DreINT0078586 @ danRer10
Intron Retention
Gene
ENSDARG00000059351 | hnrnpa3
Description
heterogeneous nuclear ribonucleoprotein A3 [Source:ZFIN;Acc:ZDB-GENE-060224-1]
Coordinates
chr9:1700375-1701653:-
Coord C1 exon
chr9:1701595-1701653
Coord A exon
chr9:1700498-1701594
Coord C2 exon
chr9:1700375-1700497
Length
1097 bp
Sequences
Splice sites
5' ss Seq
GAGGTACCT
5' ss Score
7.63
3' ss Seq
TTTTTCTCTTTCATGAACAGAGT
3' ss Score
9.27
Exon sequences
Seq C1 exon
ATTATTCTCTCAGTGAGGCGCCGTGCAGAGCGAGGGGGCGCAAAAGCTACAGCATGGAG
Seq A exon
GTACCTGTTATCAATATTCCCACATTAAAATGAATTTGCTTTATGTGTGTCAGCAGTGTTTACGATAAGGCTTATCTTAGGCCAGTTTATTACGCTGTTTTTGCGTTAAGAATGCTGCGTGGTGCAGTTATGATGTCGAGCTAACGTTAAATGGGATACAGCTGTGGATGCTGGCATCAATATAGCATAAATACACTGTATGCGTGCTGTTAAGGCGAATAGGCTAATGTTTTTTCTTTAAATAAGTCTATTATTGTTTTTCTTTTGAATACTCGTGCTTCAGTTTCATAACGTGTTGATGTTTTGTTCAGCAGCGTAAACCTAATGTTTAGCCTGATTTTGTAAGTTAAACACGTGTTAATAATACAACAACATATTGAATATTTCACTGTATTTAATCTTTTTTAACAAGTGAAATACGGAGGAAACAAGGAAAATACATCTAACGTTAATAAAATGGCGCGTGTACACTTTGGTGTGGAATATTCTAGACGCTTCGAGCCGTTGGATTGTTTATTATCGGTCTCTTCCTGAATTTTTACGGTAATCCTTAATTTTATCTGAAACTACTTCCAACTCCACGTCCTCTGTTTGTTCAGAAGTAATTCGACAGAAAGCAACCGGCTGAAATGCGAATCATACTATGGCGTAGGCACGGCTAATGAATCTTATTACGCTTATCCTTATTAATATTCATAACTTTGGCCTTTTTTAGTAGCCTAACTGGTCAGTTGACCAGCGCCCACCTTTCAACGTCAGTCTTTCAACCAATTGGGAAGGATTGATTTGAAAGCGTCACTCACCTCATGAATATTAATATACATCCTCGCCTAATTTGGTAAAAGGGTGACCGGATGTCATTCATTCTCTTCCCCTGGAGCTCTCAGCGTTCAGAAAACACCCACACAGAGAATCCAGCTGTGGTTAATATTGTGCAATCAATAGTCATGTGTTATTATCAGATTTAAACAGTTATCTTAATTGCTTCAGCATTATGCAACACATGGAGCATGCCCTGCAGGGATCATTTTATCAGTCCGGTGATGCATATTTATGAAAAGTCAAAGGTGTAATTTTTTTTTCTCTTTCATGAACAG
Seq C2 exon
AGTCGCGACAGTAAGGAGCCGGAGCAGCTCAGAAAGCTGTTCATTGGTGGACTCAGTTTTGAGACTACGGAGGACAGTTTACGAGCTCACTTTGAGCAATGGGGCAAACTCACAGACTGCGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000059351:ENSDART00000137210:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=0.122
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF142591=RRM_6=PU(40.0=68.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATTATTCTCTCAGTGAGGCGCC
R:
CACGCAGTCTGTGAGTTTGCC
Band lengths:
182-1279
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]