MmuINT0180851 @ mm10
Intron Retention
Gene
ENSMUSG00000037017 | Zscan21
Description
zinc finger and SCAN domain containing 21 [Source:MGI Symbol;Acc:MGI:99182]
Coordinates
chr5:138124978-138126646:+
Coord C1 exon
chr5:138124978-138125690
Coord A exon
chr5:138125691-138126453
Coord C2 exon
chr5:138126454-138126646
Length
763 bp
Sequences
Splice sites
5' ss Seq
CAGGTGGGC
5' ss Score
8.07
3' ss Seq
CCATTTCTTATTGTCTCTAGGTC
3' ss Score
9.87
Exon sequences
Seq C1 exon
GTTTGAAGAGTGGCACTTTAAGAACCAGAAACCCAAAGGTACCAGGTCTACTCCTAAAAGTCCTGCTGGCTCGGGAATCTGTGATGACTAAGGTGGTGGGCATGGCCACAGTTCTGGGCCCCAGGCCACCTCAGGAATCTATGGGACCTTCGCCCATTAAAGTAGAAGAGGATGAAGAGAAAGACAAGTGCTGCCCTACCCTAGAGCTATCCCATAAGCACTTCAGACAGTCTGGGAACCAAGATACCCTTGAGCCAATGGGTCCTTCGACCATTAAAGCTGAAGAGGATGAAAGCAAAGACAAGTGCCGCCCTAACCTAGAGATATCCCGTAAGAGCTTCAAGCAGTTTGGGTACCAAGACACTCTTGAGCAGTTGGGACCTTCGACCATTAAAGCTGAAGAGGATGATGAGAAGGATAAGGGCCACCCTAGCCCAGAGATATCTCGACAGCGCTTCAGGCAATTTGGGTACCATGACACTCCTGGGCCCCGAGAGGCACTGAGCCAGCTTCGGGTGCTCTGCTGTGAGTGGCTACAGCCCGAGATCCACACCAAAGAGCAGATTCTAGAGCTACTGGTTCTGGAGCAGTTCCTGACCATCCTGCCCCGAGAGCTCCAGACCTGGGTACAGCAGCACTGCCCTGAAAGTGCAGAGGAGGCCGTCACTCTCCTGGAAGACCTGGAGCAAGAACTTGATGAGCCAGGACTGCAG
Seq A exon
GTGGGCGGGAGGCCATCAGATGCTAGGAGACCGGGAATATAAAATCCTAGGCAGGAATTGAGGCTTGTCCTTCTGTTGTATGCAAATTGTCCATGGGGAGATACAAGACACACATCAACTCACCTCAGATAGGGAATCTATGGCAGACCGTACAGATACCACCAAAGTCCAACTTGGTAAACGTGGACTTTGATTGGGGTTTTATTTGGGTTGCTTACAGGAATATGGGTAGGTGATTACTTACAGGAGCAGAAATGGCTCAAAGACAGCTGCATCACCATAGCCCACCCCAGCATTTGTGACAGATCAGCTGGATACCTGGAGCATCCTCACTGCTCAACAGGGAGAGAGTTGGATAGTACTCTGTTTCAGGTGGCTCAACTAGTCTGCATCTCCTTTGCAGCTCTGTTTCTAGTCTCAGAGGAATTCTAGCTGTTATTGCTTCTTCTGGCAGGAAGGAGCCTAGTGAATCTGGTCAGTTTTAGGAACTTCCTGAAGCTAGTTTAAGTTGTTTACCTTTCTATAGGATGGAAGGCAGAAACTGTTATTCAACACTGTCCAACAAGATTAACCAACCAGACAGAAGTTTCTGGGGAGCTGGATATGTTTCTCCCTATTGTCTGCTCTTATCTTGAAATAACCTTGGGAACCAAGTGGGATGGGTGTTTTCCTTCCCTTCTAAAGGTTCTGCATAGCGCTCCTGAGATTTTTCTCATTCTTGAGTCAGCTGTGCACACACCTAGCCATTTCTTATTGTCTCTAG
Seq C2 exon
GTCTCATCTCCTCCAAATGAACAGAAGCAGTCTTGGGAGAAAATGTCAACTTCAGGAACGGCAATGGAGTCCTTAAGCAGTACTGAGACCCAACATGTGGATGCCAGCCCTAAATATGAGTTTTGGGGGCCCCTGTACATCCAAGAGACTGGTGAGGAGGAGGTTTTTACTCAGGATCCAAGAAAGCGCCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000037017:ENSMUST00000110961:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.661 A=NA C2=0.777
Domain overlap (PFAM):
C1:
PF0202312=SCAN=PU(97.9=44.8),PF034808=SBP_bac_7=PU(67.9=26.2)
A:
NA
C2:
PF0202312=SCAN=PD(0.1=0.0),PF034808=SBP_bac_7=PD(29.6=36.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
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:
GACAGCGCTTCAGGCAATTTG
R:
GCTTAAGGACTCCATTGCCGT
Band lengths:
344-1107
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