GgaINT0136546 @ galGal3
Intron Retention
Gene
ENSGALG00000002602 | CSMD2
Description
NA
Coordinates
chr23:5164244-5166471:+
Coord C1 exon
chr23:5164244-5164361
Coord A exon
chr23:5164362-5166291
Coord C2 exon
chr23:5166292-5166471
Length
1930 bp
Sequences
Splice sites
5' ss Seq
TCCGTAAGT
5' ss Score
10.27
3' ss Seq
TCTGGTTTTGTGCTTTTCAGCTC
3' ss Score
9.38
Exon sequences
Seq C1 exon
AAACAGGTGGGAAGCATGATTTTCTTCAAGTGCCAGAAGGGCTACCTGCTGCAGGGCTCCACCACCAGGACCTGCCTGCCCAACCTGACGTGGAGCGGCGTGCAGCCCGACTGCGTCC
Seq A exon
GTAAGTGCTGGGAGCTGCGGGCACAGTGGTCATTGCTGGCACACTCAGTCATTGCTGCAGATGGCCGTGTGAATTGCTGGCTCTGAAGAGCTGGTAATTTTTTGGGAGAGCTGGAAAAAAACACAGTCTTGAAGAAGAAGGGAGACGGCGCTGTCATCTCTCTGCTGACGTGGTTATGCCAGCAGCCACTTCTGCTTTCAGATGAGATTTTTTCTTAGCTTGTCCCTTCCTCAGAGACGTGGTTTGAGGTGAGACTTCGCTTTGTGCTTCTGAAACCACATCTGATGGCAGAGATGTGAGCTGGTGCTCCAGGCGCTGCAGTTAACACTGAGCCAGAAGGGCTCTCCGGCAGAGCCATGTTCTCCCTGCCTTTAATAACGTGTTGCTCTTCCTTTTAAGCTGTCCATCATCTCTTTCCCACTATACCAGAAGGAATTTGAGCTAATGTACTTAAGCTGTAATATCCACAGTGGCCTCTGTATCATAAGCATTACAAAGCTTCTCCCTCTCCCTTGTGAGGTGGGGTAGTGGTGAGATAGTGTGCAGTGAACAAACCCCAGAGGTGCACCTGAGAGCAGCCAGGGGGGCTTTAAAACTTCTGAGCAGTGCTATTGGGGAGAGGGGCCGTGGTGCTGGGAGGCAGCTGCCCTTCCCCACCACTCCCTGCAGTGAAGGGAGTGTGACCCTAGAGTTACCAGCTCCTCTTTGCTGGATTGAAGATGGCAGGGTTGCACAACAGCTGTGAGTGTGAATGGGATTTTGCTTTTGGTGTGAGGTGCACTGAAACAGAAGGTGTTTTGTACATCTCGTGCTGCTGAGTTGTTGCCTCCTATACCTGCAGCATGGAGCTGGATGTGGTCCCTGCTGACACAGTGTGGGGTTCTGGGATGCAGCGCTATGGCTGTGTGAGCTCCATCATTCTCTGAGCCTTCCTGGGTTTTATTTTTCATCTTCTGTAAAATGAGGATGAAGATAATACCTCATGAAGGCTGCCGAGGATTTGTTTTCATTCATGAGCACTTTGAGAGCTACAGAAAGGGGAAATTTACAGCGTGGGTGCGGGCGAGCTTCCTGGCCCCTGATTGATGAGCCCTGGGCCATAACTTCTGGGGAGCAGTGGTGACACATTGCCAGCAGCACAGCCAGGCGCTCTCTGGTGGCAGCAGCTGGACGAGCTCAGCCCGGATCCCTGTGGCCAAATCCTGGAACTGAGCAGTGATAGGAATTTATGGTTATTGCACACTCCTGAGGACTTGCTTTGTAATGCTGTGGATAGATAGGTGCAAATTAGCAGTAGGACAGAGGTCCTATGACGTAAGGCTGTACAAAAGCAGACCTGTGGGGCACCCACTCGCTGGCTTAGCTTGCTGGGCCTCCATGTCCTGCAGAGGTGCATTTTGTCCATGAAAGTTAAAAGAGAGGAGGAAGGCAGCTGCTCAGTTTCTTTTCCTGGCCCTGCAGCTGCAAAGGAAGGCATCACAAACACTCCCATCCCTGCTGGGTTGCAGCAGTGGCAATCTGATCACAGGCTCAAACTCCTGCTCAGCTCTGGGAGGGTGAACAGAGCTTCCTCATCCTCCGTGTGTCAGGCACGAGGTCCTCAGCATCATTGGGTTTTGGCTTCCTTTCCAGGAAAGGGGAGGGATAATGGAGCCTGATGTTGAGTTCATGGAGGCTGGAACTGAGTGAAGGATCCCCTGAGAGCTTCAGATAGGAAGAGCAATCTGGCAGCAAAGCATGGGAAATGGTCTCATTAATTCCTCTGGCTGGTAAAAATCCAGGCATGGCACTGTGTCCCTCAGTGAGCAGAGAAAGCGTTGGCTGAAGAACTCTCTTCTGAGAGCTCTGTCTCCCGGCTGACATCGCTGGTGACTCTTCTGCCTTTCTGTGACTGCCTGCTGTATCACATCTCTGGTTTTGTGCTTTTCAG
Seq C2 exon
CTCACCACTGTAAGCAGCCTGAGACCCCCTCCCACGCCAACGTCGGCGCTCTGGATTTGCCATCTCTGGGCTACACCTTGATCTATTCCTGTCAGAGTGGGTACTACCTCACCGGGGGGTCTGAGCATCGGACCTGCAAAGCAGATGGCAGCTGGACGGGGAAGCCTCCCATCTGCCTCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000002602:ENSGALT00000033174:68
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=0.049
Domain overlap (PFAM):
C1:
PF0008415=Sushi=PD(64.9=92.5)
A:
NA
C2:
PF0008415=Sushi=WD(100=91.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Mouse
(mm9)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACAGGTGGGAAGCATGATTTTCT
R:
GAGGCAGATGGGAGGCTTCC
Band lengths:
295-2225
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]