GgaINT0136507 @ galGal4
Intron Retention
Gene
ENSGALG00000002602 | CSMD2
Description
CUB and Sushi multiple domains 2 [Source:HGNC Symbol;Acc:HGNC:19290]
Coordinates
chr23:4716449-4718042:+
Coord C1 exon
chr23:4716449-4716640
Coord A exon
chr23:4716641-4717915
Coord C2 exon
chr23:4717916-4718042
Length
1275 bp
Sequences
Splice sites
5' ss Seq
TGGGTGAGA
5' ss Score
6.04
3' ss Seq
AACCCATGTGTTCCTTACAGCTG
3' ss Score
9.74
Exon sequences
Seq C1 exon
GTTTTGAGCTCATCAAATGTGAGGACCCCGGCATCCCGCAGTTTGGCTACAAGGTCCACGATGAGGGGCACTTCGCCGGCAGCTCCGTGTCGTTTAACTGCGACCCCGGATACACCCTGCGGGGCAGCAGAGTGCTGGTCTGCCTGACCGGGGAGCGGAGAGCCTGGGATCAGCCCCTGCCAACCTGTGTGG
Seq A exon
GTGAGAGCTCTTGCTTTCAAACAGTCCTCCAATGAGTCCTTTGCTGGTGGGCACCGCACCACCGCCCTTCCTTTCTCTGCAGCTAACACATGTGATAGTATCTTTAATATTGATTGCGGCCATCTACATCAAAAGGTAATGATAAGGATCCCGTGTAAGGCATCTGCAGATCGAGAGCAGCGATAGCTGCAGAGCTTCTCCAGGCAGTGTGAACGTGAGGCACTGCTGTGAGCACAGATCTGACAAGGTTTCATGCTTCTCGGCAAGGAGACTGCTGCTTTGCAGCCCTTGTCCTTTCGCTTGATGAACACGCTGTGTTAAATGCAGCAGCACTCCCTGGCAGTGGCAGGCAGCAGCGTGTCCTGGCGTTTGGCAGATCAGAGCCGTGTTGACTTGAGAGCTACATGACGTCTCATGCCAATGCTTCGGGTATTTTAATTCTCTCAGTCTCCTCCTCGCCAAGTCCCGGGTTCCCCTTTGCCCGTGACTCTCCAGATGGGTGTCCTATGGCTCAGAAAACTCTGCTGTTGAGTTCTGTGTATCCAAATGAAGTGTGCGTGTCCAAACCCGTGTGAGCAATGAGGGTTTCCAGGGCACGGAGAGGTTCTTACAGACTTTGTCCCCTCGGAGCTCCCAGCAGCTGCTTCCATGTGGTGCTCAAACGTTGGCACACCAAATCCTCCCCCATTGGGAGCTCTGTGCTGCAGCTCTGCTGAGTTTCAGCTTTGCCTTTTGAGGGGAAAAAGACGAATTTCTGTGATTTATCCACCCTGTTAGCCTTCATCCTGTTGTCTGGATATCCGTGAGAATGATTGCGTCTTCATGAACACGTGGGAACCTGGAGAGTTTTAATGGCCTTATAATGAAAACACATTCAAAATCCTCAGGTTGGGGTTCATTTAGCAGCCATACATATGCTGGCTCCTCCGTTTTATCACTCATGGATCGTTAAGGCTTTTTGCAGATGCAGGCAGGACTGAGCTCTTTGGCCCCACGCGTGGATCAGGATGTTGGCAGGCTCTGCCTTTATTCACTGCGGAGCCAAAAGGGGAAGAGGAGCTCTGACGACACGTCAGGTGTTAGGAAGGGCTGTTGTCTGATGACTCTCTCTTAGCTGAACGCAGCGACTCCTCAGCTTTGCCTGGCAGGCTGTGAGAATCTCCTTCAATGGGGACAAATTCTGTGTTGTATTGACAGGCTGAGGTTTGTGCTGTTGCCAGGTAGGAGCCATGAGGATGCACTGAATCTTCTCACTAACCCATGTGTTCCTTACAG
Seq C2 exon
CTGAGTGTGGGGGTTCTATCAAAGGAGAGACGTCAGGACGGATTCTGTCCCCCGGTTACCCCACACCCTACGATCATAACCTGAACTGCATTTGGTCCATAGAGGCAGAAGCTGGCTGCACAATAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000002602:ENSGALT00000004092:24
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=87.7)
A:
NA
C2:
PF0043115=CUB=PU(37.4=93.0)
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:
TCATCAAATGTGAGGACCCCG
R:
CCTATTGTGCAGCCAGCTTCT
Band lengths:
310-1585
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]