GgaINT0078171 @ galGal4
Intron Retention
Gene
ENSGALG00000016341 | CSMD1
Description
CUB and Sushi multiple domains 1 [Source:HGNC Symbol;Acc:HGNC:14026]
Coordinates
chr3:89742044-89743960:+
Coord C1 exon
chr3:89742044-89742217
Coord A exon
chr3:89742218-89743886
Coord C2 exon
chr3:89743887-89743960
Length
1669 bp
Sequences
Splice sites
5' ss Seq
TTGGTATTA
5' ss Score
0.6
3' ss Seq
TGTTTCATATTTTACAATAGATC
3' ss Score
7.34
Exon sequences
Seq C1 exon
CGGTGTTTTGTGGTGACCCTGGTACACCAGCAGAAGGACGCTTGAATGGAAAAAGCTTTACCTACAGATCTGAAGTTAGCTTTCAGTGCAGACCTCCTTTTATTCTAATAGGCTCTTCAAGAAGATTTTGCCAAGCAGATGGTACTTGGAGTGGAATACAACCAACATGCATTG
Seq A exon
GTATTAATTACCATTACTTGTGCTTTTTCTGCTGAGAATATTTTTTGATACACTATTACACTATCACAAGTCTAGCAATTAGCTTTCCAAATGCAGAAAACTTCTATGTAATATAAAAAGAACCAGATAAATAAGGTAATGTTTTGAGTTTAAAAAGACAGGATAGACACAATCACATATGAAGTCATTTATAAATTCACATGATTGCTTGTCTACTGGAAATGCGGAATGTCAATAAATTAGTTCCATCTATTTATGAAGCATTATAGATACACAGAAGATTTTTGCAGATTAAAGACTGCATTCTGTCACTGGAGAGTTAAAGGCTTTTATCAAAATCAATCCTAAATCAAAAAGATTTTTGGACCTTATGTATGTGGCTGGTAGAGTTCAAAAAAATGAAGTGTGCAGGGTCTGATCATTTGAAATACTGGTAAACTGCCAAGCACTATCCATTTCTCATTGACTGATGTACAGGTGATAGACTTTTAGCATGATACATAATCAGATTAACTGTGAGAAATGCTGGACACCTGTAACTCCCACTGACATCAGCATTTGACCCAGTGACTTGATAAAAAAAAAAAGATTTTGGTGTGATCATGAAAAAAGACTCTTGTATTTCTAAATAAACTCATTCCAATATAGCCTGTATATCCATGTTTTTTTAAGAGATGCAACAAGGTTTGCAAAATCAAAATGTAAGGTGAATCAAATTTCAAAATGATATCATGTCAATTCTGTTCACATTTTATATAGCATAATATAGATGTATATGAAAATGCAGTTTCTATTTCTATTACTAGCAGTAGTATTCCAGCTTATGATAATTTGTAAACAGTCCTTGAACTTCTCAATATGTTTGACTTTTATTTTCACATGTTAGGTTAACATCCACCAAAATTTTTAAGATTTTAGTAATATCAGTCCAGTTGAACTGTAGTGCTCTTGTGATAGTGAACATGAAAAGGGAAGTTGACTGAGAGTGAAATAACATATGTTATATATGTCAATTTTTCTTCTACAGAAAATTACAAATTGTTACAGATAAAATATGGGCCCAAATTCTGTTCTTCAAATTGCAGTCTACACAGAAGCAGACTTGATTGCCAAGAAGGAATCATATAGTACAGCAACATCTATCAGATCTGGTGCTTTGGCATTCTCAGTGAAAATACACCATCAGAATGTGAAGTGGGCATAAGTGAATCAAAATTGATTTTAAACTGTGTTAATTTATACTTATGAAAATTATCATTCATTTTTATGGTCATTTAATTAGCCAAACTCTATTGGTGTATCTTTTTTTGGGTAGGAAGAGGGCTTTATTTTTATTCTCCAGCAAAATCTGAGATAATAGTCCATTTGAAACATTTATTTTCATGATGACATGGGACAAATTCTATAAAATATAGGACAAATTCTATAAAATGTAAGTAATTTACATGCTATAAGAAAGCAAATTTTTTTGTTGTTGTTAGAAATCTGAATTAACCATTGATCTCTTTATTGGATTCACCATTGGATTTCATTGTATACTGAAATACACACGTGTATTAAATATGTGATTATTATTATTACTTTACATTGATGAATTAATCTTTGCAAATAGTAGCCTATTCTTTCTGTGTAATAGTAATATCTGTAAATGTTTCATATTTTACAATAG
Seq C2 exon
ATCCAGCTCACAATACGTGTACAGACCCTGGCACTCCACATTTTGGAATGCAAAACAGTTCCAGAGGTTATGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000016341:ENSGALT00000026359:60
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.017 A=NA C2=0.200
Domain overlap (PFAM):
C1:
PF0008415=Sushi=WD(100=91.5)
A:
NA
C2:
PF0008415=Sushi=PU(32.7=72.0)
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:
GTGTTTTGTGGTGACCCTGGT
R:
CTCATAACCTCTGGAACTGTTTTGC
Band lengths:
246-1915
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]