MmuINT0149578 @ mm9
Intron Retention
Gene
ENSMUSG00000036281 | Snapc4
Description
small nuclear RNA activating complex, polypeptide 4 [Source:MGI Symbol;Acc:MGI:2443935]
Coordinates
chr2:26223664-26225132:-
Coord C1 exon
chr2:26224659-26225132
Coord A exon
chr2:26223929-26224658
Coord C2 exon
chr2:26223664-26223928
Length
730 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGGC
5' ss Score
10.08
3' ss Seq
GGACTCGTCCACCCACCCAGAGT
3' ss Score
2.4
Exon sequences
Seq C1 exon
AAGAAACAGCATCTGCAGAGGAAGAGAGGGCAGAGGCCCCGTCACAGTAGCCAGTGGAGCTCTAGCGGCAGCAGCAGCAGCAGCAGTGAAGACTACGGCAGCAGCAGTGGCAGCGACGGCAGCAGCGGCAGTGAAAACTCAGATGTGGAGCTGGAGGCGTCTCTGGAGAAGAGTAGAGCACTGACTCCTCAACAGTACAGAGTGCCAGACATTGACCTGTGGGTTCCTACCAGGCTGATCACCAGCCAGTCACAGAGAGAAGGGACAGGGTGCTACCCACAACACCCTGCTGTCTCCTGCTGCACTCAGGATGCCTCTCAAAATCACCACAAGGAAGGTTCTACCACCGTCTCTGCTGCTGAGAAAAACCAGCTGCAGGTGCCCTATGAGACCCACAGCACTGTTCCAAGAGGAGACCGGTTCCTACACTTCTCGGACACCCACTCAGCAAGTTTGAAGGATCCGGCCTGCAAG
Seq A exon
GTAGGCCCTAGAATGTGAGCAAGGGGAATAGTGTGTGCTCTGTGCTCTTAGTGGTCACTATAGCTGTCACTCTGGACAGTGTGGCAGTTTGGTTTCTGACCTGGCAAAAGCCTTGTCCTTTTATTCACTAGAATTGTTGCTTAGAACTGGTTTCAGAGTTGTGCAGTAGCAGTGGCCTTCATAGGAGCTGCAGCCTCCATTGTCCCCAAGTCATTTGCTTTAAAGGTTGTAAGAATTTCTGCTTAAGGGCACTTAGATAGTAGGCAGTTCCCCATCCTCAACTGCCATGAGTCGTGGAGGTGTCCTTGGGTAGTGTCAGTCCAACTTGGCTGGCTGTGCATTGACCTGTCCCCCTCTGTCCTCAGTGCTGGGCCTGGGGCCAGCCAGATTAGCTCTGGCAGTGGCTGGAGCAGCCTTTTGGACTATACAGGCTGCTCTGCTGCTCTGCACTGGGGATTGCTGGAGGGACAATGCAGTCAGCTCAGCCATGGTACTGCCTGCCATTGGGCCAGAGCATCTGTCTTAGAGAGGGCACTAAGACAGGCCCTACTTTAAGGCCACATTAGCCTTACCACAGAGTATTTTCGCAAATAGCAAGTGGTGTTCTTACAAGGGGGCGTTAAACGTGCACAGTGGCAGGCCTGTACCAGATCCTCTTGATATACAGCCTGTGTTGAAGGTGCCCCTAGAGAAAATGCCGAAGTTAATCAGGACTCGTCCACCCACCCAG
Seq C2 exon
AGTCACACACTGATGAAGGAAAGACCGAAGCAGCCACTCCTCCCTAGTTCACGCTCAGGGTCTGACCCTGGCAACAATACGGCTGGGCCCCATCTGCGGCAGCTATGGCATGGAACTTACCAGAATAAGCAGAGACGCAAGAGACAGGCTCTACATCGCAGGCTCCTTAAGCACAGGCTTTTGCTGGCTGTGATACCCTGGGTGGGTGACATCAACCTGGCCTGCACACAAGCTCCCCGGAGACCTGCAACCGTTCAGACTAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000036281-Snapc4:NR_033572:17
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.839 A=NA C2=0.712
Domain overlap (PFAM):
C1:
PF061126=Herpes_capsid=PD(94.7=45.6)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGATCACCAGCCAGTCACAGA
R:
AAGTTCCATGCCATAGCTGCC
Band lengths:
357-1087
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
Other AS DBs: