GgaINT0136552 @ galGal3
Intron Retention
Gene
ENSGALG00000002602 | CSMD2
Description
NA
Coordinates
chr23:5169885-5170749:+
Coord C1 exon
chr23:5169885-5170023
Coord A exon
chr23:5170024-5170589
Coord C2 exon
chr23:5170590-5170749
Length
566 bp
Sequences
Splice sites
5' ss Seq
CAGGTGGGT
5' ss Score
8.56
3' ss Seq
TTCTTTCTGGCACCCTGCAGGAG
3' ss Score
8.02
Exon sequences
Seq C1 exon
ACGTCAGCATGATGGAAAACGATCCGGAATCGATCGGACACCATTTTGCATCCAACAGCAGTTCTGTGGCAGCTGCCATTCTTGTGCCTTTCATAGCCCTGATTATTGCAGGGTTTGTGCTTTATCTCTACAAACACAG
Seq A exon
GTGGGTTCCAGGAATGACGCAGTAAGTGAAACAAAATAAGAGGGCTGACAGAAGTATTTGTGAGCTTGTCTTAAAAGCACTCCCTCCAGACCCGGTTTCTCATTTAGTTCAGAAGGTAAAATAAGTAATAGAGCAAAAGTGCACGGAGATGGAGGGGTGTTGGGAGAGCAGAGTGCTGAGGGCTTTTATGGCAATCAGTAAGATTTGTGGCAACGTTAAGGAGGATAAGGCAAAGTAAATTTCATACTTGGGCTTTGCGTGTGTTGTAAATGATTTCTTTCTCCTGATCAGTGCATTGCTGTGGAAATGTTCCTGCACTTCAAAGCATTGTGTGGACTGGATGCTGTGCAGGGGGAGCACGTGTAGGACTATGGCAAAGCCCAGAGAGCTTCCTGCACCACAAATCCCTAATAAGATTTGCTGTAGATCCCTCCTGCCTTTCCCGCAGGTGTTTACCTTCTTCAAAAGCAGCTTTTTCTTTCCCACTGGCTTGGTCACTGCTGTTCTGTGGGCTGCAGCGGGAGCAGCCCTGACCTCTCTGGGTTTTTCTTTCTGGCACCCTGCAG
Seq C2 exon
GAGAAGACCCAAAGTCCCATTCAATGGCTACGCGGGCCATGAAAACACCAATGTCAGAGCAACGTTTGAAAACCCCATGTATGACCGAAACCTGCAGCCCACGGACATCATGGCCAACGAGACAGAGTTCACAGTCAGCACTGTGTGCACAGCTGTATAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000002602:ENSGALT00000033174:74
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.094
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:
ACGTCAGCATGATGGAAAACGA
R:
GCTGACTGTGAACTCTGTCTCG
Band lengths:
278-844
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]