MmuINT0023896 @ mm10
Intron Retention
Gene
ENSMUSG00000034384 | Barhl2
Description
BarH-like 2 (Drosophila) [Source:MGI Symbol;Acc:MGI:1859314]
Coordinates
chr5:106452523-106455675:-
Coord C1 exon
chr5:106455450-106455675
Coord A exon
chr5:106453670-106455449
Coord C2 exon
chr5:106452523-106453669
Length
1780 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGG
5' ss Score
9.16
3' ss Seq
GCCCACCCGATTTCTTTCAGAAC
3' ss Score
7.68
Exon sequences
Seq C1 exon
GAACAAAGGAGGAAGGAGACCGGGAGATTACAAGTAGCCGAGAGAGTCCCCCCGTGAGAGCCAAGAAACCTCGAAAGGCCAGGACAGCTTTCTCAGACCACCAGCTCAACCAGCTGGAGCGTAGCTTTGAGCGGCAGAAGTACCTAAGTGTCCAGGACCGAATGGACCTGGCGGCCGCACTCAACCTCACTGACACCCAAGTCAAGACCTGGTACCAGAACCGAAG
Seq A exon
GTGAGGAGAGCCACTGGGTCCCTGCAGGCCAGGCCGGTACCATCTTCTCTCCTGGAGATGCGGGACAGAGAGTCACAGGGTCTGTAGTGGGTATTCTTGGGGCAGAGGTTAGGCACACATCCAAATGGGAGTGACTGAGGACACCGGGAGTTTGAACACTTTTGTGCTCTAAATGTCTTAACATTTGGTTCTCTCTCCCTGCCCCCCAGAAACTCGAGGCACCACAGTTTCCCTCATTTTGTCCTCAAGTCAAGCCGCACTCAGGTTGAAATATCTGTGTAACTGACACCCAGGAGGAATCTGTGTGCGCAGAGTACCCTTAGAACTGCCACAAGCTGGCTCCAAATATCTGTGTCAAGCAACATGGCCTAGCTATTGAGATCTTCACAGAGCTGTCCCACCAGCCTTGGCTTAAATGTTAGGCAGTTGGGAAAGCCAAAGTCCAAGCCTTGGTTGCCATAACATGGAAGATCAGGGAAACCCATCTGGATTAGAGCTGGACTGGAGGCCATGGGCTGGAGAATCAGGCAGCTGCTTGAGCATCTACTCAACAGTGTGCGTGGGGGAAGGGGAGGGAATTGTCTGTCCCCATGTCCTGGCTGTTTCTGCAGTCTCATAAAGAGGAAGGGTGGGGAGGGGACACAAACCCTGTCCCATGTGACTGATTAAAAAAAGACATTAAGAAAGTGTCTGGCCTCACCCTGGTGGCTAGGGACAGACTTGGGCAGTAGGAGTTGAGGTTATGTCCTGTTTCCACACCTGGTGCTAAACTCTCTAGGCTCAATTCTCTGCCCCCTCTGTCGTTTGTGTCCTAATCGTTCATAAGTGGGGTTGGAAATGCCCGTCCAGTTGTCATCTTACCATAATTTTCTGTCTCATTACATACGGTTTCAGCCACCCTAATTCTGTCGGAGAACATTAGTGTCATCTGTAGCCAATTTAAAACCGGCGACATGTTTATTAATTTGGCTAGAGCTGCTGGGTATGGATGCTCCACCAGGCTTGCCTTCCTAGGGCATTCGAGTAAAGTCCTCTCTCCCAGCTTGGTGCAGTGGGAAGAGAGGAGACCCCCTCCCCCCAAAAAAAATGGATCACAGGGTTTAAGCACTACTTTCTCTTTTAAGGAGAGAATATCTTGAGACCCATTTCCTTCCACCTAGAATGGTCGGAGGTACCGCTCCCTAGGGAGAGCTCACTCTCAAACGAATTCCAGTTTGAACCTCGTCGCCCTTCTTCCCTAAGCCTGTAATGCCTGGTCAGACTTAGGGAGGAACTGTCCCGGCAGCCATGGAGAGTGCAAACCCGGAGTGTCAGCCGCCCTTTGTTTCTGGTTTTGGTTTCCTTGGGTGTGATGGGGGGAGGGGCCGAGATCCAACCTTTCTGAGATTTCTGGTCAGAGAAGATTGGAGGAGAATTGGGGGACCAAGGGAAGAAGGCTGGTGAAAAGATGGGATTTCATTTGGCCTCCGGGAAAGTTGCAGGATATAGTTAAATCGTGGGGCAGACTGTAGGGCAGAGGGCCAGAGAAGGCAGTGAAGCTTGTACGACTCCATCTGCGAGTGTCCCCACGTAGAAGACGTAGTTTGAAGAACTGATTTTGGGCCTGGGCCGTCCTGAGAGCGCGTGGGTGAAGCAGAGTGGGGGTGGGGGCAGGAGAGGTGTATTTGAGGTTCCCCAGGCCTTCCTGAAGTAGGGAGGATAGGGGAGAGCGGGGAGCGGCGGGCGCGGTCCCGGGACCATCCTCCGCAGCCGCCACCCGCGCCCACCCGATTTCTTTCAG
Seq C2 exon
AACCAAGTGGAAGCGGCAGACTGCAGTGGGCCTGGAGCTGCTAGCCGAGGCCGGGAACTACTCCGCGCTGCAGAGGATGTTTCCGTCGCCTTATTTCTATCACCCAAGCCTGCTGGGGAGCATGGACAGCACCACGGCGGCGGCGGCGGCCGCGGCCATGTACAGCAGCATGTACCGAACTCCTCCAGCACCTCATCCGCAGCTGCAGCGGCCGCTGGTACCCCGCGTGCTCATCCACGGCCTGGGGCCTGGGGGACAGCCGGCCCTCAACCCTTTGTCCAACCCCATCCCAGGCACCCCGCATCCCCGGTGAGGAAGGAGGGACAGGAGGGACAGTGCCACAGCCCTCCAGGTTCCCACCTCACCCCGGACGGCTGCCCCGCCTCTTCCCGCACCAAACCAACTGGAATAGAGGCAGAGGAGTAAAAGGGGGAGCTCACCGGTGGGCTGGGGTCCCCAAGGACCAGCCAGCTCTCAGATCTCCATCTGCCCACTCAGAGGCAGGGCTGCAAAGCTCCCCGAGTGTGACTGGAGAAAATACTGAAAAGTGCAACCAGTAAGTGAAAACACCCATCCACCCACACATACACACACACACACACACACACACACACACACACACACACACACACACACACACACAAAACGAACCCTCGAGTTCTTTCTTTCTTTCTTTTTTTTTTCTTTTAAACAAAATGACTTTAGGGACATGCAGCAGGGAGGGAGGGGGGAGGGCAAAGAGGGGAGAGACTGGATGGAGAGGAGCCTTCGGGCAGAGAGAATTGTTACTGGACAGAAGCCTGAAGTTCACCCCCAGGCAGAAGGTGGTACCCTGGACATCCAGTCTGCCTCAGAGCAGAGGAGGGTGATGGAGAACTTTGCACTGATTTTTCATGAGCTTTTTTTTTTTCTTTTGGAAAAGTGGCATGCTACATAATATGAAAAAAATGTACATTTGAAAGACTGAGCGATGAGTGATATATCATATTTATTATATGTTGTCCAAAAAAGAGTCACTTATATACGTCAGTAATAACATGACTTTTCTTTTCATGTCTTTTTGATTCAGTAAAATAAATGCTTAGACAAAAGTATAGATTTTTTGTGATTGAAAATTACAAAAATAAAGTTTATCTTTTTTTAACAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000034384:ENSMUST00000086795:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.618 A=NA C2=0.375
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=PU(89.5=67.1)
A:
NA
C2:
PF0004624=Homeobox=PD(8.8=4.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCACTCAACCTCACTGACACC
R:
CTGGGATGGGGTTGGACAAAG
Band lengths:
343-2123
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- 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