RnoINT0042646 @ rn6
Intron Retention
Gene
ENSRNOG00000007057 | Csmd2
Description
CUB and Sushi multiple domains 2 [Source:RGD Symbol;Acc:1565728]
Coordinates
chr5:146656049-146658353:+
Coord C1 exon
chr5:146656049-146656097
Coord A exon
chr5:146656098-146658236
Coord C2 exon
chr5:146658237-146658353
Length
2139 bp
Sequences
Splice sites
5' ss Seq
TCGGTAAGA
5' ss Score
10.53
3' ss Seq
GATTACTCTTGTTGTCACAGCGC
3' ss Score
6.86
Exon sequences
Seq C1 exon
ATGCCCGGGACTGTGCGTAGATGGAACTACCCGCCTCCGCTCTGCATCG
Seq A exon
GTAAGAGAACCGACTTCAAAATCCACTAAAGCCCAAATCCCCAGGGATCGGAGCTCCCAGCCGTACTTCTGTGTTCAGGTTCAAGTCAAAAGAAATTCTGATGTTCTGGATTTGTTCCAAGTCAGTAGTTTCTGAAAGACATTTTGTAATTTCTAACTCTCATTCAAAGCTGTCCTGACTTATAGAAGGCTCTACCCACCCACTAAAAAAAAAAATCACAAGGTTGCTCACCTGAGACTATGGTGAGGGCCACTGTGGTCCCACAAAACCAGCCAGAGCCCAGAAGGCGTTTTTAGGCGCATTGGTTTGTCTGATGACTTTGTCAAAGGACGGACTAACAGACCTGCTTGTCATGTGGGTTGCACATAAGATAAGGACTTGACTTGGTTTCATGGCTTAGCTCATGCTAGGCAATGTTGAGGAAATTAGCAGATACAAGGATGCTGCAAAGAATTTTGGTCAAGAAAGTAAGAAATAAACAGTAGCTGGGTATCTCCTAAGTGCCAGAAGGGATGCATTAGCGCGTTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTGTTGTATATACACGTGTGGGGGGAGTGTCTGTACATGTCTTCCTCAACCACTCTCCAGATGTTTTTTGAGACAGGGTCTCTCCCTAAACCTGGAGCTCACCCGATGAGCTAGGTTGGCAGACCAATGAGCTCTAAGAGTCCTTCTCCCCACCCCCACCCCTCAACACTCAGATTACAGGTATAGCACTGCACTTGGTTTTTACATGGATGCTGGACATCCAAACTCAGGACCTCACACTTACACAGCAAGTACCTTACACATGAGTCATCTTCCCCAGCCCAGAAATCTTTCTTTGAAGGTTAAAGGGAAATGAGAAACGGAAGGGGAAGGTTTGTCAATGCTGGGCTGATCTTAAAGCACATCCCAATTGTCCCTGGGAAAGTAGTGACTCAAGGGAGTGTCACATTGGTGTGACAGCATTTCATTTCTGTGCTTTCACTCACATGTTGAGAGGGTCACACATGTAGCCTGAAGCTCTAGGCGCTCACCTGGTGTACTTCAGACACTTGGCCCAGGAAACCATCGGAGCAAGAGGTGTCACTCACGCCGTCTGTTGCACACATCAGCTCTCCTTCACCAAGTGAAAGGCATTCTTCCCCGTGTCCCCTCAGAGCAGCTCCCTGACGGGTTGTTCTTCGTGCCTTTTTGCTGCTTTGGAAACTGGACTTGGAGTGGTCAGGGTGACATAGAACTCACCCATAGTCCCACAGGACGTTCAGTGGTCACTGTGACATAGTGGTGGTCCCTTTTCCATCCTGGTGTGCTTCCTAGTCACCTTCTGCCCCAAAAGTGCTGGTCTGGATCCTGCCTGGCATTTCCATCCCTGAGCTCCTTTCCCTGGGCCCCCATGGCTGATAAGCCCCATTCTTCTTCACACAAGCTTTCCTCATAGAATGTGAAATACAAAATAATTTTCAACTGAACAGCTGCTGAGGTGTCCTGCACGACTTGAAATCAGATGTCTCCCTTCGTCACAGCTAAGTGGTCATGGCAAGCCTTGACAGTCAGCCACTCTACCCCATAGATGATAGGTCTGGCACAGTTACAAGCACATGAAGAGGACACAATGTGTGCCTGTCCCTTCTCGTCCCTCTATCCTTTGCTGTCATGGAGACTGGATTGGGGAGGAAGGAGAGAGAGAGAGACAGAGAGAGAGAGAGAGAGAGGGGGAGGGAGGGAGGGAGGGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAACGCTGGGCTATCGTATAAGGAGTGGAGGACCTCTCTTGAAGCAGAGCTTTGTCACTCCCTATATGTCCTTGATGAAGTCACTGACCTGTGAAGGGCATGGCCAAGGCTGGCACTCCTGGTATCTTGAGCTGTGCTTTAGCCCTGACTGGGTTTTACCCGTGGGTACAGATGTTCAGGGAGACCCTTTGGGTTCTCCCTGAGGCCTGTGGCTCATGATGTGTTTTTAAAATGGGGCTCTGGACACTTGCATAGCCCTGCACTCTCCTTGACGACCTAACCTGATTACTCTTGTTGTCACAG
Seq C2 exon
CGCAATGCGGGGGAGCAGTGGAAGAGATGGAAGGGGTGATCCTGAGCCCCGGTTTCCCAGGCAACTACCCCAGTAACATGGACTGTTCCTGGAAGATCTCGCTGCCTGTGGGCTTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000007057:ENSRNOT00000036029:1
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=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0043115=CUB=PU(34.9=92.5)
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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]