DreINT0116942 @ danRer10
Intron Retention
Gene
ENSDARG00000076542 | pogzb
Description
pogo transposable element with ZNF domain b [Source:ZFIN;Acc:ZDB-GENE-100609-3]
Coordinates
chr16:38175591-38177542:+
Coord C1 exon
chr16:38175591-38175745
Coord A exon
chr16:38175746-38177441
Coord C2 exon
chr16:38177442-38177542
Length
1696 bp
Sequences
Splice sites
5' ss Seq
CTAGTAAGA
5' ss Score
5.2
3' ss Seq
TGTTGTGCTTTTGTGTTCAGCCA
3' ss Score
7.38
Exon sequences
Seq C1 exon
ACTTATGAACCATATGAGGTACCATGTTGAACTGGATCAACAAAATGGGGAAATGGACAACCACACATCCTGTCAGCATTGTTTCCGTCGCTTTCCTACACCGTTTCGTCTGCAGTGCCACCTTGAGAGTGTCCATACCTCCATTGAATCATCTA
Seq A exon
GTAAGAACTATTTCTATTTTATTAATCTTTTTGTTTAAGGGTGCCACATACAGCATTTGTTTAATAAGTTAAATTGTTCTCTGATATATACATAGTAGGTTTATGGCTTTGGTATTTAAAAAAAAATCTCCAGAAACAGTTTTATAAGCACTTTTATTACTCCATAAAGTACCAACAGAATCAAAAGATCCATGATTTGACCATATATGGCTCGTGTGATGAATATTAATTACAGACACACAAAGAGCATTATCAAAGACAAATGTAAACCCTATCAGAGTAGCGTTAACCTATTTTGCTGACCAAATCTGTTGTGGATAAAGGCTAAATTCTAATTAAAGTTGACAAAAGAGAGGGGTGGAGATGTATGGTGTTGTACTTTGAAGCTATAGTCAAAGAAAACACAGCCAGGAATGATCAACCTCTGCATGAACAGATGACAGTTGAGCTGAATGTTTGTTGAAATATACACATCAAATTTCACAATAAACATGATAAATGAACAAAAGATGTAACTAAACACACCTCATGCCTCTTCAGAGTGAACATGACTAAATGTTTAATCTGTGAATCTTGCATTTTGCTTCCTGAGCCGATATTGAAACATGCTGCAGTAACGCACAGTAAACAATTCATACATGGTAAATATATGCTTAAATATAACTAGGGGAGGAAAATTATCACTGTTGTCTCTCCAGAAAACATTGTTGCAAACGCTTTAAGAGGCTTGCAAATATTAATGATCTCAGAGCTTTTTTTTAATGATCTCAGAGCTTGATGGCATGGCTGCTTGTCAGATCCGGATGAACGACCTAAATTAGATATACATGCAAATGCGGAGGGCATGGTCAGTGAGTCTCGTCACAATTTTGTGTTCTGATTGGCCCGTTGTCCACCTAGGTTTTCCACTTGTGGAATTTACATGAAAATGAGGAAACGGTGGTGTCTGTGGCTCACAGTATTCTTATTTCCATATGTTGCTCTTTTATTATTCCTCTATGCTTTGATATATCCAGATTTTCTCTATAGGCAACCTTTAAGGCATAAACTACAGTTCTAAAATTAAGGGTCTGTACAGTAAAAAATTAAAGAATATTTAACAAAACTACATTTGTTTGATGAATAATATAATAAAAAGCTGCAATATTGTAAAATTTGCTGTTTTAAAGCTGCATGAGTAACTTTATTTTCTGTTTAATAAGCAAATGCATCTTTCAGATTTGTTTTTGTCATATTTTGATATACATCTATAGATAAACCATTTCAGATCAGGGAAGTTAAAATGTATTCTGCTAAGATTTTTGTTATTTTTCTATTCTGCAATTTTTTTATTAGATAGATTGATAGATTGATTGATTGATTGATTGATTGATTGATTGATTGATTGATTACAAAAAACAAAGTGCTTGCTAGACTGGTTATGCTAGTTAAAATCTATTTAGGCCCAGTTCTTCAACAGACACACACTCTTGTCGTGCATACTAATTTATTTGACTAAATTCAAATAAGGAGGGGTCAATGAGGCAATGTTCAGTCCCAACAAATGTTTAGTAAAGTTCTTCATTCACCATTGTTCTGCAATGCTGCAAAGATAGTAAATGATAAAAGTTTGTATTTTGGTTTGCCACAGTGTCTATAAACTGCAGGACTCTCAATTTGTCAGCAGTTTAAGTAACTGTTGTGCTTTTGTGTTCAG
Seq C2 exon
CCAAGTGTAAGATATGTGAGTGGTCCTTTGAGAATGAGCCAGTGTTCCTGCAGCACATGAAGAACTCCCACAAACCCGGAGAGATGCCTTATGTATGCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000076542:ENSDART00000132087:11
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.057 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF134651=zf-H2C2_2=PU(70.4=55.9)
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:
ACTTATGAACCATATGAGGTACCATG
R:
GGCATACATAAGGCATCTCTCCG
Band lengths:
254-1950
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]