DreINT0085312 @ danRer10
Intron Retention
Gene
ENSDARG00000078133 | kdm2ab
Description
lysine (K)-specific demethylase 2Ab [Source:ZFIN;Acc:ZDB-GENE-101007-5]
Coordinates
chr14:21474662-21475730:+
Coord C1 exon
chr14:21474662-21474694
Coord A exon
chr14:21474695-21474864
Coord C2 exon
chr14:21474865-21475730
Length
170 bp
Sequences
Splice sites
5' ss Seq
TCGGTGAGT
5' ss Score
11.11
3' ss Seq
CTGTCTCTCTTTCCCCAAAGCTC
3' ss Score
10.18
Exon sequences
Seq C1 exon
ATCAAATTGGAAAGAAACAAAATCCTCCAGTCG
Seq A exon
GTGAGTGTTATGAGCTTAAAGCATCTGCTTCCCATCATCGCAGCGCATCCATAATCCTGCTCTTACCATTCTCACATGTTTTCTCTGTCATTCTTGGCTTCTGCTTTTTTTCGTTCCTTCTGTTTCTGTCCATCTCTCAGACCCGTTCGCCTGTCTCTCTTTCCCCAAAG
Seq C2 exon
CTCCTGCGTCAGCGGAGTCTGGAGAGGAGGGGTTTAATCAGAGCAGGACCTGGACAAAGCCTTTCCCGCGGCCGAGGGTCATCCTCCTTCCGTGGCCGAGGGTTAAGAGTGCGAGGCGGCGGAAGGGGTGGAGGTCTAAGAGAAAGAATGGAGATGGTGGTAGAAAGAGAGGATTCTGCAGAAGAAGAACAGCAGGAAAGGAAAGAGAACGGACAGTATAATGGGAAAGAGAATCGCCCTCAGAGGCTAAGTGGAAAAGCGGGAGAAGATGAGAATGGCGACGCTCATCGAAATGGAGAGAGCGAGGAAAGCAGTGAGGGAGGAGAGCCCACTCTGTCTGACACTTCTGTAGCACTTACCGATGATGTCAGAGGCCAGGAGTCTTGCGTCACGGTCAAGTTACAACCATCAAGAGCTAAACGAGATCCTAGCACCATCGTTCCCAAATTGGAAGCCAACTTGTCTTCAAGAAGCCTTCCGCCAAACCACAAAGCCCTCCTCCGCCCCCCGCTCCGAAACGGTGCCCGTTGTTCAGACGCTCCTCATTCTCCTGGGGACAGATTGCACGTAAACAAATCACATGCTCTTTCATCATCGTCACACACCCTCACGAGGCGCGCATCCAAAAACTCAAATCTGAGATCAAACTTTGAAGATTCCACTCACCGCCTGACTCGAGAGAGAATCCAGAAAAATGCTCGATCGGAAAGAGCCAAGTCCTCCGACTCCTGTCCCAGTTCCACCTTCCACTCTGGAGGAGGGAATGAGCCAGGCTGGGAGAAAGAGGTGTGGGTGTCCGTGTTCCGCTATTTGACTCGTGCAGAGCTCTGCGTTTGCATGGCTGTTTGTAAAAGTTGGTACAAATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000078133:ENSDART00000111839:18
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=0.855
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF129372=F-box-like=PU(66.7=9.7)
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
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGAAAGAAACAAAATCCTCCAGTCG
R:
ACTGTCCGTTCTCTTTCCTTTCC
Band lengths:
242-412
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]