MmuINT0180846 @ mm9
Intron Retention
Gene
ENSMUSG00000061894 | Zscan20
Description
zinc finger and SCAN domains 20 [Source:MGI Symbol;Acc:MGI:2679268]
Coordinates
chr4:128265260-128267385:-
Coord C1 exon
chr4:128266696-128267385
Coord A exon
chr4:128265689-128266695
Coord C2 exon
chr4:128265260-128265688
Length
1007 bp
Sequences
Splice sites
5' ss Seq
TTGGTAAGA
5' ss Score
8.85
3' ss Seq
GAACTCTTCACTTCTGACAGCAG
3' ss Score
4.12
Exon sequences
Seq C1 exon
GAGTTCCAGCTTCAAAGCCAAGTGCCACCTCCCAGCAAGAGCAAGGACCGGAGATTTGGGGTCTGAGCCTTATAAATTCTGGGAATGGGAGTGCTGCAGACGATAGCCTGGACAGTGCGCAAGACAAGCCAGTGCAGGCAGTGGCCCAGGCAGACTCAAGGGCCTGGGGAGAGCCGTGCCAATGGGGTGCGGAGGACATGAAGGTGTCAGGTGTTCACTGGGGCTATGAGGAAACCAAGACTTTCCTGGCCATCTTAAGTGAGTCTCCTTTCTCTGAAAAGCTCCAGACCTGTCACCAGAACCGCCAGGTATACCGGGCTATCGCAGAGCGACTGAGGGCACGGGGCTTCTTGCGGACTCTGGAGCAGTGTCGCTACAGGGTCAAAAACCTTCTCCGGAACTACCGGAAAGCCAAGAACAGCCATCCGCCAGGGACCTGCCCCTTCTATGAGGAGCTGGAGGCCCTTGTGAGGGCTCGGACAGCCATCAGAAGAACCTCAGGTGGGCCAGGAGAGGCAGTGGCACTCCCCAGGCTGGGTGACAGCGACACTGAGATGGATGACCAAGACGAAGGGAGCTGGGAGCCCGAGGAGACCGTGGAAGACTGCAGTGGTTCTGGCCTGGCCGCCGAGGAGTCTCTTCAGGGGCCCAGGATTGCAGGGGGCCCAGCTCTGCTCCAGAGCCGTATTG
Seq A exon
GTAAGAACATGGCATTTAACTAGATGAATATCAGCCAGGCTGCTGCCTCGTGAGGTTAGAGCTCAGCCTGTGAGTCAGTAAGACGCCAAGTACCTGGGCCCTCCTCAGACTCACTCTTCTCTGCACCACGTCTCTTAGTTATAGGAGCAAATAACTCTGAAGCCTTGCCAGACCGGGAGAGATTCCAGTTGCTTCCAAAGGGTGTCGCTGAGGACACTCCGAGGTGGTACCCGAGTGATCTTGTCATTTCCGTAGGCGTGTTTCTCATAATGCGGGTGAGAATGGCCAATTAATTCACAGATAGCAAGTCTTGGGTAAGAAAGTGTGTGAAATACTGGCGTATAGAGAAGAAAGTGACAGTGTAGCCTTGAGAGTCACTATGTGGCAAACACCTGATACTGCAAAGGGAAAGTCTGTGACAGCCATCTGAGGCTTTGGAAGCCACATTGGCAGGAACAGAGCCTGGTCTCCTGCCTGGAGTTCATGTAGCCCCTCCCCCACTCCACCTCCTTGGGTTATGCCGCTTACCCGAATGGAGACTAAACTGTGGCCCTGCCCGTGGACCAGTGAGGAAAGCTTTTCCTTAGTCATAGTCTGTGCCCTGGTCACTGAAGTCCATTGATGTCTCTGATCCTTGTGGATTCTCAGGTTCCAAATATTGTTGAAGAGAGGATTCACAAAGGAGACAGGGGATGCGTTTAGAGTGACTGCAGGGAGAATGTCATGGATGATACCATTTGTCAGCTGAAGCCACGGGGTGGGTCACTTGATGCAGTTGCTAAAAGCATGGCCAGTCGGCCTCTCCTTCAGCAAGACTGTCTCTTGAAATGGTGAGAGAGGATGCCTTGGCCGGCTTCCCTAGCATGTCTCTTGAGTTTGTGTTGCCAGGTGCTTGGACAGTCTCTGAGATCTGTGTTCTGGATCTGTAGAAGTGCAGGTGACCCCAGTCCTAATGACCTAGGTAAAGCTCCTAAGCCTCACATGTCTGAACTCTTCACTTCTGACAG
Seq C2 exon
CAGGCGTGCACTGGGGCTTCGAAGAGACCAAGGTCTTTCTGGCAATTCTCAGTGAGTCCCCCTTCGCCGAAAAGCTTCGCACCTGTCACCAAAACAGCCAGATATACCGGGCCATCGCTGAACGGCTGCGTGCGCTGGGTTTCCTGCGGACGCTGGAACAATGCCGCTACCGATTCAAGAACCTTCTTCGAAGCTACAGGAAAGCCAAGAGCAGCTGTCCACCAGGAACCTGCCCGTTCTATGAGGAGATGGACTCACTGATGAGGGCTCGGACTGTGATCAGAGCCGTGGAGATGGTAGGAGAAGCCACAGGCCTCCCTGGATCTGGGCAGAGCAGTACTGAGGCTGATGACCAAGAGGCCTGGGGTGAGATGGAAGATGAGGACGCCGTTAGACTTCTGACTCCAGACTCCCAGCCTGCAGATGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000061894-Zscan20:NM_177758:6
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.408 A=NA C2=0.271
Domain overlap (PFAM):
C1:
PF138371=Myb_DNA-bind_4=WD(100=37.2)
A:
NA
C2:
PF138371=Myb_DNA-bind_4=WD(100=59.7)
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:
TTCTATGAGGAGCTGGAGGCC
R:
CTGGCTGTTTTGGTGACAGGT
Band lengths:
348-1355
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: