MmuINT0178711 @ mm10
Intron Retention
Gene
ENSMUSG00000063894 | Zkscan8
Description
zinc finger with KRAB and SCAN domains 8 [Source:MGI Symbol;Acc:MGI:1913815]
Coordinates
chr13:21525138-21527021:-
Coord C1 exon
chr13:21526519-21527021
Coord A exon
chr13:21525307-21526518
Coord C2 exon
chr13:21525138-21525306
Length
1212 bp
Sequences
Splice sites
5' ss Seq
CCAGTAAGT
5' ss Score
9.09
3' ss Seq
TGCTGTCCCATTGTTTCTAGGTC
3' ss Score
9.93
Exon sequences
Seq C1 exon
AAGTGCCCTGGAGGTTCTTGGAAGACTTGTAAGAAGATACAGAAGGTAGAGGAAAGAGATCTTCTGAGCTTTACTGGCCCTAAATGGCTACAGAACCAAGAAAGCCTTCTTCAGCCCCATCTCCACCAGACCAGGCTCCTGAAGAGGATCTTGTCATTGTCAAGATAGAGGAGGATCATGGTTGGGATGAGGAATCCGGTGTGCATGAGAACAACACACCTGGCCAAGAACTGTTTCGTCTACGCTTCAGACAGCTCTGCTACCAGGAGACATTAGGACCTCGGGAAGCTCTGATCCAGCTCCGTGCATTTTGCCATCAGTGGCTGCGGCCAGACTTGAACAGCAAGGAGCAGATCCTGGAGCTGCTGGTGCTGGAGCAGTTCCTGACCATCCTGCCAGGGGAGCTGCAGGCTCTGGTTAAGGAGCACCAGTTACAGAATGGAGAGGAGGTGGTAACCCTATTGGAGGACCTGGAAAGGCAAATTAATGTCCTAGGGCGGCCA
Seq A exon
GTAAGTAGCTGTGCATGCTGTGACTGAATTCCTGAAAGCTTTGTAGAAAGACATTGGCTTCACTTTGAGGAATAAATTCTATTCACTGGTTTCTTGTAAATGCAGATGAAAATTTTAATTTTGTAAAAGGTAGAATCCATTTTCATCCTCCTAAGATCCATCCCACACTTGTATTATTGTCCTTGCTTACTATATGGGACCATAATACACAAGGAGCTTATATTACTTTTTTTCTGGGGTACCTGTAACACAAACAGTCAGGGTTTGGGCCAGATATTTCTACATCTTTGGCCTCTTATTCAAGGAATTGGAACAAAGACCCACACAAATTGTACAGATAGCAAGGAAATGTTATTCAATGGCAGAACAATGGTACAAAGTAAGAAATACAATCAAGAGTCCTAGGCTACTCAAGTGAAACTACTCAAGTACTCTAGGGCCTCAATTATTTGGGGCTTCTTCTGGGGTTCAAGAGAAAAGGGAATTTGTTTGCTAGTAGGCATGATGAAGATGAATCTTTGTTTTCTTGGAGGATACAATTTGTCTTATTGGCTCATGCACCCAAAATCAGTCTAGGCCTGTTTGACCCCTACCTTCCTTACCCAGAAGTAACTGGAATGTGATTGGGTACAAGCTTTCTAAATGTCATGGTTGTTAGAGGGAGGAGAGATTTATTCCCTTGTTCTGAGTAGGGTGTAGGTACAGCTCAAAGCAGGTGAGGTCCTATATCACTAGCAGGTGCTAGGTGCATTGTTCAGAGAGCAAGGATGGGGGACAGGTCTTAATAGGAAGCGAGTAAGCAAAGCCCAGCTTGCCTTGCCTGGATAATGAAAGATGACTACTTCCTAGAATATGAGCTTCCTAGGGTTGTTTTGTTTTTGTTTTTGCTTCCTAGTTTCTTATCAGAAGAATATTTTGCTATTGTGTGACCCTATTTTAGTTTTGTGGGTTATTCATCCTAAGTTAGAGTTCTGAATCCTAATATTGGTGTTTGATATAGTAGAGAAATATCAACAGAAATTGTTTCTTTAGTACTAAACCGAAACAAATACCTTCTTTCTGTACTAATTTCTTGCTGCCCTAGGAAGTAAATGACATAATATTGCTTGCTTTCCCAAATATGAACACCCATGAAAGGCGTTGACTCCACTACCACCTTCACTTCATTTCTCAAAGGAACTCTGTGTAACTCTGCTGTCCCATTGTTTCTAG
Seq C2 exon
GTCTCAACTCATACACATGGGCACAGAGTACTCTGGGATGAAGTCATACCTTCAAAATCTGCATCAGAACCTCCAAGTATTCACGTACAATCCTTGGCCACCGTGCCCAAATCTCCAGTGCCCCAGAAACCACAGGACAGGGGAAAGAGGCCAGATTTCACTTACAACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000063894:ENSMUST00000045228:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.307 A=NA C2=0.649
Domain overlap (PFAM):
C1:
PF0202312=SCAN=PU(97.9=67.1)
A:
NA
C2:
PF0202312=SCAN=PD(0.1=0.0)
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:
CCGTGCATTTTGCCATCAGTG
R:
TTCCCCTGTCCTGTGGTTTCT
Band lengths:
347-1559
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