MmuINT0179457 @ mm10
Intron Retention
Gene
ENSMUSG00000045519 | Zfp560
Description
zinc finger protein 560 [Source:MGI Symbol;Acc:MGI:1915280]
Coordinates
chr9:20352753-20354249:-
Coord C1 exon
chr9:20354064-20354249
Coord A exon
chr9:20352842-20354063
Coord C2 exon
chr9:20352753-20352841
Length
1222 bp
Sequences
Splice sites
5' ss Seq
ATGGTAAGT
5' ss Score
11.01
3' ss Seq
CAGTTTCTTTTTCTTACTAGGTT
3' ss Score
8.59
Exon sequences
Seq C1 exon
ATAATATTTGATGATGAGTGATCCGTGTCCTCAAGAATGCAAGTAACACTGTAGAGAGAGGAAAGATCACCAGTGGCCACTTATGCGTATAAACTGCCAGGACGTGTCCTTCAAGTTCTGGAAGAGAGTGCTCCAGTGCATTTCACCATCATCTTCACAGGATGGAAGCTATCAGTTTGTCCTATG
Seq A exon
GTAAGTCTTGCTTATGCATTGTGGATTCCTTGTACCGACAGAAGTGTTGGTGCTCTTGGCTTGAACAGCCATGCTTCCAGTTCAGGGGTGCTTCTGTCATTTGAATATGAAATTACCCCAATGACTTACTGGCACCCTTAGTTCCCCGCTTATTGTACTGTTTGGAAAGGTTGTAGAACTTTCAGGAGGTGGAGCTTTGCTGGAGGAAGTGGCTCAGTGTTAGGTGGGCCTTGAGGTTTTATAGGCCAGTCTTACTTCCTGGTTCATTCTGTTTCCTGACTGCTGATGCGGTGCAGTCAGCCAACCTCTCCACCCCTGCTGCCATGCCTTCCCCTATAGAGAGAGTTGAAGATCACCATCAGCCACTTATGTGTATAAACTGTCTAGACGTGTTCTTCAAATTCTGGAAGAGAGTATTGCAGTACATTTCAAGGATTATATCCTCTGAACTATAAGCTGTAATAGGCTCTCTCTTAAGTTGTTTCTGTTTTATCTTTTAAAAGATTTATCCATTTTATTATTTTCTATATGTGTTTTGCCTGCATGTATGCCTATGGACCACATTTGTGCTTGGTGCCTGTGGAGATCATAAAAGGGCATTAGATCTGGAACTTGAGTTCTGGATGGTTGTAAACTACTGTGTAGGTGCTAGGAGCCAAACACAGGTCCTCTACAAGAGCAACAAGTGCTCTTAACAACTGAGCCATCTCTCTAGCCCCCAAAGTTACTCCTTGGTAAGTATTCTTTTATCATAGCAATGAGAAAAATAACTAATACAGATGCTGAAATTGGCAAAAGTTGCTGAAGTTGTCTGTTTTATAAACCAGCTTGCTGATATGTGTTCTTTGGTCATAGGTTCATGAGTTTTTCCACCATGGGCAGGTAATAGGCCATGTTTCTAGGCTTACTAGTCTTTACCTGTAAATGAGACCGATACTCTGGTCTTCACAGGCAGTGTGGCTCACCATTCTTTTTTCTGAATTTGATTGCTCTGGCACTGTGTGTTAGTCTTGTATACATGTAAAATGAGGTGGAGGGAGGGTAAGACAGGGAGGGAGGGAGGGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGCACTTGATTTCCTATGTTGGACTATATGGGAATTTTGACCAAGGATAGAGTGACATCCATGTATGTAAATGTGAGAATTATAGCTAACTCCAGTTTCTTTTTCTTACTAG
Seq C2 exon
GTTTATTTTCTAGGAACCCAAGCTACTTTCATAATGAAAAAACAGAGATGGAAAAGACGGTGTCTGACTGCTGGACAAGTAGTTACCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000045519:ENSMUST00000068079:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
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:
ATTTGATGATGAGTGATCCGTGTCC
R:
CTGGTAACTACTTGTCCAGCAGT
Band lengths:
270-1492
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