GgaINT0136549 @ galGal3
Intron Retention
Gene
ENSGALG00000002602 | CSMD2
Description
NA
Coordinates
chr23:5167937-5168735:+
Coord C1 exon
chr23:5167937-5168098
Coord A exon
chr23:5168099-5168622
Coord C2 exon
chr23:5168623-5168735
Length
524 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGG
5' ss Score
8.3
3' ss Seq
AAAAGTCACTTATTTTCCAGGCA
3' ss Score
5.64
Exon sequences
Seq C1 exon
TGCCTGCTGATGTGTTTGCTAGAAATTCCCTTTGGAAAGGCTCCTACGAATACATGGGAAAAAAGCAGCCTGCAATGCTGTCTGTCACCAGCTTCGACCCCGTCACCAGTAAAGTCAATGCCACTTTGATAGACCACAGCGGCGTGGAGCTCCAGGTTTCTG
Seq A exon
GTGAGGGAACCAACGTGGCTGTTTGTTGGGATTTACACTCACTGCACTGTAGTCAATGGCATTGCTGGGCAAGGGGCAGTGTGCTCTGTTATCTGAGTGCTCTGGCCTTTGTGATACAGCTGGACAGAAGTTGGAAGTCTCCAGTCTTGGAGTGGACCAAGACGAACAAATCCTGTGCCTGAGTTTGCTTTGACTCATCCTGGAAAGCAGCACAACCCAGCTCACTGACCTATAATTTAATCCACACAATTAAATGGTGTGAATACCCCTTGTCTCTGCCCCCCAGGGGGCACTGTGTTACTGATCTGGTGGCACTTAGGAAATACAGCTGAATTGCTTCCCACATGCAAAATGTCTTTAATATCCTGGGGGACAGATGTGAGGTTGAGAGTTTGTGGTGTGGTTCCAGGTGATCCCACTGATTGAAGCATAGGAAGAGTTGCTGCCCACTCTGAGACAGTGAATTACTTCAAGTTTGAATTGAGACATTGTGATCCAGTGGTTAAAAGTCACTTATTTTCCAG
Seq C2 exon
GCATTTACAAGAAAGAAGACGTGCACCTGCTCCTCCAGGTCTATCAGATTATGGGGCCAGTGGAGATCTTTGTAAACAAGTTCAAAAACGATAAATGGGCTCTAGATGGACAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000002602:ENSGALT00000033174:71
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:
NO
A:
NA
C2:
NO
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:
TGCCTGCTGATGTGTTTGCTA
R:
TGTCCATCTAGAGCCCATTTATCG
Band lengths:
274-798
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]