCAAACATTCAAGGCGTCTGATGACAAGCCGAGCTTTCTTTCCTGTGTGCAG
Seq C2 exon
GGATGGGCCACAGCAGACATCACTGCAGCTTGGGGTCTTTACAAGGAGTCTGTCCAAGAAAATAGCATACAGCTCCTCTAACCAGGTCCTGCTCAAGTTCCATCGGGACACGGCCACAGGTGGGATCTTCGCCATTGCCTTCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000007057:ENSRNOT00000036029:5
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:
PF0043115=CUB=PU(54.3=95.0)
A:
NA
C2:
PF0043115=CUB=PD(44.8=94.0)
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:
TGGTGGGAACATCACCTCTTTC
R:
TGAAGGCAATGGCGAAGATCC
Band lengths:
314-1375
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]