GgaINT0002804 @ galGal3
Intron Retention
Gene
ENSGALG00000013286 | KDM2A
Description
NA
Coordinates
chrUn_random:27616110-27617979:-
Coord C1 exon
chrUn_random:27617267-27617979
Coord A exon
chrUn_random:27616274-27617266
Coord C2 exon
chrUn_random:27616110-27616273
Length
993 bp
Sequences
Splice sites
5' ss Seq
GTGGTGAGT
5' ss Score
8.95
3' ss Seq
ACCCTTGTCCTTGTCTCCAGGTG
3' ss Score
12.25
Exon sequences
Seq C1 exon
AAGCGCAAGGTAGAAGAGAGCGATGATGACATGGCACAAGCCAAGGTGCTGCGACCCCTGCGGAGCTGTGAGGAGCCCCTGACCCCGCCACCCAACTCGCCCACCCCCATGCTACAGCTGATCCACGACCCGGTGTCACCGCGAGGTGTGGTAACACGCTCGTCCCCAGGCGCCGGTCCCAGCGAGCACCACAGTGCCAGCAGGGATGAGCGATTCAAGCGGCGCCAGCTTCTGCGGCTCCAGGCCACGGAGCGAACCATTGTGAGGGAGAAAGAGAACAACCCCAGTGGCAAGAAGGAGCTGTCAGAGGTGGAGAAGGCCAAGCTGCATGGCTCCTACCTCACCGTGACGCTCCAGCGCCCCACCAAAGATGTCCATGGCACTTCCATTGTCCCCAAGCTGCAAGCCATCACCGCCTCCTCTGCCAACTTGCAGCACTCTCCCCGCGTGGTGATGCGCCACACGCCTGCCCGGATGCACCCGCGGGGTGGGGGGGAGGACGAGGTGGCCGCTGAGGAGGACGAGGAGGACGAGGATGAAGATGATGAGAACATGGAGGAGGGGGGGGCTGCCCGCCTCAATGGCAGAGGGGGCCGGGTGCAGGAGGGTGAGGAGAGCTGGATGCAGCGCGAGGTGTGGATGTCTGTCTTCCGCTACCTCACCCGCAGGGAGCTCTGCGAGTGCATGCGGGTGTGCAAGACCTGGTACAAGTG
Seq A exon
GTGAGTATGGGAACAGGCAGTGCTGCCAGGACCATTTGTGTCGTGATCCACGGAGCCTGGGGCCTGATGGGCAGCCAAGAGGGGAAGGGGCACAGGATCATTTACCCCCTAACCTATCAGTGCCTTCCTCCCCTCCCCAGCACAGGCATTTGCCAGGCAGCATCACCCCACTGCCTCTTCTGTCCCATCTTCAGTCTGCGCTTGACTGTCCCCTCTGCTGGGAGATGGTCACACGGTGTAACTTGCATCCCACACACCACGTTGCTGTGAGGTGCTGGTGCCCTTTCCTTACCCACTGCCCTGTGCAGCCCTTGCCCTTCCTGGCCCCACAGCACGGGTTGAGTGGGGATGGGTTTGCTGCCTGGGAATGCCTCAGGGGGCTCTGGCTGAAGACAATGCTGGCAGCGGGACAGCTGTGGATGGAGAACTGGGAACAGACAAGGATGGGGAACTGGGAGGTTTCTAGCTGCCTAGCAGCGGGAATGGCACAGCAGGGAAGGGCTGGCACGCTTTGATCAGCAGGCGTTGGGCTTGGCAGGCTGTAGGGGACCCTGGCATGGCTGCTCTGGGGGCGGGGCAGCGTTGGGTCCGGCTCCTGCGGCAGAGGAGGGATTCACGCCACCTCCAGGCTGCACAGCAGCTCCTGGTGATGCAGGGAGCACTGCTATGGCTGTGGGATGGGACTAGGTGGAGCATTTTGCCCACTGGGAGCAGGGATGCTGAAAATCTTTGCTGTATCTGGGGAGCAAGCAGGCTGGCAGTTGCTATGCAGTTCTGTTACATGGCAGTAAAACTCTGCTAGGGCTGTTCTGCGTATCCTGCATGGCCAGGCACCCCCAGCGTCCTCCCATGTCAGGGAAACCCCAGCCAACTTGGAGGAGTGGCTTTGTTCTATGGCTGGAGCTGTGCCAGTGCTGGGGTCCTCCCAGAACGACTGCCTCTTGTCCCATGACACCCTCAGCACTCAGCTTTCACCCTTGTCCTTGTCTCCAG
Seq C2 exon
GTGCTGTGACAAGAGATTGTGGACAAAAATAGATTTGAGCAGGTGCAAGTCCATCACCCCCCAGGCACTGAGCGGTATCATCAAAAGACAGCCTATCAGCCTTGACCTCAGCTGGACCAACATCTCCAAAAAGCAGCTCACATGGCTTGTCAACAGACTGCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000013286:ENSGALT00000021696:16
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.845 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0064628=F-box=PU(71.7=13.9)
A:
NA
C2:
PF0064628=F-box=PD(26.1=21.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GACGAGGAGGACGAGGATGAA
R:
ACAAGCCATGTGAGCTGCTTT
Band lengths:
344-1337
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]