DreINT0116941 @ danRer10
Intron Retention
Gene
ENSDARG00000076542 | pogzb
Description
pogo transposable element with ZNF domain b [Source:ZFIN;Acc:ZDB-GENE-100609-3]
Coordinates
chr16:38175159-38175745:+
Coord C1 exon
chr16:38175159-38175442
Coord A exon
chr16:38175443-38175590
Coord C2 exon
chr16:38175591-38175745
Length
148 bp
Sequences
Splice sites
5' ss Seq
TAGGTACGA
5' ss Score
7.12
3' ss Seq
ATCACTTGTTTTCTTTGAAGACT
3' ss Score
6.5
Exon sequences
Seq C1 exon
TTTTGCTGCCCTGATCTGGTCCACATGACTGAAACAAGCAGTACCCCAACAGCTGTGAAACCCCCAGCAACACCACCTAAGAGTGCCTCTGTTGTGCCTAGTGCCAAGGTGGATAGCCCACCTAGCAAAACAGGAGATAGCCATCCCAGACTCGTCATGCTGGTTGATGATTTCTACTACGGCACATTTGAGGGAAATCGAGTCTATGTACCAATGGACAACTCAAAAGAACCATTATCATTCAGATGCCTGACCTGTAGCAAGAAACTAAAGAATAATATTAG
Seq A exon
GTACGATTATGGACTGATTTTAGAAGTCTTATTGTAAATATCTAGTTGAAAATGATAGGTTTTATTTTAAGTAATTTCCTAGTCTTTGTTTATTCTGTCTTTGATATGTTGGAACTGTGCCATTAGTGATCACTTGTTTTCTTTGAAG
Seq C2 exon
ACTTATGAACCATATGAGGTACCATGTTGAACTGGATCAACAAAATGGGGAAATGGACAACCACACATCCTGTCAGCATTGTTTCCGTCGCTTTCCTACACCGTTTCGTCTGCAGTGCCACCTTGAGAGTGTCCATACCTCCATTGAATCATCTA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000076542:ENSDART00000132087:10
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.379 A=NA C2=0.057
Domain overlap (PFAM):
C1:
PF139121=zf-C2H2_6=PD(8.0=2.1)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CATCCCAGACTCGTCATGCTG
R:
CGAAACGGTGTAGGAAAGCGA
Band lengths:
251-399
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]