GgaINT0136491 @ galGal3
Intron Retention
Gene
ENSGALG00000002602 | CSMD2
Description
NA
Coordinates
chr23:5040146-5041517:+
Coord C1 exon
chr23:5040146-5040233
Coord A exon
chr23:5040234-5041392
Coord C2 exon
chr23:5041393-5041517
Length
1159 bp
Sequences
Splice sites
5' ss Seq
TAGGTAAGA
5' ss Score
9.14
3' ss Seq
CCCTTTGTTCTGTCTGCTAGGTT
3' ss Score
11.83
Exon sequences
Seq C1 exon
TAACTCAGGTTGGTGTGTCCCAGGGACATAATATGTGTCCAGACCCTGGGATTCCAGAGAGAGGCAAAAGAATAGGCAACGATTTTAG
Seq A exon
GTAAGAACCTTTGATGTGTGTGTTTATGCATGCTGCAAAGCTTTTGTTACAACCATTGTGTGTACTCCTTGGCATTACAGAGTCTGTTTGTAGAGCCCCTCTGCACACATCTCAATGTGCCGTGTCTGAAAAGCTTGCTGAAGCCAGTGATGCAGAAGAACGAGCGTGTCTAAACGTGCATGTGTGTGTGCAATCTACTACAGAGATCTGTAATGATCTCTCTTTGAGAACGTTTCTCTTGCCACAAAGTGGGCGCCTGGCCACGCTGCTGCAATCCCTATTTGTCGTCACTCCCTTCTCCAGTTAAGCACAGAAAGAGTCCTCTCAAACAGCATCACTTCTAAATTAGCTCAAGTCCCAGCACAACCCTGTGCCCAGAGAATTTCGGGTGACTTCCTGAAGCAGTGGTACAGTTCCTTGTCAATAAGTAAATGTGGTGCTGGATAATTGTTTTCTTATAAAGCTTAAAATAATGGTGTTATTCCCTTGTAGTTGCTAGCGTTCATTTAAAGCGTGTTGGAATGAATCAGCCTGTTGTTAGCAATGGTGAATCAATATTTAATCTTATTTTGCTGTCAATAGCTGTTTTGTTCACTAAAAATGTCTTTCAATTTAACCTGCGTCTATCAGACTCTCCTGGAATCCAGAGAACGTATTGGAGGAGAGGGAACGAGGGTTAGGGAAGGGTATTCCCAATAGAGTCCCTAAATGCCATAGGATAAATTCTCAGCTGCTGTGAATCTGGCATTGTGTCGCCTCGGTGAATAAGACAGCACTGCTTTAAGCAGCAAAGGATCCGAATCCAAAGCGACAGAACAAAGAACAAATCTTTCAGTAGTAGATAAAGATTTTGTTCTTTATAAGAACGCTGAGCACTGTCATCTCCTGGGACTGAGTGTGAGCTCCGAACTGAACAAAACTCCCACTGAAGTTGCATTGAAAGACTCAAATCTGTTCTTGGACTCTCACCACCTCAGGCAACCGGCGCCCAGCTCAAGGAAATGAATGAGGAAGAGCTGGCCCCTCATTCATTTCCACTGTTGCCTGGAGGGCCGGTGATCTCTCTCTGTTCACAATTTGGATAGTAAAAAGCAAGAGACAAAGCTGTTGCTGCAGAAGCGCCTCAGTCGCTGACTTCCCCCTTTGTTCTGTCTGCTAG
Seq C2 exon
GTTAGGCTCCAGCATCCAGTTCACCTGCAACGAGGGCTACGATTTGCAGGGGTCCAAAAGCATCACCTGTAAGAGAGTGAGCGACATCATTGTTGCCTGGAGCGACCACAGGCCAGTGTGCAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000002602:ENSGALT00000033174:13
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.411 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0008415=Sushi=PU(29.3=56.7)
A:
NA
C2:
PF0008415=Sushi=PD(69.0=93.0)
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:
AACTCAGGTTGGTGTGTCCCA
R:
CTCTGCACACTGGCCTGTG
Band lengths:
212-1371
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]