MmuINT1020746 @ mm10
Intron Retention
Gene
ENSMUSG00000046434 | Hnrnpa1
Description
heterogeneous nuclear ribonucleoprotein A1 [Source:MGI Symbol;Acc:MGI:104820]
Coordinates
chr15:103242922-103243780:+
Coord C1 exon
chr15:103242922-103243080
Coord A exon
chr15:103243081-103243624
Coord C2 exon
chr15:103243625-103243780
Length
544 bp
Sequences
Splice sites
5' ss Seq
GTGGTAGGT
5' ss Score
7.23
3' ss Seq
AGAGGCTTTTCCTTTTCTAGGAA
3' ss Score
9.49
Exon sequences
Seq C1 exon
GTGGTTATGGAGGAGGCAGCCCTGGTTACTCTGGAGGAAGCAGAGGCTATGGAAGTGGTGGACAGGGTTATGGAAACCAGGGCAGTGGCTATGGCGGGAGTGGCAGCTATGACAGCTATAACAACGGAGGAGGCGGAGGCGGCTTTGGCGGTGGTAGTG
Seq A exon
GTAGGTATCCAGTGATGCAGGTACTTGGCTTGGAGCTAGATTAGACTTCTAGAGTTTATTATGCCCGTGTTGGACTTTAAAGCTCTTAAAGCATTGTGGGTGCAGTGCATGGTGCGTTACAGTAGGCCTGCTCTGCTGTGCTACCTCCTCCTGGCTTTAAGCTGGGGCCGCCTCCCCCAAAATAAGTAGGTGAATGAGTGGTTAGTGTTGTCTTCAATGTGAGATAGTTAGATCCACACTACAGTTGGATTGAATGTCTAAACTCTGTTGGGACTTCAGGCATTTAGTTGATACATCCAAGAAATGTATGTATTGACCTGGAATACATAAAGGCCTTCAATTCTAACTTGCCACTGAGAAACTTAAGTTGGGTTGATTTTACTTTAAATGCTGGATTATTAACTGAATGCCTCACTCAGAGAATGAAGCCGAAGGGTTTGGAGTTGACAGAAGGTCTATAAATATCATAATCTTTGATTCAGACCCTAAGCACTATTGGCTTGTCAGTCCTCAAAGTCATCAATAGAGGCTTTTCCTTTTCTAG
Seq C2 exon
GAAGCAATTTTGGAGGTGGTGGAAGCTACAATGATTTTGGCAATTACAACAATCAGTCTTCCAATTTTGGGCCGATGAAGGGAGGAAACTTTGGAGGCAGGAGCTCTGGCCCTTATGGTGGTGGAGGCCAGTACTTTGCTAAACCACGGAACCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000046434:ENSMUST00000036004:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.815 A=NA C2=0.792
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF116273=HnRNPA1=WD(100=67.9)
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:
GTTATGGAGGAGGCAGCCCT
R:
TGGTTCCGTGGTTTAGCAAAGT
Band lengths:
310-854
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Ribosome-engaged transcriptomes of neuronal types
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types