GgaINT0078154 @ galGal3
Intron Retention
Gene
ENSGALG00000016341 | CSMD1
Description
NA
Coordinates
chr3:92913988-92915743:+
Coord C1 exon
chr3:92913988-92914133
Coord A exon
chr3:92914134-92915662
Coord C2 exon
chr3:92915663-92915743
Length
1529 bp
Sequences
Splice sites
5' ss Seq
ATGGTCAGT
5' ss Score
6.57
3' ss Seq
ATTTTCACTTAAATTTGCAGCAT
3' ss Score
7.95
Exon sequences
Seq C1 exon
GGATGGTCCTGACCATAATTCACCTCAGCTGGGAGTGTTCAGTGGGAACACAGCTCTGGAAACAGCTTACAGTTCCACCAATCAAGTCCTCCTCAAATTTCACAGTGATTTTTCAACAGGAGGATTCTTTGTTCTCAATTTTCATG
Seq A exon
GTCAGTTTTTTTTTTTATGTGATCAGTGTCTAATTACCACAATCAGTAAGTGAATTTTAAAAATAATTCTTAACTATGGCAGGTACTGATTAAATCTATTTACATTCATAAGTTTGCTACTTTTTAAAAAATAACAGTATAGATTAGTTTTTAAAACAACACATCAAAAATATCTTAAAATTCATTTTTACTTTGAATAAATGATGTTCTATTGATAATATTAATTACTGCTATTTAATATCATTCTTTCAGTTGTTTAATTTATTTAGCCCATTTATTTATCAATTAATTTATACTGCTGTAACAAAAATCCTCACCAGCTTAATAATTTAATGATCGTTTATTGAAATCTTGATGGGACAGCATGGAGCATTGAACAGCAGCTTTAAGTTTAATATGTAGTAAAGTACTGTATTCAAAGTTAAAGTCATGGCTGTAGCTGTGGCCCTGCAAGCTAGGCCTCTCACCTGCGAACTAGGCAAGTTAGGTCTGTAACTCAGACACGAAATGCAGCATTTCAGTTCTACTTCTGATTCTGAATTCTAATTCATTCAGATTTTATATTAATTTGTTCATGTTTTGGATTGAAATTCGAAAAGAAACAGTGAATTATTTCACAAGGACAGGAGGCAGTGAGACAGAAAGAGTGTACCTGAAGATATCTATCTGCATAAAGTAGTTTTCACAGAGGTAGTACTCATATTCTGCGGTCTTTTTCATTGTCTATGTTTTTCTCGCAAAAGAAAGAAGTGATGTAGCCTATTGTCTAGACTCCGGAGCATTTATCTGAGGAGCAAAGACTAAAGTAACAGTCTTTAGACATCATGCAGGGGACTCACATATTCCAGGACTGTGTCTGCACAGCAAACTACAGGGTCAAAGTACAGTCAGTGTCAATTAATGAACTGGTCATATTCCTTATGAGGCTGCTTACAATTTTTTGAAACATTTTAAGAGTGGAGAAAGTATTTTGTTTTAAAGGTATTGCTGTTTTCTTTTGTTTAACTTGTAAGCATTATGATCACTGTTGTTACTATTACTGTTTATTTTTAAAGTAAAGATATGTACTTCTACCTGATAAACCTTTGTTTCTCCAATATGCTTAAATCACGAATGCATATGACAAGCCAGAAGTGTAACTGATACTTATAGATTTTCCAGGAAATTGAAATAATCTGTAGTTAGCCTTATGACAGGCTGTAAAGGCAGCCACATAAAACAGCAGCCTTGTGGATGCAAATACGTCCTCATAAGCGTCGCAACTGCATTCAGTCCAGCAGTGGATCTATCTATAACTATGTAGGCAGAGTAGTATACTGTCTATACTGAGAATAAATATATTATTTCTCTCTCTGTATATAGACATAGTGTGTGTGTGTAATGTCATGACATTTAAATTGGAAACTGTTTTAACTGAAAGACTGTAATTTTTAGTGTAACTTTGGTGATTTGGCAGGTGTAAATATGAAATGATTTTTTCTGTAAAATAACATGCCATTACTTAACCTTATTTTCACTTAAATTTGCAG
Seq C2 exon
CATATCAGCTGAAGAAGTGCCAGCCTCCACCAATAGTTCCTCATGCAGATTTGTTTACAGAAGATGATGACTTTGGAATAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000016341:ENSGALT00000036950:37
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=PD(44.2=92.0)
A:
NA
C2:
PF0008415=Sushi=PU(36.2=75.0)
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:
TGACCATAATTCACCTCAGCTGG
R:
TCCAAAGTCATCATCTTCTGTAAACA
Band lengths:
214-1743
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]