DreINT0052631 @ danRer10
Intron Retention
Gene
ENSDARG00000001559 | csmd2
Description
CUB and Sushi multiple domains 2 [Source:ZFIN;Acc:ZDB-GENE-030616-39]
Coordinates
chr19:36580767-36582882:-
Coord C1 exon
chr19:36582709-36582882
Coord A exon
chr19:36580941-36582708
Coord C2 exon
chr19:36580767-36580940
Length
1768 bp
Sequences
Splice sites
5' ss Seq
TTGGTGAGT
5' ss Score
9.27
3' ss Seq
ACCGTTTTTTTTTTCAACAGCTG
3' ss Score
10.95
Exon sequences
Seq C1 exon
TAATTTCCTGCGGTGACCTTGGAACCCCTCCGAATGGGAATAAAATTGGAACATTAACTGTGTATGGAGCGACTGCCATTTTTTCCTGTAATACGGGTTATACTCTAGTGGGCTCCAGAGTGAGAGAGTGTATGTCCAATGGCCTGTGGAGTGGAGCTGAGGTCCAGTGTCTTG
Seq A exon
GTGAGTAACTTCACTTCCCATATGGCTTAAATTAGATTCAGTCATTAATAATTATAATTATACTATGCTTAAATCTGACTTGTTGAAGAATAAAAGCTTGGTTCGGGATACTGGAGGTTTTAAATCCTAATCGAAATCTGGAATTATGCTAATTAGGAAAATCGTAGATGTCAAATCTCAAACATAAACGCACTAAACAGTTGAATTTTTCAACAATAAGACAACAAAAACATCAACCGTTTCTCCTAATGCACTTCTCTTTATTACTGTTGTATGTGTTCCACAACTTCCACAATAACCAGCTTCTCCATCTCTGCTATCCATAGGACCAATATAGTAGCTTGTTTGGCAATCGTTGAAGCACTGACATAATCGTAATCACCTCAGTTTAAAATCCGAAAAATCGGATGGCCTGATGTGTTAGGCCAGAAAAGGATGCTTTAGATTAGATCAGTAAACACCTCACATTGCCAGATGACATTGAAACATGTTCTATCACATGTTAAAATCACTTCTTACATGGCTGTCTGGGATACTTGCTTCTGACTGGCCAGTCGTGACTTTCCAATGTATGTTAATCCCAGGTAACAACCTCTGAATAAAGCAGAATCAACTGGGAACTTTAAATCACCTTGACCATCAGTGAATAGGCTGACATCCGTACACTTATATCCATATCCACAAATATCTGCTTGTCTGTTACACCAAGGTTTTTGACTGATATCAATAAACTGTTTGCCACCGTCTTAAGATTGACTAATTTGTAGATACTCAATGCTTTACACAGCCAGTTTTGTTTCTATCAGCTTTGCGTTTTTGACAGTTTGGCATCATCTTGTGCCTGAATATTACACAGGTTGGTGCAATGTTATAAAGTATTTTTTATTTTTTTTTAACTTAGAGGTTTTCTTGTTTTTAGTCCAAATATGTAGATATAAATTAAGAAACATTTTTAGACAAGAAAAAAATTTTCTAGCTTTTGTCAAATTTTAGTAAGTTTAGAGAAAGGAAAATAATCTGCCAATGGGGTAAACAAAATAATGTTATTTCAAAGCGAACAATTGGCAGATTATTTTGCTTGTTTAAAGGAAAAATGCACTTAATTTTGACCTAATATTTTTGAAAACAAGAGAATATTTTGGTTTCTCTAGTAAATGTTTCACGGTTTAATAATTTTTGTATTTTTGAACTAGAAACAAGACAAATACTCTAAGTACACTTTTAGAATTAATTCATGTTTACGGCTTAGAACATGTTCATGTAATAAGTGGGATGAACAGAAGGTTGTTTTCACAGAATAAAGCCCTTCAGTTTTATACAAATGCAGATAAGCCTGTCGGGGTTTATCTTGCGAAAGTAACCTTCTGGATGTACTTTATCCCTTACATAAAATATGTAGAACAGCTATGCAAAACATGTGACACATGAAAGCATGAGGTTTTGGAATATTTTTATGTAAAAACCATGACATCACATGAGTTGCACATGAATATCTTCCATAACCACACATTTTTACGTGTTCCACATATTTCAGATGTAATTTTAACATCACTGCACATGTGTAGCTTATGTCTATAAGGGACGAGGACCTGATCAAGATTTTAGTTATTTCAAAATTCATTAAAGCCTGCAAAAGCTAAATTAATTAAACCTAAAGTTATCAAGCAAATACATTTAAGAAATGGATGCAGTATTATTATTAATAATTCAGTCAATCACTCTTTTATGTGCTCTAAACAAGCATTTGCACCGTTTTTTTTTTCAACAG
Seq C2 exon
CTGGACACTGTGGCACACCAGAGCCTATAGTGAATGGTCAGATCATTGGAGAAAACTACAACTACAGAGGCAGTGTTGTTTACCAGTGTAATCCTGGATTCCGGCTCATCGGCGTGTCCGTTCGCATCTGTGAGCAGGACCACCGCTGGTCCGGGAAGACTCCTGTCTGTATCC
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000001559:ENSDART00000132471:52
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:
PF0008415=Sushi=WD(100=91.5)
A:
NA
C2:
PF0008415=Sushi=WD(100=90.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AATTTCCTGCGGTGACCTTGG
R:
GACAGGAGTCTTCCCGGACC
Band lengths:
340-2108
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]