DreINT0119324 @ danRer10
Intron Retention
Gene
ENSDARG00000005382 | prdm9
Description
PR domain containing 9 [Source:ZFIN;Acc:ZDB-GENE-040426-1319]
Coordinates
chr12:9751155-9751595:-
Coord C1 exon
chr12:9751324-9751595
Coord A exon
chr12:9751223-9751323
Coord C2 exon
chr12:9751155-9751222
Length
101 bp
Sequences
Splice sites
5' ss Seq
GTAGTAAGT
5' ss Score
8.01
3' ss Seq
TATATATTTATTTTCTCCAGATT
3' ss Score
8.56
Exon sequences
Seq C1 exon
ATTGTGAGATGTGTCAACAACACTTCATAGATCAGTGTGAGACCCATGGTCCACCTTCGTTTACATGCGACTCTCCAGCGGCTTTGGGTACACCTCAAAGAGCTCTGCTAACACTGCCACAAGGCTTGGTTATTGGTCGATCAAGCATCTCTCATGCAGGACTTGGGGTTTTCAACCAGGGCCAAACTGTTCCTCTAGGGATGCATTTTGGGCCTTTTGACGGTGAAGAGATCAGTGAGGAAAAGGCACTGGATAGTGCCAACTCTTGGGTA
Seq A exon
GTAAGTGTCTACCTTACTGTTTTTTTTTCTGTATTTGTCACAGTCCTAATTGTTATTTTAGTGTTGGATTAAATGTATATTTATATATTTATTTTCTCCAG
Seq C2 exon
ATTTGCAGAGGAAATAATCAGTATAGTTACATAGATGCAGAGAAAGACACTCACTCTAACTGGATGAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000005382:ENSDART00000027321:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.048 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGGCTTTGGGTACACCTCAAA
R:
AGAGTGAGTGTCTTTCTCTGCA
Band lengths:
251-352
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]