GgaINT0102987 @ galGal4
Intron Retention
Gene
ENSGALG00000016111 | CSMD3
Description
CUB and Sushi multiple domains 3 [Source:HGNC Symbol;Acc:HGNC:19291]
Coordinates
chr2:132875747-132876503:-
Coord C1 exon
chr2:132876315-132876503
Coord A exon
chr2:132875894-132876314
Coord C2 exon
chr2:132875747-132875893
Length
421 bp
Sequences
Splice sites
5' ss Seq
ATGGTAACT
5' ss Score
6.06
3' ss Seq
TTTTCCTTCCTTATATCAAGGAC
3' ss Score
7.58
Exon sequences
Seq C1 exon
TGCTATGTCCAGCCAATGAAATGCGTCTGGATTCAACAGGGGTAATACTGAGCCCTGGGTATCCTGACAGCTACCCAAATCTCCAGATGTGTGCATGGACCATTACTGTGGAAAAGGGTTACAATATCAGCATGTTCTTCGAATTCTTCCAGACAGAAAAAGAATTTGATATACTTGAGGTGTTTGATG
Seq A exon
GTAACTATAAAATACATGATTTTGGATGATTCTTTTTCTTATATAGTGTATTTTTACTTTACAGCTACATTGAAAATCTCAAATCACTGTTATTTGTTCATACCATATTTTATGTATACAAAATTAAATAAGCAATCATTTGGATTTGTTGTGCTAAAAAATATCTTTTGTTTATACTGCATTTAAAAACTGTACTGAAAAAGTTATGAGAAAGAAATAATTTTGTTTCAGTACAAATAGTACTCTGCAGTACATGACATGTTCTGTCTACATCAATTTCTAAATCAAATTAATTTACAATTTGCTTGGAAGATGTTTTCTATGCATAGTAATATATATATATTTTGTTGTATGTTATTTAAGACTTTGTAACTTCTTGGTGTTGTGTTTTTTGGTTTTTTTTTTCCTTCCTTATATCAAG
Seq C2 exon
GACCAAATATTCACAGCCCATTGCTCATTTCTCTCAGTGGGGACTATTCCTCATCTCTCAATATAACCAGCAATGGGCACGAGGTATTTCTCCGATGGTCAGCAGATCATGGCACAAATAAAAGAGGTTTCCGGATAAGGTACATAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000016111:ENSGALT00000025958:48
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:
PF0043115=CUB=PU(56.0=95.3)
A:
NA
C2:
PF0043115=CUB=PD(43.1=94.0)
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:
TGCTATGTCCAGCCAATGAAA
R:
ATGTACCTTATCCGGAAACCTCT
Band lengths:
334-755
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]