GgaINT0078170 @ galGal3
Intron Retention
Gene
ENSGALG00000016341 | CSMD1
Description
NA
Coordinates
chr3:92976073-92976926:+
Coord C1 exon
chr3:92976073-92976246
Coord A exon
chr3:92976247-92976752
Coord C2 exon
chr3:92976753-92976926
Length
506 bp
Sequences
Splice sites
5' ss Seq
TGCGTAAGT
5' ss Score
9.73
3' ss Seq
TTCTTTTTTTCATATATTAGCGG
3' ss Score
5.22
Exon sequences
Seq C1 exon
CTATCACCTGTGGCCCACCTCCACCAGTACTCTATGGAAAAGTGGAAGGATCTGATTATCACTGGGGTGCTAGTGTGAGTTACAGCTGTGCAGAAGGCTATCAGCTATCTAACACAGCTATTCTTTCCTGTGAGGGTCGAGGAATATGGCGGGGAGACATCCCACAATGTTTGC
Seq A exon
GTAAGTTTTCAGGATCCATTGTGTTGGGGTTCACCAAACTGTCTCAGACTTACAGTAATTTTTTTTCCTCTCAGTTTAAAAAGCACTTGGCTAGATCACATACTCTGTTTGCCATTTGTTTTTCAGTTTCTTCTTAACCTGTCATATTCTGACCTTGAATGCTTGAAATTCGTCAAGACCCTGACAAGCATTTTTCCCTTTACTTAGTTAGTTCAAAAATTTTGAGCAAACTCACTTGAGGGTGAATGATGTGAGAATTGCATGCATTTAGCACTGAGTACTTTGAAATTACTTTGTGAACCAAATCTAATAAACATTTAAGTGTCTCAGTTAAAAGGTCTGTTTTTACAGGTTTATTTTGATGCTTACATTAACTATAATAGTGACAATTATTTTTAAATTGCTGTCAATAATTCATTTGAGCTACACAGATAAATGAACAAAGATAGCATTTCCTCTCATATTCAGTATTCCTGATTTGAACTTTTCTTTTTTTCATATATTAG
Seq C2 exon
CGGTGTTTTGTGGTGACCCTGGTACACCAGCAGAAGGACGCTTGAATGGAAAAAGCTTTACCTACAGATCTGAAGTTAGCTTTCAGTGCAGACCTCCTTTTATTCTAATAGGCTCTTCAAGAAGATTTTGCCAAGCAGATGGTACTTGGAGTGGAATACAACCAACATGCATTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000016341:ENSGALT00000036950:53
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=0.017
Domain overlap (PFAM):
C1:
PF0008415=Sushi=WD(100=91.5)
A:
NA
C2:
PF0008415=Sushi=WD(100=91.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTATCACCTGTGGCCCACCTC
R:
GCATGTTGGTTGTATTCCACTCC
Band lengths:
344-850
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]