GgaINT0136523 @ galGal4
Intron Retention
Gene
ENSGALG00000002602 | CSMD2
Description
CUB and Sushi multiple domains 2 [Source:HGNC Symbol;Acc:HGNC:19290]
Coordinates
chr23:4752291-4752925:+
Coord C1 exon
chr23:4752291-4752407
Coord A exon
chr23:4752408-4752715
Coord C2 exon
chr23:4752716-4752925
Length
308 bp
Sequences
Splice sites
5' ss Seq
TTGGTGAGG
5' ss Score
6.9
3' ss Seq
TGTTTGTTCTTCCTCCCTAGGTG
3' ss Score
13.22
Exon sequences
Seq C1 exon
CCCAGTGTGGAGGAACAGCAGAGGAGATGGAAGGAGTCCTCCTGAGCCCGGGGTTTCCAGGAAACTATCCCAGCAACCTGGACTGCACGTGGAGGATATTGCTGCCAGTGGGATTTG
Seq A exon
GTGAGGCAGTTGGTTTTGGTGTGAGCTGGCTACGTGCAGTTTGGAAAGAGACAGGGCTGTGTAGCTGTGTGCTTGCCTTCATAATTCCTTTGCTGTCAGGCAAAGTGAAGAGAGTGCAGGGGAACTCAAGCATCCTGAAACCACAGCACTTGTAGCCCGATCTGGGCTGAAACTAGCAGGACAGTCGCCCTTTTCCTCCAGTGCACTAAATGTTTCTTTTTCTAATTGACCAGGCTGTATTGGACAGTGCTGATGTGCCGATGCTTGTGGATATCTTTGAAGGCAAACTGTTTGTTCTTCCTCCCTAG
Seq C2 exon
GTGCTCACATTCAATTCCTAAACTTCTCCACTGAGCCAAACCATGACTTCGTTGAAGTGCGCAATGGGCCATACGACACCAGCAACGTCATCGGGCGCTTCAGCGGCACCGAAATCCCAGGCTCCCTCCTGTCCACATCTCATGAAACCACTGTGTACTTCCACAGTGACCATTCGCAGAACAAGCCAGGCTTCAAGCTGGAGTACCAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000002602:ENSGALT00000004092:40
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=0.028
Domain overlap (PFAM):
C1:
PF0043115=CUB=PU(34.9=92.5)
A:
NA
C2:
PF0043115=CUB=PD(64.2=95.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTGGAGGAACAGCAGAGGAGA
R:
TGGTACTCCAGCTTGAAGCCT
Band lengths:
319-627
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]