GgaINT0136518 @ galGal3
Intron Retention
Gene
ENSGALG00000002602 | CSMD2
Description
NA
Coordinates
chr23:5112099-5115807:+
Coord C1 exon
chr23:5112099-5112223
Coord A exon
chr23:5112224-5115710
Coord C2 exon
chr23:5115711-5115807
Length
3487 bp
Sequences
Splice sites
5' ss Seq
CAGGTACTG
5' ss Score
9.04
3' ss Seq
CCCTTTCGTTATTACTTTAGATA
3' ss Score
8.2
Exon sequences
Seq C1 exon
TGCCATGTGGTGGAAATCTGACCGAGCGCAAAGGCACCATCCTCTCCCCTGGCTTCCCAGAGCCGTACCTGAATAGCCTCAACTGTGTGTGGAAGATATCAGTCCCCGAGGGAGCAGGAATCCAG
Seq A exon
GTACTGAGTTAGCAGCACAATACAGAAAGGAGAAAACACAGCATCTAGTGCACTTAGAGGCTTTGTGTTAGGAAGCTGAGATGGGTTGAATGTGTAATTCTCTGGAATCAGACATTCATTTACACTGCAGCTGCCATAAGTGGGTAATATTCCCATGGATTTTTGCCTCCTGGAGGCACTCTCCATGGGAAATAGTTGGAACCATGTGGCTGTTTTGCTGTAACAGAATAATTGTGATATTTTGGGCAAATACCTTTATACCCCTTGATTATGCAGCCTTGAAAGCATTGTAAGCTGTACCAAGGAAGAGCAGCTTGCTCAGAGAGCCGGTGCAGCTTTGTTCTGCCAGCAGAGTTACAGCAGTATGATTATACAATTAGAGCTTTGCTGTTCATTGTCTCCAGGTAAATGGGCTCTCCAGGTTTTGTGTGGTCCTTATCGTTTCTCTGCAGAAAGAGTCCTGCCTGCTAGAGGATGGTGAGAATTAAGCCCAACATTAGAGACCAAAGTTTAGATTATGTTCCCATTCAGCACATGTGCACTTCACCCTACAGAAAGTATCTCATCATGCATTACACTGGCATCAGTTGATGCAGAGAAGATGGATTCTTTAATAGGTTCATTCTTCTCATTAACAGAGGGTTTCTGTCTTCTTTTCACCTCTTTGTCAGTGAGGGTTTTGTTCCCGAAGTGCTTTTATTTCTCTATCATGGTTGGCCAAAAGTCTTGCACGTGGATTCCTCCTTCTCTGCCATATTGTGCTTCTCTCACCAGTTATACTGAGACGTCAGGTCTGTGCAGTTGGATTACAGTTCTGTTTTTCTGCAGGGATAGTCTTACGTGATGTCACCAGTGTAACTCAGAGCTGAAGCGAGGGCTGGGGAGCGTGATGGCCAAGCCTGGAACACCAGCTTGTGCCCTTTGCCAGGTCCAGCAAATTCCCATTTTCTATCATCTGTTTTTGAAGCCATTTAACCTAGTGTTTTCAAAAGCCTCAGCGCTTATTGTCAATTTCTTTCTGTTCATCTGAAATTTTAACCATGCTCCAAACCCCTAAATGGCAGGGGGATCCATTTAGCTCAGCTAAACATCTCAGCAGTTGAGGCCGTTTGCAAGTTGCGCGGGACTCCTGGGATCAGGAGGTGATAATTCACTTAATTTTTAAAGTGATGTAAATAAATGTCTGTATTTTGCACTGCTGTGTTCTGAATGCAGACTCTTGCTGCCAGTTTCTCAGCCCGTGGAGCTGTTTTTGTGTACATCTGCTGAGCTTAGAGGAGAGCAGCTATTACAGCAGGCTGCTAAAAGCATTTGTTTCTCACCTCTTTTGCTGTGCAAATGCAGCTATTGCATGTAGAAGTAGAAAATGTAACGTCAAAGAAGTGTTTTAAAGGATTCTTCCTTCCTGCTACATACAATATTTTGTGAGAGAAGTAGATGTTTGGGGATCTAACACAGAGTGTAAGCAAATAACAATGAAAGAGTGCATCCTGCAGCTGAGTGTTACCATGTCAAACCTGAAGCTGAGTTTCCAGTTCTAGAGTGGTGTTCTAGTTCCAGTTTTAGTTCTCTATAGCCATGCAGTGTCCAAGCTCAGTCCCATCTGTGCCAGGAACACCACACCTCCCCACCCAGCTCTGCCCCTCCACATGGGCAGGATGCAGGGTGATATTTTCCCTGACAGCAAACCAGTTCTGATACTTCCAGTGGAGGTCCTTTGATGGAAGGAACCTGGCCTGCTGCAATCAGCTCGCCCTGCACGCACCACCCTGGTCACCCACTGCTGAATGCAACATGCTCTGGGTTATTAGATACTAATTTAAACATCAGTTTACCCTCATTTTGTACAACAATTAAAGGTTAAACAGCTGTAAATCAGAGGAGGAGGTGAAATTAAAGCTTTCTTAGTAGCGGCGAGTCACTAGTAGGATTTTTATGTAATCCATGTATAAGCAAGCACTTCTGCCATGAATTATTCATTCCTGTAGCAAACCTTCCTGGGTGAATTAATTTATATACATGGCAGTAAATAGATGCAGATCCCTTGTGAATCCACATGTCAGACTTGAATTAGGCCCTTAAAAATGTTTATTCCGTTAAGTTGGGGACATGGGGGTGGATAAATAATTTAAAAAATGTAAGAGCAAACAAAATGCACATTCTCAGTCCATGGCCTCTCAATAATGTTAGTCACAACAGGAATGTAATTATATGGGCTGAAAGGTATTGACGTGGTCAGTGCCATCAGTAATGGCTCTGTAGGGGTCATTGCAATTTCTGTTAGATGAACTCTTACTTTTTTTATTGAAAGAAACTTTGCTGGAACTTTTTCATCTGCTTTATTATTCAGAATAAATCAATGAGAAAAAAAGGTTAAAATGGCAGAAATCATGGGATTTGATTTTATGTATTTTGTGTTTACCAGAGCAAAAGGAAACGAGGTATTTGGAGTAGATGTGTAAGTACAGAATGAAAGGGAAGAGGAGAGTATAAGAGTGCACGTGTGAGCATGCTGTCTAGGTTTCCAGTGTGTTGAAGTCTCTTCCAAGAGTTCTGTCCAGCAAATGTGTCCTGCTGAGCTCAGTGCTTAAGGGAGTAATTCTATTGAATTCAGCAGGGCTGCTGAGATCAGAAGCATCAGGCTTAGTAGGAAATCTCCATCCAAAGAGACCTCAAAGAATGGAGGCTCTCCAGTAAGCAGATGCGTGAGGGTGGATGTAAACACACATCTACCTGCCAGAGCTGCCAAACCTTTCCCCCCAAACGCAGGAGTGGTGCTGAGCAGCAGTGCCACTGCCACGGGGATATGGAGCCTTTTGTCAGGGGCCTATTCTGTGTTCCTGGTTGTCTTTAAGAACCTCGTTTTTAGGTTGGTGGCCTAGAAAATAAGTTTGAATGTCTGAAAAATTCACCTAGAGCATGCAGATTCAAGGGGTTTTTTCCATGTAATCCTGGCTCTCTCTCACGTTTGCTGTCTTAGGCAGTTCACCAGACCAGATCTACAGCCCAGCTTATTTTTCATATTGGGTCACTGAACACTTGGACTCCCAGTACTTAGAAATAAAGGCAGAATTCATTTGAATAATAATTAAGGAAAACAAATCTACCATGCAATTACATCTCTATCATTACAAGAGCTGCTTTTCAGGGTAAATGCAGATTTATGAGATACCATGATATTACTCATTTAAGGTTTGTATTGAAGTTCTGACTCATGGAGTCAAGTGACTTGTATAAACCTTCAAACCCTACGGTGCATGGCAGAGAAAGGTGGGAAATTTGAAAATGCAACTTGAGCGATAGGATTAAAAGCTGGGAAGCAAGACAACTGCAAAGAGCTTCATTGGATTAAAAAAAATTGTGATATAATGGAGGTTTCCTTCTTCTTGTAATAGTTTCTGGGTGGCTAATGATTGCTTTCATGTGAAAATAGTGCCGAAGTCTTCAGGAATCTCTTTTTTTCCCCTCCCTTTCGTTATTACTTTAG
Seq C2 exon
ATACAGGTGATCAGTTTTGTCACTGAGCAGAACTGGGATTCCCTGGAAGTGTTTGATGGAGGAGACAACACAGCCACCATGCTGGGAAGTTTCTCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000002602:ENSGALT00000033174:40
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=PU(36.8=92.9)
A:
NA
C2:
PF0043115=CUB=FE(30.2=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]