RnoINT0071385 @ rn6
Intron Retention
Gene
ENSRNOG00000036839 | Hnrnpa1
Description
heterogeneous nuclear ribonucleoprotein A1 [Source:RGD Symbol;Acc:69234]
Coordinates
chr7:144867633-144868744:+
Coord C1 exon
chr7:144867633-144867707
Coord A exon
chr7:144867708-144868588
Coord C2 exon
chr7:144868589-144868744
Length
881 bp
Sequences
Splice sites
5' ss Seq
ATGGTAAGT
5' ss Score
11.01
3' ss Seq
CAAAGACTTTTCCATTTTAGGAA
3' ss Score
8.61
Exon sequences
Seq C1 exon
GTGGCTTTGGTGGCAGCCGTGGTGGTGGTGGATATGGTGGCAGTGGGGATGGCTATAATGGATTTGGCAATGATG
Seq A exon
GTAAGTTTCTTAAGGAGTCTGTAAGGAGTGGTTTCTGGCGACCTCTACCTTTAGAATAGGCTACTAGAGACTAAACCTAGTGCATGACAAAGTTCAGTCAGCCCCGTAAAATGCATGCCCTGAGCAGCCTTTAGCTATTTAACTTGCGTAGATTTTTCTTGTTAAATACTTTTGTCTTATTGAGAAGACTTGTATTCTTGTAGGTGGTTATGGAGGAGGCGGCCCTGGTTACTCTGGAGGAAGCAGAGGCTATGGAAGTGGTGGACAGGGTTATGGAAACCAGGGCAGTGGCTATGGCGGGAGTGGCAGCTATGACAGCTATAACAACGGAGGAGGCGGAGGCGGCTTTGGCGGTGGTAGTGGTAGGTATCCAGTGACGCAGGTACTTGGTGCGGAGCTAGATGAGACTTCCAGGGTTTATGCCCGTCTCAGACTTCACGGCTGGCTCTTAGAGCATTGTAGGTACATTGCATGGTGCGTGCAAATAGGCTTGCTATGCTACCTCCTCCTGGCTTTAAGCTGGGGCCGCCTCCCCCAAAATGAGTAGGTGGATGAGTGGTTAGTGTCTTCCTTCCACATGAGGTAGTTAGAGACATAGCTGGATTGTCTACCTTCTGCTGGGACTTCAGGCATTTAGTTGATATATCCAAGAAATGTCTGTCTTGACCTAGAATATGTACACAAAGACCTTCGATTCTAACTTGCCACTGAGAGAAACTGTCATTAGTTAGGTTGATTTTCTTTAAATGTTGGATTATTAACTGAATGCCTCACTCAGAATGAAATGTAAGGGCTTGAAGTTGACAGAAGGTATATATAATCTTTGATTCAGGATCCTAAACACATTGGCTTGTCAGTCATCAAAGACTTTTCCATTTTAG
Seq C2 exon
GAAGCAATTTTGGAGGTGGTGGAAGCTACAATGATTTTGGCAATTACAACAACCAGTCATCAAATTTTGGACCGATGAAAGGAGGAAACTTTGGAGGCAGGAGCTCTGGCCCTTATGGTGGTGGAGGCCAGTACTTTGCTAAACCACGAAACCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000036839:ENSRNOT00000055285:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.635 A=NA C2=0.839
Domain overlap (PFAM):
C1:
PF116273=HnRNPA1=PU(2.8=3.8)
A:
NA
C2:
PF116273=HnRNPA1=WD(100=67.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTTTGGTGGCAGCCGTGG
R:
TGGTTTCGTGGTTTAGCAAAGT
Band lengths:
225-1106
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]