GgaINT0006048 @ galGal3
Intron Retention
Gene
ENSGALG00000004225 | KDM2B
Description
NA
Coordinates
chr15:5529942-5530818:-
Coord C1 exon
chr15:5530732-5530818
Coord A exon
chr15:5530212-5530731
Coord C2 exon
chr15:5529942-5530211
Length
520 bp
Sequences
Splice sites
5' ss Seq
AAAGTGAGT
5' ss Score
8.4
3' ss Seq
TTGTGTTTTGTGTCTCTTTGGCG
3' ss Score
1.27
Exon sequences
Seq C1 exon
GTGAAGGAATCAGATGGTGTGGTTAATGACGAGCTGCCGAACTGCTGGGAGTGTCCAAAGTGCAACCATGCAGGGAAAACTGGAAAA
Seq A exon
GTGAGTTTAATGGGGATAAGTGGTGCTGGAATGAAATACAAGATCTCAAACGTTCCCTCTGGCTTGTAGGTATAATTTTGCCCAGTACCGCTTTTGTTTTTGTGTTCAATTCAGTCGAGTCGAAGGAAATAAGCTGTTGGCTTTCTGTTCCCTAATCATCTTTTTATTTTTCTTCTGTGCACTAACACCAAAATCTGGAGAGTGTTTAGGTTAGTTCTGTGCAGTGCTGCATGCTAAACTCTAAGATACTTCTTTGGATTGTGTAAAAGGGAAAGAAAAAAAGTCATGCGAAACCTGAAGTGTCTATTGGAATTAGGGAAGCTTTTGTTTTCTTTTGTAAAGCGAGAGGCTGCAAGTGTGCATAAAAACTTCTTAAAGGTTGAAACTGCTTCCACTGTAACTCCTTGTTAATGATTTTGTCTGTTACAAAGTGATCAACCCGCCAGTGCTGGAGGCAACGTACATAAGTAGCTGAGAAAGGCATAAGATATAAAGTTTGTTTGTGTTTTGTGTCTCTTTG
Seq C2 exon
GCGTACAAGCAAAAGCGCGGACCAGGATTCAAATACGCATCAAATCTCCCAGGCTCATTGCTGAAGGAACAGAAAATGAACAGAGACAATAAGGAAGTAACAGATGCTGCAAAACGGAAAGGGGACTGTGAAGAAACTCCCAGGCGGAAATCTGAGGAACATTCCAAAAAGCCTCAAGTTGACTCAATTCTGAGGAGAAAGTCAGACGAAGTACATCTGCGGAGGAAAAGGAAATTTGAGAAACCCCAGGAACCCTCTATGAGAAAACGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000004225:ENSGALT00000006725:15
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=0.933
Domain overlap (PFAM):
C1:
PF0062824=PHD=PD(35.4=79.3),PF0030115=Rubredoxin=PD(60.0=93.1)
A:
NA
C2:
NO
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:
GTGAAGGAATCAGATGGTGTGGT
R:
AGGGTTCCTGGGGTTTCTCAA
Band lengths:
343-863
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]