RnoINT0107853 @ rn6
Intron Retention
Gene
ENSRNOG00000010736 | Pbx4
Description
PBX homeobox 4 [Source:RGD Symbol;Acc:1305100]
Coordinates
chr16:21303837-21305591:-
Coord C1 exon
chr16:21305485-21305591
Coord A exon
chr16:21304138-21305484
Coord C2 exon
chr16:21303837-21304137
Length
1347 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGT
5' ss Score
10.65
3' ss Seq
TCTTGTCTCTGTCTTTCCAGGCC
3' ss Score
11.52
Exon sequences
Seq C1 exon
ACTCCTGTGGCCCCTTCCCACTGACCAGTGGAAGTGACATGGTTCTCACCCTGCGGACCCTGGCCTTCCTCCAGCCCCCACCCGGAGGAGTCTGCCTACAGCCCCTG
Seq A exon
GTAAGTCAGCTGCAGCCACCCTGGGACCCCTTCAGGGCTTTGGGGAAGTAGAAGAGCCAGGTGCTGGGTCTTGGGAAGGAGACTCCAAGGAAAGGTGGGAGCATTTAACCTCTAGGCTCAGACCCGCCCACTGGGGACTGGAGACCTGGTGGGTTGGGGGTGTCTCACACTGGAAGGGCATGTGCCAGACTGAGATACATGTTGGTAACTGGGATCTAGACAGCCAAGTTGCCTCCAGAACTTTGCCAGGGTGATACTTGTCTCCTTTGTAGAGTCTGTGACCTTCCAGTCTGTCCTGGTGTGGGACCACAGCCCCTCCCAAGGCCCTGTGAGGGCCCTGCATAAACAGAGTGGGCTCTGGCACAGTGCACCTGCCATGGTCCCATGAGCCCAGCAGCTTCCCAGAAGCTCCCTCAGAAGCAGCCCCAGGGCTCAGCCCCAGGGATGGGGTTGGGGGAGCCTGGCACACTCAGGCCCTGCCTGCCACCACCTTAGTCCCAGCCTAATGCAAGCGTCAGGCTGTGGAGCAGAGTCTGGGCCTGCTTCTTGCACACCTGAAGCTCAGGTGCTCTGGGACAGAGCCAGCAGGAGTGAGGGAGCGAGTCTGCCCTGCTCTGAACCGAGCACACCTGTCCATTCCAGCACTGAGCCAAGAGTCAGACTGAGGGCAGTGCCATGCCCTGCAGGCACCCACCTAAGTCTCCTTTAGGTAAACTATGACCCAAGCACACCCTGTATCTTGTTGTTGTTGTTTGTTTGTTTGAGATGTTCTTTCTACATAGCCCTGGCTGTCCTGGTATTCACTTTAGATCAGGCTAGCCTGGGATTCACAGAAGTCTTCCTGCCACTGTCTCCTGAGGGCATAAAGGAAGGCACCATCAAGACAGATCCATGCCAACCCCTTCATGCGCATTTAGCCATTCAGCTGGTTCTTGTTAAAGGTCACTCTGCCAGCATGGCCCCTGCTCAGCCATGAGGCAGTGCCTTGCCTGATACAGTGTACCCCAACAGTGTCCCCTGAGCTTAGCACACCTGTCCAGCCGTCCCTAGACAGATGGGCAGAGTAGCCCCAGTGTGTGCTGTGGTCATGCACACTGCAGACAAGCAGAGGCTTCTGCTCCTGTGAGGAAGGGCTCTTACTGCCTATGAGCCATGGCCCTGCCACAGGCTGGTGGCTCTGACATTCACAAGGCACTTAATGGAGGGATGTGGGTTCAGTGCCCACCCTGTCACCCTGCCGCTCAGCTGGTTCTTTCTGGACACCTCAGCTAGCATGTTCTACATTCCTCTGGGGACCCCAGAACTGGATGGTTACCCCCTCTCGTGCTCTTGTCTCTGTCTTTCCAG
Seq C2 exon
GCCCATGGTAGCTGGCAGAGGGCCACCACCTCACAGCCATCCTCCTCACCTGCCGGAGACTCCGGCAGCTTCAACTCAGATGCGTCTGACTAAGGTTTTGGAACCTGGCTGAGTGCTGTGGATGTCTGGCCCTGGGTCCTGCTGATCACCTCAGAAGCCCTGGCTGTGGCTCTGCCCTTTCCAGGCCACTCACTTCCCTGCTTTGGCGCGATGTTCTTTAAAACATGAATTGAGTGGCTGGCAGTGGAGTGTTCGCCTGGGGCTTGTTCTGAGCACCCCATTAAAGTTTTGACCTGTTTGC
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000010736:ENSRNOT00000014265:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.361 A=NA C2=1.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTGACATGGTTCTCACCCTGC
R:
AATGGGGTGCTCAGAACAAGC
Band lengths:
356-1703
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]