DreINT0052622 @ danRer10
Intron Retention
Gene
ENSDARG00000001559 | csmd2
Description
CUB and Sushi multiple domains 2 [Source:ZFIN;Acc:ZDB-GENE-030616-39]
Coordinates
chr19:36630627-36632148:-
Coord C1 exon
chr19:36631971-36632148
Coord A exon
chr19:36630773-36631970
Coord C2 exon
chr19:36630627-36630772
Length
1198 bp
Sequences
Splice sites
5' ss Seq
TTGGTGAGC
5' ss Score
7.43
3' ss Seq
TAATGTTCTACCTTCAACAGGGA
3' ss Score
7.11
Exon sequences
Seq C1 exon
TGCCCTGTGGAGGTAACATTACATCAGACAATGGCACAATCTTCTCTCCCGGTTACCCAGAGGACTATCCCACATCTGCGGATTGCAGCTGGCTGATTACGGTGGCACCAGGCCTGGGTATCCGTCTTAATTTCACCCTTCTGCAAGTCCACGGCCCTCAAGATTTCATCACAGTTTG
Seq A exon
GTGAGCTGTCGATTATCCTACAACTAGTCATTCTTTGACGCACACATTTCTGCGCGGGAACATAATTACAGCACACTCCTTCTAGTGATTAATTAACAAGCTTCCCAGGGAGCATCTTGATGTCAAAAGGACCTCAAGCAACATGTCAAAAATCGACAACAATGTAAGATGTCAATTTGATGTCATTTTGACATCAATGTAGTTTACATCTATTAAAGTGATACACAATATAGTGTACATTTGTCATTAAAAATTGAGGCTTTTAGATTAATAAAACCTTTCTTATATTGTATTAGGTTTTGTGTCATTATTTTTGTGGTCAAACGAGCATCAATCTGTAGATGCCAAATAGACGTCAAAGTTTGACCCTTCTGTTTTATTTCTTGAGTCACTTGAGGCCTGTATTTACAGATATGACATTATCTTTTTAAAAAATACTGATATTAAATAGCACATTACACTTAAAGAATATGTTAGGCCATTGCCTCTCCTGAGACTACAACTTTCTGTTCGGATTAAATGAGGAAACATTGATTCTTTTCGGTATCCTGGGATCCTCTTTCTTGAGGCATGATGTACTCTCTTACATTCAGGTTTCATCCACTTCAGCTCAAGCTAGAGGTAGAGTATAACCTGAAGTGCCAAGAAAAGCTCCATCAAGACAGCTTGGCCTCAGTTCAGTGAGCCAGCATTCCCTTTAGCCAACCAGATGCTTTTTTTTGAATGCACAGGACAGGCCATAATCTGTAGTGCAAGCTCAGATGGCCACAAACAGATGGTTTTAAAGCTGAATGGTCATGGTTAAAACTGGGATTAGGTTGGTGCCAGGTTGTTCCCTCCTAGATTGAGGACTGCAGAGATGGAGATAAGGAGATGTCCTTGTAGATGGTGGCTACGTTTTTACTATGTCATGACACACATTTAGGGTGAGTGTGAAGGAACCAGAGTGCAATATCTAAGAGAGTGTGAAAGGAGTCCCTGAAATTGGAGAGGTAATCAGTATGGCTGGGATAGTCTCTCAAATCAGTAAAGTAATCAATATTTAGAGAATCGTTCTGCAAATCAGCCGGGTGATCAATATGGATCTCACTTACTGTGCGTTTTCAGGCAACAAAGGCACGTGGTGTTCTCTTGTTGTATTGAATGCCCACTGTTAATGGGTTTTATACTCTGAATCCTAATGTTCTACCTTCAACAG
Seq C2 exon
GGATGGACCACAGGAAACAACTCGTAAACTTGGAGTGTTTACCGAGGGAGAGCCAAACAACCCACCGAGCAGCACATCTAATCAAGTTCTGATACGTTTCCGAAGCAGTTCTGAGAAAGGGGGGTTGTTCAAGATCAACTACCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000001559:ENSDART00000132471:43
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.050 A=NA C2=0.460
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:
TGCCCTGTGGAGGTAACATTAC
R:
AGTTGATCTTGAACAACCCCC
Band lengths:
318-1516
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]