MmuINT0180855 @ mm10
Intron Retention
Gene
ENSMUSG00000050619 | Zscan29
Description
zinc finger SCAN domains 29 [Source:MGI Symbol;Acc:MGI:2139317]
Coordinates
chr2:121169199-121170268:-
Coord C1 exon
chr2:121169810-121170268
Coord A exon
chr2:121169404-121169809
Coord C2 exon
chr2:121169199-121169403
Length
406 bp
Sequences
Splice sites
5' ss Seq
TCGGTGAGG
5' ss Score
8.99
3' ss Seq
TAACGGGGGGTTATTTCTAGGTC
3' ss Score
5.15
Exon sequences
Seq C1 exon
AGCGCCATTTCTCTCTACTCTAGGATAAAACTCCTTTTTACAGAGAGACTCATCTGCAGGTGTTTCTCCAAGGGCATGCAAAGATAGTGTAATAAGTCCTAGAACCCAGACAGTGAGGAGAGAAACGGCTTTCTGCTGTGAAAGATGGCCAAACCCACTCGGAGAGGAAATGGCACAAGCTCTGAAAGCTTACGACAGCGCTTCAGAAGATTCCATTACCAGGAGGTGGCTGGGCCCCGGGAGGCTTTCAGCCAACTATGGGAACTTTGCTGTCGGTGGCTAAGGCCGGAGGTGCGGACCAAGGAGCAGATTGTAGAATTGTTGGTGCTAGAGCAATTCCTGACTGTGCTACCTGTGGAGATCCAGAACTGGGTACAGAAGCAATGTCCAGAAAATGGAGAGGAGGCGGTGACACTGGTGGAAGATTTAGAAAGAGAGTCTGGAAGACCTGGACATTCG
Seq A exon
GTGAGGAGGAGGGGGAATACAGTCAGAAGTGTGTGGCTGGGGAGAGACAAGGATGGAGGGGCAGTTTAAGATCAGTCGGATGTAAAGAGGTTTGGTGATTTTGATACTTCTGATCTGGAAGGGTTACTTTTTCAGGTAGGGCTTGCTTGGAGATGCCTACTCTGTTACAGTAAGTCTTTCACTTCAGTTTCTTAAGAGAAAAAATGGGGGAAGTTTCTTTTCCAGCTGCTATTTGGGTTTCTGTTTGATCTTTCTGCAGTTTCAACCACTCTAAGCTGATGATAACGGAATAAACACTTGTCTGTCCTACTCCCCACCCTCCACTCTGGCCTGGCCTCAGAGGATGGTCTCCCCCTGGGAATGCCCCTTGTTATGACCATGTCAATTAACGGGGGGTTATTTCTAG
Seq C2 exon
GTCACAGTCTCTGTGAAGGGGCAGGAAATGCACTCGGAGAAGATGACACCCCTGAAATCATCACAGGAGTTATTAAGTGTTCTGCAGGAGTCAGTGGAACCCCAGCCCAAGGGTGTATCCAAGAAAGAGAGGGCAAGAAGGCCAGCCCTGAGACTACAGGAGCAGATGAACCCAAAGGAGAATCTCAGACCTTTTCAAAGGAGCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000050619:ENSMUST00000110661:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.292 A=NA C2=0.768
Domain overlap (PFAM):
C1:
PF0202312=SCAN=PU(97.9=89.5)
A:
NA
C2:
PF0202312=SCAN=PD(0.1=0.0)
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:
ATGGGAACTTTGCTGTCGGTG
R:
GGCCTTCTTGCCCTCTCTTTC
Band lengths:
345-751
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