GgaINT0136504 @ galGal3
Intron Retention
Gene
ENSGALG00000002602 | CSMD2
Description
NA
Coordinates
chr23:5082191-5085951:+
Coord C1 exon
chr23:5082191-5082379
Coord A exon
chr23:5082380-5085781
Coord C2 exon
chr23:5085782-5085951
Length
3402 bp
Sequences
Splice sites
5' ss Seq
TTGGTAGGT
5' ss Score
7.03
3' ss Seq
GGTTCTGTGTCTTTCTGTAGCTG
3' ss Score
8.63
Exon sequences
Seq C1 exon
AATACGACCTGGAGCCCTGCGATGAGCCAGAGGTCCCAGCCTACAGCATCAGGAAGGGGCTGCAGTTCGGCGTGGGCGACGTCCTCACCTTCTCCTGCTTCCCCGGGTACCGCCTGGAGGGCACGGCGCGCATCACCTGCCTCGGGGGGAGACGGCGTGTGTGGAGTTCGCCTCTGCCAAGGTGTGTTG
Seq A exon
GTAGGTGGTCATGTGCTTTCATTTTGCTTGGCTGGTTGCAGTGTGCTGGAGCGGTTAGCGGGGCTGGGAGGTGCGTGGTGTTATCCCAGGGGCACCTCCGGGCTGGGCGGTGCGGGGAGGGAGCTGGGATGAGCTTCAGCCCTGTGACTGTACGTGGGGAAGGGGAGGGATGGGCAGAAGGGCTGCAGCCCCCTCTCGGGTTGGGACACACGGTGTGTGGTGGTTTGGGGTCCCGAGAAGCGCCGTGTTGTGGCCCAGTGAGTGAGTCCCAACCTGGGGCAGCTCCAGCAGCCCTTTAGGGACAGGTTGTGTAAAGCAGAGTGGTTTTAGGGCCAGCCTCCCTTTGAATCAGAGTGCTGTAAAACGTAATAGGCTGAAGATGAAGGCTGCTTCGGGGGGAGTGCTCCTAAGGAGCACAGACTGCACCTCAGTGTGGTTGTCTCTTCCACCTTCAATTTCTCCTCCTCCAACCACTGCAAGTTCTTTTTTGCAGTTATTCATACTAATAAATAAACATGGGGGGAGAGGGGAGGAGAGGAGAGGAGGTCACCTGCAGCACCGAGCCAATTGCTGGCTGTCATCCCTAATGCAGAGGGGCTGCGGGTGACCTGGTGAGCTGCTCACAGTGCCCTCTGAGCACAGCAGCACAGGAGCACCCGTGTAACAGCAATAAAGCAAGGAGGGAAGGATTGCCAACGCCTCAGGGCTTTGCAGAAGGAAGGTTTAACATATTTCTGGGTTTGTTGTACAGTGTGGTAAGTAGGAAAATATTCAGTGCTCTGCTGCTGCTGCCTGGGTCACCCAGAGCAGCGTGGGGATGAGACAAACCACATTCATACCTGGTATCACTCCAGCAAAGCCTGCTAGGTGGATGTTCCTCATCTGTGGCCCTTGAGGGATGTTACAAAGAAGGTGTCCCAGCAAGAGCCGGTCTGCTTTCGCAGTCTGTTGAGCTTTGCTGTTGAGCCCTGTCACGCTGAATGCGTTTCCCAGCACTGTTTAATGCCTGGGTCACAGGGCTGCATCATCCTGCTGTGACAAGCAGCCTCTTCAGGGCATGAATAATAATCAGGTTGCAGAGAAAGCTCATCAGGGGAATAGAAATCAAAAAGCATCATAACACGGCTTTAAATGTGGTTTTCAGGCATCCCCAAATGGACACAGGAGTTCGGTGTGCCCAGCTCCCCGCGGTAGCTGGCTCAGAGTCAGCGTGCTGCTTTGTGGTGATGGATCGGGTCGCCTGTCTGGTGATCTGTGCACAGCTCTGGTGGCAGCTTTTTCCAGGCTGTGTGAGGGGACAGCTGCAAACTGGAGCCCTCCTTCCTAAGGCCCACTAAGAGGTCTGTTTTAGCTGGCAGCCCAGGCACATCGTATTCAGTTCCTGTTCGAGGGATGGATCTGGATGAAGACAGGAGCAGCTCATCCCTTCGTCCTGCCCCTCTCTCAGGTGGCCATGCTCCGTGCTGACCCCTGCAGCAGACCAGGTCCTGCACGGCGACATCCCCAGCATCAGCCCCAATATCAGTGCTGCAGGGAACGCTGTCCTCCAGGGAAGAGGGGAGGAGAAAGTCACCTCCCAACCGCTTCCTCTCGCTATGTCTGCTGCTGCTTCCTTACATTACTTTCCTGCTTGACTGGGAGGAGCAGCAGAGGTGGGAGAGGTGATGCACAGAGCTGCACATGCACTGCTGTGGTTTCCTGCAGTCCCAGCAGCGCTGTGTGCTGTGTGAACAGCTGGGCCACCAGAAAGCTGCTCTCAGGGTGGGTTGGAGCACTTCTCCCCAGCTGTGCATGCAGAATGGCCGGGCTCAGAGGAGCAGGGAGAAGTGTGTTACAGCTGAAAATCTATCAGGGTGAATAGGCCGAGAGAATGAAGGCTCGTGGTTTGCTCATGTAGGAGCTCATCAGGGAGTAATGAGAAATCCTAAGCCCGGGGTGGCTGCAAAGCACATTGACACATTTTGAGGGGCTGCATGTAAACAGCGGGTGGGCTGTAGTGCTCTGAGCTGCAGTCAGGAGCATGGGCAGGACTGGGGCTGCTGGCAATGGGTGTCCTTGCAGGGGAGCATCCCTGCCATGCTGCTCTGCAAGCAGCTCCTTGAGCTGTACCATGAGAGCTGTGAACTTTGCCTCCTCCCTCTGCTGCCAGCAGGTAAGAGCAGTTCTCATGTTGCTCCGTGGGCTCTGGGATTGCTCAGTGCTATCACAGTGGTGCTGCTGTCTGTCCTCAGGGGCACTGGGATGTCTGTTGGCTGCATTGTGTGGGGCAGACATGTTCATAGCAGTCCTGTTCTACACACTGTGGCATGTTCATATGGGAGAGAGAGAGAGAGAGCATCCTTAAAAGCCTGCAATTACAATACATAAAGCAGAGAGGTGAATGTTGGTGTGTGGGGTTCCCACATCAGCATCTCCTCGTCTGCCTCCAACCCTTTGTCTTTCAAACAAGAAAGGTCAGTGGTGTCTGTGCTGCAGCCCCTGTGGGGCACAGAGGACACATTGGGAGGAAGCAGATGTATGCAAATCAGAGCCACTTTCTGAGACTGGGGGCCAAAAGGATTTCTGGTTTTCTCTCTTTTTCTAATGGGAGTGGATGTAATTGGCAGCTGCAGAGCTGGGAGGGATGAGAGGTCCTTCAAAATACTGTCAGATGGGGAACTGAAGGGCCGAGGTCAGAATTAACAGCCGATGAGAGAAACATCACTGCTTTCCCTCTTAGGTTTCACGAGGTTATTTTGGGGAAGATTTTCAAGTCCACGTATAGCTTTGTGATGTGTGATGATATCAGAGTGTCACTGAGCACAGCTTTCTGCACAGAGACCTGCATGGAACAGCGTGCCAGCAGCCCACGGTGTGCTACGTTGGCTGTTAATAGAAAGCCATTGCAGTGCTCAATACATTGCAAATATAAGACTCACAGAGATACAGGATGAGCTTTGCCTCAACAACGTGGCAAAAGATGTTAAATATTTCAGTTTAATTATGTATGTTTTTAATCTCCTTCCAGTTCAGAGAGCTGGGAGGGACGTAACCACATGCACTGCTTCGAGCAGGTGGTGATACCCCATGGATTTTGGACTGCCTTTCTAAATTAGGATCCAGGATAGCATTGGAATACACCAGCGTTGTGTGACTCAGGTTCCCTGTCCACGCAGCGAGAGGATATCAACTGCTTCTGTAAAGCACCTGAGGTTTAATGGTGATAGAAGCATTAGTAAGAGCTGGAACTGAGGGGGGGTTGGCTTTGATTAGCAGCACTTGGAAGTAAAGCTCATGGCTGTGGTAGCAGATGGGTGCAGGAAGGAGTGAGCATCTGTGGCCATTGGAAGGAATCACCTGCATGTGCTGTACGGCTCCAATACGCACGTGGGTGTTAAAAGGTGGTTCTGTGTCTTTCTGTAG
Seq C2 exon
CTGAATGTGGTTCGTCTGTAACTGGAACTCAGGGTGTTCTGCTGTCCCCCAACTACCCAATAAACTACAACAACAACCACGAGTGCATCTACTCCATCCAGACACAGCCAGGGAAGGGGATCCAGCTGAAAGCCAGGACTTTTGAACTGGAAGCAGGAGATGTCCTCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000002602:ENSGALT00000033174:26
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:
PF0008415=Sushi=WD(100=87.5)
A:
NA
C2:
PF0043115=CUB=PU(50.9=94.7)
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:
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]