MmuINT0142294 @ mm9
Intron Retention
Gene
ENSMUSG00000058153 | Sez6l
Description
seizure related 6 homolog like [Source:MGI Symbol;Acc:MGI:1935121]
Coordinates
chr5:112890167-112892069:-
Coord C1 exon
chr5:112891875-112892069
Coord A exon
chr5:112890306-112891874
Coord C2 exon
chr5:112890167-112890305
Length
1569 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGC
5' ss Score
8.7
3' ss Seq
CTCTTGTCTGTCTGTTGCAGCCA
3' ss Score
10.88
Exon sequences
Seq C1 exon
CCTTTGAGAAAGGTCACTGCTATGAACCCTACATCCAAAATGGGAATTTCACCACATCGGACCCCACCTACAACATCGGCACCATTGTGGAGTTCACCTGCGACCCCGGCCACTCTCTGGAACAGGGCCCGGCTGTCATCGAGTGTGTCAATGTGCGTGACCCATACTGGAATGACACAGAGCCTCTATGCAGAG
Seq A exon
GTGAGCCGCCACCTTCCCCAAAGCCAGAATGCCCAGGGCCTCCACCCCAGCAAAGAACAAGACCCCAGCCTAGAAGGGGTGGCCACATTACACACTTGTTTTACCATGAGACCTTTTCCGGACCAGTGGTCATCTGGGTCTGGTTGCTGCTGTTTCTTGGGGTAATTCTTTTTTCTTTTAAATAATTCCATTTTGGGAAATGTCCAGAAGAAACATACCCACAAAGGTAGAAAGGGGATTCTAGTCGCCAGGGCCTGGGAGGGGACCTGAGAGGGAGGATGGATGTGGTTACTCTTTTTTTTTTTAAAGATTTATTTATTATTTATTTTATGCATGTGAGTACACTGAAGCTGCACAGATGGCTGTAAGCCTTCCTGTGGTTGTTGGGAATTGAATTTTAGGACCTCTGCTCGCTCCGGTCGGCCCCGCCCACTCAGTCACTGCTTACTCCGGCCCAAAGATTTATTTATTATTACAAATAAGTACACTGTAGCTGTCTTCAGAAGAAGGCATCAGAACTCATTACAGATGGTTGTGAGCCACCATGTGGTTGTGGGATTTGAACTCAGGACCTTCAGAAGGGCAGTCAGTGCTCTTACCCGCTGAGCCATCTCTTCAACCTCCGACAATGCCCTTTCGACAGCCATACTATGGTAGACACCAGCCCCATTCATGACGAGGAATCAGACATGGAGAGAGCATGCCCAAGAGCATTCTAGGGTCACTGGAAAAAAAGTGCACTTAGCCTCTCTGTGTTCAGAGCCCAGGCAATATTGGCTGTGACAACCTTCAGTCACACTAATTCCCGGGTCACACTGACTTCCCAGGTCTTGTATCCATGGCCAATGAACCCTAACACATGGAGGAATGAGGGAGACCCTCACTCCCATCAACCACCTGGCAGTTGGTGTGACGTCATTGCCTTGCCCTGGTGAGGATTGGCCCCTGAACTAAATGTACTTCATTAAGGGAGAAGAATGTATTGAGGCTTCAGCCTCTGCCATATTGAGGGCTTACCCAGGAAGGATTGGGAGAGCGGCCTCTGTATCTCTGCTGCCGGTCCAGGATAAACCTTTCAGAGACTGGAGCCTACTTGCCACCTGAGTACATTCTGGGGTCAGGCAGGGTGCTGCAAACTGGCATGGTGACCTTAGTAGTGATCCGTCATAAGCCAGTGGGCTGGAAGAGCATTTCCTGACCTCTCAGAGGAGGAAGCTGATGCTATCAGACCATATACACACCTTATCCAAAGCTGGCAGAACAGTGGAGTGGGAACTGGGGGCTGCCCTCAGTGGCGAAGACATTGCCTACCTCTGCCCCCTTGGAGCAGCAGGTGAGGCCAGTAGCCTTTTTTCAACACGCACACAGACATATGCACGCACATACATGCACACTCATGTAAATGCACACACACACACACACACAAATAGACACACATGCTGCCCCCCCCTGCCTGCTCCACCCCATGCTACACAGGGATCCACAGATGCCAACCTCACCCCCCAAATTTCTAACCACTATGCTGTATTGTCTTCCTCACAAGAGTGTCCTCTTGTCTGTCTGTTGCAG
Seq C2 exon
CCATGTGTGGTGGGGAGCTCTCTGCTGTGGCTGGGGTGGTGCTGTCTCCAAACTGGCCAGAGCCCTATGCAGAAGGTGAAGACTGTGTGTGGAAGATCCACGTTGGGGAGGAGAAGCGGATCTTCCTGGACATTCAGTT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000058153-Sez6l:NM_019982:8
Average complexity
IR-S
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:
PF0008415=Sushi=WD(100=87.9)
A:
NA
C2:
PF0043115=CUB=PU(40.4=93.6)
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:
AGAAAGGTCACTGCTATGAACCC
R:
CTGAATGTCCAGGAAGATCCGC
Band lengths:
326-1895
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: