MmuINT0149575 @ mm10
Intron Retention
Gene
ENSMUSG00000036281 | Snapc4
Description
small nuclear RNA activating complex, polypeptide 4 [Source:MGI Symbol;Acc:MGI:2443935]
Coordinates
chr2:26370786-26372825:-
Coord C1 exon
chr2:26372731-26372825
Coord A exon
chr2:26370881-26372730
Coord C2 exon
chr2:26370786-26370880
Length
1850 bp
Sequences
Splice sites
5' ss Seq
CCGGTGAGT
5' ss Score
10.9
3' ss Seq
CTGTTTCCACACATTTCCAGCTA
3' ss Score
7.13
Exon sequences
Seq C1 exon
AAATTGCTTCAAGCTGTTGCCAAGTATGGGGCGCAGGACTGGTTTAAAATCCGGGAAGAGGTGCCAGGTAGGAGCGATGCCCAATGCAGAGACCG
Seq A exon
GTGAGTTGCCCGCACTGGCTGAAGGAGCGACTTGCTTGGGTCACACTTCTGTAGGCAGGCTAGGTGACAGTGGGCCAAAGTTATATGCCCACGGGGGCTTTTCAAACCGGGGTTGGCACTGTTAGGAAGCAGGACTTTGGTATTTCTGTTGCCCACAAGTTGTCAAGTACTAGTGATGACTCATGCAGATGTCCTTCCACATTGCTGGTGGGAAGGTCCCCAGCAGAGAGGTTCTCTCCTTTTCTCCCTATTTTCTTTCAGTGGTTTGTTCAGATGTATTTTAGTTTACCTACACTCAGCAGCCCTGCAGAATCCCATTCAAAACAGGCAGACATTTTCAACAGACTTGTCTCCAGAGATGCACAAGTAACCAGAAGGCCCATTAAAAGATGCTCAGTCACTTATTTCAAGAATGCAAATCAAAACCACAGTGAAATATTTCGCACATGTAGGGGAATTGTTTTAAAACACACACACACACACACACACTAACAAGTATTCCTGGGGCACAGATCATAGCCTCCAGAAAAACCAGAGCATGGGACAGCATTGTGCTGGGGCAGTATAGTCTGTACCTGCAAAACTCCCTTGTCCCAAGTGTCCCAGGAGCTTGTATATTAGACAAGAATGTTAATAGAACATCCTTCATTGTCAGAAAGAAAGTGTGGGGTACAAAGCCGGAGTGTGGCATTTGCAGGGAAGGTCCTGATAAGCGCTGTGTGATACATGTGGCGCCGTGGGAACATTCTGAACATTCCGTCAAATATTTATCAAGACATGCTCATTTCTCTCAAGAGCGTCTTTGGGTCGGTGACTCTTGTGCTTGGCCTTTGGAAGAACTGTCATCTGTGCAAAATGTCTCTATATTGTGCTCCCACAAGCAGCATGTGAGGCTTGTGGCTGAAGCCGTCCACGTGTTTGTGGAATAGACTTTGACACAGTTGTCTCACAGCAGCCCCTCATGGCTAACCGTGTGTACAATTGCTTGTACCTGCTGGCTTCTTACATGTGTACATCTCTTTGGAAAAACACCTGTCAAGTCCCTTCCTAGGTTTAAATTACCTGTCTTTGGATTACTGGCTTTTACATGTTCAAAATGCAAGTCCCTAGTCAGATGCACTAATCAACGGCTCTTCTCTCCCTTCTTCACAAGGCGCCTTACAGCAGTGGTTCTCACCGTGTGGGTCTCACCGTGTGGGTCTCACCGTGTGGGTCTCACCGTGTGGGTCTCACCATGTGGTTCTCACCGTGTGGGCCTCACCGTGTGGGCCTCACCGTGTGGGTCTCACCGTGTGGGTCTCAAGCCCTTGGTAGGGAGGTTGTTGAATGAACCTTTCACAGGGGTCGCCTAAGACACAGAAACACAGATAATTATATTACAATTCATAACAGTAGCAAAATTAGTTATGAAGTAGCAATAAAAATAGCTTTATGGTTGGGAGTCATCATATCATGAGGAACTATATTAAAGGGTCACGGCATTAGGAAGGTTGAGAACCACTGCCTTAAAGCATAAAATTCTTGAAATGTTCTGGGCAGTGGTGGCTCATGACTAATCCTAGCATTTAGGAAGCAGAGGCAGGAGGATTTCTGAGATCGAGGCCAGCCTGGTCTACAAAGTGAGTTCCAGGACAGCCAGGGCTACACAGAGAAAAGCTGTCTCGAACCAAAAAAAAAAAAAAATGATGAATTCCATCTTGTCTTGGTTTGCTTTGGTTTTGGTTTGGTTTTTGCTTTTGCTTTTGCTTTTGCTTGTTGTGGTATTGTCCTAAGAAATCACTGAGAAGGCCAGAGAGCAGTGAAGGGGGTCTTAGCACCTAAAGTGTCCCTCTGTTTCCACACATTTCCAG
Seq C2 exon
CTACATCAGAAGATTACATTTCAGCTTGAAAAAGGGACGGTGGAATGCAAAAGAAGAACAACAGCTGATCCAGCTAATAGAGAAATATGGTGTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000036281:ENSMUST00000114115:13
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:
PF139211=Myb_DNA-bind_6=FE(50.8=100)
A:
NA
C2:
PF139211=Myb_DNA-bind_6=PD(36.1=66.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AAATTGCTTCAAGCTGTTGCCA
R:
CAACACCATATTTCTCTATTAGCTGG
Band lengths:
190-2040
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