MmuINT1017189 @ mm10
Intron Retention
Gene
ENSMUSG00000109398 | Gm3854
Description
predicted gene 3854 [Source:MGI Symbol;Acc:MGI:3782026]
Coordinates
chr7:6348437-6349813:+
Coord C1 exon
chr7:6348437-6348563
Coord A exon
chr7:6348564-6349717
Coord C2 exon
chr7:6349718-6349813
Length
1154 bp
Sequences
Splice sites
5' ss Seq
TGGGTAAAG
5' ss Score
4.2
3' ss Seq
TTTTTTCTCCTCTTCTCCAGGTC
3' ss Score
12.66
Exon sequences
Seq C1 exon
GGTTCGGAACTGTTCAGGGATGTGACCATAACTTTCTCCCAAGAAGAGTGGGAGTGCTTGGAGCCTGTTCAGAGGGATTTGTACAGAGATGTGATGTTGGAGAACTACACCCACCTGGTCTCACTGG
Seq A exon
GTAAAGTGGTCTGGTTTGTTAGTGTGGATCTTATCCTGGGAATGACCCTTCCTGGTCAGCTATTGGGAGTTGTGTCTGGCCAGTAGATCACAACATGGGTTCTAGCCTGGAAAGGCATTTTGGAAACCTGGAAGAGAAGAGGGGCTGGGCTGCACGAGATAAGGAAGGAACCAAGACAAAGCTCTCTGCTCAAGGTTCAATTTTTACTATTTCGGCACTCAGTTATAAAGGAAGGGGGAGGGGCCCAATTCCCGCCAAATAATCTTGGGGTCCAGTAGCAGGGTAATCACGTGATGGCTTCGGAACAGCAAAGCGGCAGGTTCCAGCAGTAAGCGTGGCAGAAAGATTGAGCGGGAAGCTCCACCCCTGAGCAAGCAGGTTTCAGGCTGGGGGAGGGGAGACTACAATTGGGCACCTTTGGCCTGCCCCTTCCTAGTCAGTTATTGGGCACCTTTGGCATGCCCCTTCCCGGTCAGTTATTGGGCACCTTTGGCATGCCCCTTCCCGGTCAGTTATTGGGCACCTTTGGCATGCCCCTTCCCGGTCAGCTGTTGGGCACCTTTGGCATGCCCCTTCCCAGTCAGTTATTGGGCACCTTTGGCATGCCCCTTCCCAGTCAGTTATTGGGCACCTTTGGCATGTCCCTTCCCGGTCAGCTGTTGGGCACCTTTGGCATGCCCCTTCCCGGTCAGTTATTGGGTACCTTTGGCATGTCCCTTCCCGGTCAGCTGTTGGGTACCTTTGGCATGTCCCTTCCTGGTCAGTTATTGGGCACCTTTGGCATGCCCCTTCCCGGTCAGTTATTGGGTACCTTTGGCATGTCCCTTCCCGGTCAGCTGTTGGGCACCTTTGGCATGTCCCTTCCCGGTCAGTTATTGGGCACCTTTGGCATGCCCCTTCCTGGTCAGGTAGTCATTGTATGCCTTTTAGCTCTGTGACTGGTTACTTTCAAGCTAACAAAAGGCAGCCAATTGTTTGAAGTCATATTTTCTGCTACTCTTAGGCCACTGTTACATTTTTGTTTTTGTTTTTGTTTGTTGTTTGTTTGTTTGGCCCATTCTGCAGTTCTCTCCCTACTCAGCGATTCGTCCCTGGATCTGAATTCCAAGGCCTCTCAGTATAACCACATGGTGGTTTTTTCTCCTCTTCTCCAG
Seq C2 exon
GTCTTGCCATATCCAAACCTGAGGTGATAGCCATCCTAGAGCAAGGAAAAGAGCCATGGATAGAGGAAAGGGCTACAACGGGAGGGCTATGTTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000109398:ENSMUST00000207173:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0135222=KRAB=WD(100=93.0)
A:
NA
C2:
PF0135222=KRAB=PD(0.1=0.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGTTCGGAACTGTTCAGGGAT
R:
CTGAACATAGCCCTCCCGTTG
Band lengths:
223-1377
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