GgaINT1015984 @ galGal4
Intron Retention
Gene
ENSGALG00000013286 | KDM2A
Description
lysine (K)-specific demethylase 2A [Source:HGNC Symbol;Acc:HGNC:13606]
Coordinates
JH376180.1:97052-98921:+
Coord C1 exon
JH376180.1:97052-97764
Coord A exon
JH376180.1:97765-98757
Coord C2 exon
JH376180.1:98758-98921
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
Human
(hg38)
No conservation detected
Human
(hg19)
No conservation detected
Mouse
(mm10)
No conservation detected
Mouse
(mm9)
No conservation detected
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
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]