DreINT0116947 @ danRer10
Intron Retention
Gene
ENSDARG00000076542 | pogzb
Description
pogo transposable element with ZNF domain b [Source:ZFIN;Acc:ZDB-GENE-100609-3]
Coordinates
chr16:38179880-38180480:+
Coord C1 exon
chr16:38179880-38180020
Coord A exon
chr16:38180021-38180429
Coord C2 exon
chr16:38180430-38180480
Length
409 bp
Sequences
Splice sites
5' ss Seq
CAAGTAAGT
5' ss Score
10.08
3' ss Seq
ATTTATTTTTTTAATTTCAGCAA
3' ss Score
7.3
Exon sequences
Seq C1 exon
GGCTCAACTGGGCAGACATAAGTGTGTGGAGTGCACTTTTGACATTCCAGACTTTGTGAATCACTACCCCACTTATGTTCACTGTTCACTCTGCTTCTATAGCACGTGCTGTTCTCGTGCTTATGCAAATCACATGATCAA
Seq A exon
GTAAGTTGAGTCAAACATATATTTTCACATAAATTTTATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATAAAATTTATGTGAAATTATATGGCAAAGTGATGTAAAGCTTTAAGCATCAAAATTGGTACTTTGTATCGGTTGATCACCATGACAAGAAATCAGTACTTGGTGTTGCCTGTAAAAATCCTGATCGGAGCGGCTCAAATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATACAGAAGAATATATATGTACAGAAGAAAACAGTTTCATTGGAAATTGCAGCTTGAAGTTTAGTCACATATTGCAATTTATTTTTTTAATTTCAG
Seq C2 exon
CAATCATGTTCCTGGAAGGGCTCCAAAACCTTCTAAAAAGGGGCCTCCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000076542:ENSDART00000132087:16
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=0.500
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGCTCAACTGGGCAGACATAA
R:
CTTGGAGGCCCCTTTTTAGAAG
Band lengths:
192-601
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]