RnoINT0107850 @ rn6
Intron Retention
Gene
ENSRNOG00000010736 | Pbx4
Description
PBX homeobox 4 [Source:RGD Symbol;Acc:1305100]
Coordinates
chr16:21308824-21310650:-
Coord C1 exon
chr16:21310460-21310650
Coord A exon
chr16:21308960-21310459
Coord C2 exon
chr16:21308824-21308959
Length
1500 bp
Sequences
Splice sites
5' ss Seq
CAGGTCAGG
5' ss Score
7.2
3' ss Seq
CTGAGCATCTCTGTCTGTAGGCG
3' ss Score
7.17
Exon sequences
Seq C1 exon
GCCTGTCGTGAGTTCACCACGCACGTCACCAACCTTCTCCGGGAACAGAGTAGGGTGAGGCCCGTGTCCTCCGGGGAGATCGAGCACATGGTGAGCACCATTCACAGCAAGTTCAGTGCCATCCAGAGGCAGCTGAAACAGAGCACCTGTGAGGCTGTGATGACCCTACGCTCACGGTTCCTGGATGCCAG
Seq A exon
GTCAGGGCTGCATGCCACTGGGGTCCCCAAGGGTTGGCCCTTAGGAACAGAAGCAGGATCGGAGTGGGATGGCTCTGGAGTTTGTCATAGTGTTGCTGAAGATGGGACTCAGGGCTTTGCAAGCGCTAACCACATGCTGTCCCTACCACTGAGCCCCAGCCCCGCTCTGTCTTGAGTTTAAGTCCGTCCAGAGCATCCAGCCAGGCCCCACACAGCTTTTTTGGGAGAAGACCCAAAGTACAGACTGCTGGTTCATTTTCATTTGTGTATGTGAATGGCATCAGAGGACAGCCTCGGGTACTGGTGTCCCTCTTCCACCGTGCTTGAGGCAGGTTCTCTCTTGTTTTCCACTGTGACTTCCAGACCAGCTGCCCACTTCCCATCCTGCCCCAGGAGCCCCATAACTACAGACATGCACTAACATGTATGGCTCCCACATGGGTTCAGGGAACCCAGACTCAGGTCTTCATACATGTTCATTACCCACTGAGGCATGTCAAGCCCGATTGCTGTGTCTAAAACTGCAGAAGATGAGGATGGGGAGGCAGCTCGCTCAGTCAGGTGCTCACCATGCGACCAGAAGGACCTGAGTTTGCATACCCAGCACCCACAGAAAAAGCCAGGCATGGGCCAGCAAGATGGTTCAGGGGGTAAGGGAACTTGCTGCAAAAGTCTCAGGACCTTAATTTGACCCCAGAGTGACATGAACCTGCAGGAATAAGGGTCCTGAACGGTGAAGTATCAAGTGGGGCAGGGCCAAGAGGAGAATAAGCAATAGTTGGGGCCAGGAGACCCTGCATAAGTGATGGCTTATGCTAAGCAGGTTTGTCCAGGAATATATTGCCCTATCTACTATTTGCAGAGGGGAAATGGAAGTCTGGGAGAGAGCAAAGTCAGGCAGTGTTGGCAAAGAATACACAGGGTTCTCAGACACGGCTGGTTAAGGACCAATAGCCACAGCCCAGGGGAACAGCCTGGTCCCCAGAGCTGCAGCCTTGGCTTCTCTGAGGCACTGGCCCGGCCTTGCCAAGCTGGGCAGGTACACAGAACTAGCGCTCTCTGTCATCAGATCTCTGTGAAAATCTTGGTTGGTCTGGTCTGGCTTCCCACACCAGAAGTATGCACACATACACACACATTCACACACACACACATGCATGCACTCACACACACACACAATCTTGCACACAAGCACACACTCTCGCACACTCACTCACACATACAGGTCTTTTAAAGCCAAGAGCTGCTGCAGCCAGGCACTGGCCACATGGATAAGGCTGGTCCCTGGGGCCTGCTGCTCTCCAGTCTGCCCAATCACTGGGCTCCAGGTTCAGTGAGAGACCCTGCCTCAAAGAAGCAAGGTGGAGAGTGACGGAGGACACAGCGCATCAGCCTCTGGCCTGCACGTGCACACACACATAGGCTGCCAGGACATTAGGGACACGAGAGTTGTGACTCTGCCCCATGAGAGTGCTACAGACTGAGCATCTCTGTCTGTAG
Seq C2 exon
GCGCAAGCGGCGGAATTTCAGCAAGCAAGCCACCGAGGTGCTGAATGAATACTTCTATTCCCATCTGAGCAACCCTTACCCCAGTGAAGAGACCAAGGAAGAGCTGGCCAGGAAGGGTGGCATCACAGTGTCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000010736:ENSRNOT00000014265:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.188 A=NA C2=0.239
Domain overlap (PFAM):
C1:
PF037928=PBC=PD(31.1=95.3),PF070286=DUF1319=PD(64.7=85.9),PF083976=IMD=FE(51.2=100),PF0004624=Homeobox=PU(0.1=0.0)
A:
NA
C2:
PF083976=IMD=PD(26.8=71.7),PF0004624=Homeobox=PU(75.0=97.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCTGTCGTGAGTTCACCACG
R:
CTGGGACACTGTGATGCCAC
Band lengths:
326-1826
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]