MmuINT0180328 @ mm9
Intron Retention
Gene
ENSMUSG00000029729 | Zkscan1
Description
zinc finger with KRAB and SCAN domains 1 [Source:MGI Symbol;Acc:MGI:1921820]
Coordinates
chr5:138534154-138535367:+
Coord C1 exon
chr5:138534154-138534660
Coord A exon
chr5:138534661-138535219
Coord C2 exon
chr5:138535220-138535367
Length
559 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAAA
5' ss Score
8.59
3' ss Seq
AAAACATTTTCTCCCCTCAGGTC
3' ss Score
11.03
Exon sequences
Seq C1 exon
TGGAGGAACCAATAGAAGACAGCTGCTAGGACAGAAACTGCAGCCTGACCCTGTTGGACCCCACCAGTTCACTGAGCCTGAATGATGACTGCTGAGTCAAGGGAAACCACAGGTCTATCCCCACAGGCTGCACAGGAGAAAGATGGTATAGTTATTGTGAAGGTAGAAGAAGAAGATGAAGAAGACCACATGTGGGGGCAGGACTCTAGCCTGCAGGAGACACCACCACCCGACCCAGAGGTATTCCGCCAACGGTTCAGGCGCTTCTGTTACCAGAACACTTTTGGGCCTCGAGAAGCTTTGAATCGACTAAAGGAACTTTGTCATCAGTGGCTCCGACCAGAAGTCAACAGCAAGGAACAGATCTTGGAGCTGTTGGTACTGGAGCAGTTCCTGTCCATCCTGCCCAAAGAGCTGCAAGTCTGGCTGCAGGAGTACCGGCCTGACAGTGGGGAAGAGGCCGTGACTCTTCTAGAAGACTTGGAACTTGATCTATCGGGACAGCAG
Seq A exon
GTAAAAAGAGATGACACCTGTGTGTGTAAGAAGGACACAGACTTAGGCTCAGAGGGGAGTGTGGGGAGTGTTTGGAACAGTTCTTGCCTATTGCTCTTCTGGGTTCTTTCAGAGTTCTGAGGGCTTGGCAATATAGCTCACTCTGTTCTAGAGCCGTGTGCATAGCATCTGTGAGGCTCAGGGTTCACTGGCTGACCATAGAAAGGATGTGTGTGGGGGGGTCCTCCTTTCAATATCCATTGGAATACTTAGAAGTTTTACTATTTCTAATTCCGCCAGGCATGGTGGCGCACGCCTTTAATCCCAGCACTTGGGAGGTAGAGGCAGGCGGATTTCTGAATTTGAGGCCAGCCTGGTCTACAGAGTGAGTTCCAGGACAGCCAGGACTGCACAGAGAAATCAAAAAAAAAAAAAAAAATTAATTCCTACTTTAAAAGTGATTTGCTGGACGAGACAGTGCTTCATGCCTCTAATCCTAGCACTTGACGTGCTAGAGCTGGAGGACTGTGAGTTCAAGGCCAATCAGAAGTTTTACCTAGAAAACATTTTCTCCCCTCAG
Seq C2 exon
GTCCCAGGTCAAGTTCATGGGCCTGAGATGCTTGCCAGGGGTGTGGTGCCTCTGGATCCAGTTCAGGAGTCCTCAAGCTTTGACCATCATGAAACTGCCCAGTCTCATTTCAAGCATTCATCTAGGAAGCCTCGTCTCTTATCCCGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000029729-Zkscan1:NM_029869:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.338 A=NA C2=0.876
Domain overlap (PFAM):
C1:
PF0202312=SCAN=PU(96.8=64.8)
A:
NA
C2:
PF0202312=SCAN=PD(1.1=2.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Conservation
Rat
(rn6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTTTTGGGCCTCGAGAAGCTT
R:
TGCTTGAAATGAGACTGGGCA
Band lengths:
343-902
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
Other AS DBs: