RnoINT0114699 @ rn6
Intron Retention
Gene
ENSRNOG00000053599 | Pogz
Description
pogo transposable element derived with ZNF domain [Source:RGD Symbol;Acc:1309980]
Coordinates
chr2:196021414-196023506:+
Coord C1 exon
chr2:196021414-196021522
Coord A exon
chr2:196021523-196023215
Coord C2 exon
chr2:196023216-196023506
Length
1693 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGG
5' ss Score
11.08
3' ss Seq
TTTGTCTCTTTTTTTAAAAGCCC
3' ss Score
7.65
Exon sequences
Seq C1 exon
GGATTCCCTGTAAGGAATGTTCGCCCTGTACAGAATGCCATGAACCAGGTTGGGATCGTGCTGAATGTACAGCAAGGCCAAACAGTCAGACCAATTACACTGGTCCCAG
Seq A exon
GTAAGGACATGTTTACAACCTGGCATCCAGATACTTACTCTTATTGTTTCAAAATAGTCTCGGTCATTTGGAAGTATGTATTTAAACAGAATTTTAAAATACCATGTTAACAATTTAAGTCCAATTTTAAAAAGTCTGAACTTTAGTCAAGTGGTAATTTTAGTTTTACATTTAACTTTTCACCACCATTCATGAGGTAAAATAAGTCTTATTTAGTCAAACAGTATCTGCTGATGAGGTCAGCTCTTGTTTGTTATCCTGAAAGAATATTGTTAATGCAAACCCACAAATCTAATGCTCCCCATACATTTACTCACTTATGGGATAGGATTATAAATTGAATTTTTCTTTAACTGTAAAGCATAGGTTTTCTATATGCCACTAGGTATGGTGACACACTCCTGGAATCCAACATTCAGGAGGTTGAAGCAGGAGGATTACTGTGAATTTAAGGCCAAGTCTTGTCTCAAGAAATAAACAAGCTAAGGCAGAGGTTGGGGGAATTTTAGATATAAATTAAGTAAATGATAGATGTTTTGAAGATAATACTACCATTGACCATATAATGGAATATTAAAGAATCTTGGGGGGTTGGGGATTTAGCTCAGTGGTAGAGCGCTTGCCTAGGAAGCGCAAGGCCCTGGGTTCTGTCCCCAGCTCCGAAAAAAAGAACCAAGAAAAAAAAAAGAATCTTGGGGCTGGAGTTATAGCATTTTTAGCATTGCTTGAGGCCTTGGGGTCAATTTTTCAGTACCAAAAGAAGATTCTTGTAATTTCCCCCCAAATCACAATGCTTACCTATTAGGTTTTCTACAGTTTGGCTCAAAAAGAGAGTAACTTTATTTGTGTAAACAGTCCTTAGGACCAGTAGGTGTCTCAGGGCTAAATGGACCTGTGTTCACTCCCTAGAGGCCACATGATGGAAAGAACCAGTTCCCACTTGGTTTGCTCTGACTCCACTTGCACACTGTGGTATGCATGCCACCCCCACCCCCCACCCCTCACACATATACACATACACACACTCAGATAAATACAAGGACAATAAGGGGCTTCTGTGGTTGGCTTTCCAAAGCATTTTGTTTGTTTTTTTTTTTTGTTGTTGTTGTTGTTCTTTTGTTTCCTTTGTTGTTGTTTGAGAGCCATCAGGGCATTTAAGGCATAAATCTGATGAGATGTCTCTAACATTCTGAGGTTCTCTAAATGTTTTTCCCTGGGATTGTCTACAGTAGTTCTAGAAAAAGGTCAACCTTTGGGACATTGAGGTAGAGTAGACTGCCTGTCCTATTTGAGTATACAGAAGAAAATGGAAAATTCTTTTAGAATTCTGAAAAAAGACTTTAAGGACCAAGTCTGCCCTTTGGCCTGCATATACCCAATCTTTTCCCACTTCTAATATGGAGGCCAAGCTACTGTAAAAAAGAGTGTGTGCAGGGCATCTGAAAAGAGTTGGTGGGAATTTCTTCTGACTGCTGCTTTACGAAACGTTGGATAATTCCTTTTGTTTGACGGACAGCTACAGCTTTCTTAGATGTTCAGATCGATGCTACTCTTAGTGATCTCTGGTGGTCACTCAGTCAGTTTAGGGAGTAACTTTTTCCTGTTCTTGTATTTCTAGGAAAGGCAAGAAAATATTTTATAGGTGAGCTCACTGATGAAGGTTTGGGACTTTTTTTGTCTCTTTTTTTAAAAG
Seq C2 exon
CCCCAGGTACACAGTTTGTTAAGCCGACAGTTGGCGTCCCACAAGTGTTCTCTCAGATGACCCCCGTGAGGCCAGGCTCCACAATGCCTGTGAGGCCCACCACCAACACCTTTACCACCGTCATCCCAGCTACTCTCACCATCCGAAGCACTGTCCCACAGTCCCAGTCCCAGCAGACCAAGTCCACCCCCAGTACCTCCACTACTCCCATTGCCACACAGCCAACCGCATTGGGGCAGCTAGCTGGTCAGCCTCCAGGCCAGCCCAACCAGACCTCGAATCCCAAACTAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000053599:ENSRNOT00000082849:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.351 A=NA C2=0.939
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCATGAACCAGGTTGGGATCG
R:
TGGGATTCGAGGTCTGGTTGG
Band lengths:
357-2050
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]