MmuINT0180332 @ mm9
Intron Retention
Gene
ENSMUSG00000029729 | Zkscan1
Description
zinc finger with KRAB and SCAN domains 1 [Source:MGI Symbol;Acc:MGI:1921820]
Coordinates
chr5:138538295-138538807:+
Coord C1 exon
chr5:138538295-138538386
Coord A exon
chr5:138538387-138538680
Coord C2 exon
chr5:138538681-138538807
Length
294 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGC
5' ss Score
9.6
3' ss Seq
AGGATCTCCTGTTATTTCAGGCA
3' ss Score
5.2
Exon sequences
Seq C1 exon
CTCTCCCTGCCACCCATGTTCCTGCCCCTCATCATGAGGGGAATCCCAGAGACCAGGCGATGGCATCTGCACTATTGACCGCAGATTCCCAG
Seq A exon
GTGAGCCATGGGCCCCTCTTCCCTCCTGAGACCATGGATTTGCCCCATTCTGGAGCATCTTTCATGATCTCAACCAGGTCACTTGCTTATGATGCCCAGCCTACAGAAAAGCCCACTCCCCTCACTGTTAGGGTTCTTCCACCATAACCCCTTCAGTCTATCAGGGTTGCTCATGTGTTCTCTCCTAGTGTCCCACAGTCCTGCCCTCAGCTCTGTCTTTGACCTCAGGTTTGGGCAGTATGACTGTCCCTGATGTTACAGGGAGCTGAGTATGAGGATCTCCTGTTATTTCAG
Seq C2 exon
GCAATGGTGAAGATCGAGGACATGGCCGTGTCCCTCATCCTGGAGGAATGGGGATGTCAGAACCTGGCTCGGAGGAATCTCAATAGGGACAGCAGGCAGATGAATTTGGGGAATGTGTTTTCCCAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000029729-Zkscan1:NM_133906:4
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.968 A=NA C2=0.535
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0135222=KRAB=WD(100=95.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTCTCCCTGCCACCCATGTTC
R:
AAACACATTCCCCAAATTCATCTGC
Band lengths:
212-506
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: