MmuINT0179175 @ mm9
Intron Retention
Gene
ENSMUSG00000062519 | Zfp398
Description
zinc finger protein 398 [Source:MGI Symbol;Acc:MGI:1917856]
Coordinates
chr6:47808928-47809531:+
Coord C1 exon
chr6:47808928-47809054
Coord A exon
chr6:47809055-47809417
Coord C2 exon
chr6:47809418-47809531
Length
363 bp
Sequences
Splice sites
5' ss Seq
TGGGTGAGG
5' ss Score
6.74
3' ss Seq
TTCCACTTTTCCTCTTCTAGATT
3' ss Score
11
Exon sequences
Seq C1 exon
GTGCCTGTGGCCTTCGATGACGTCTCCATCTACTTTTCCACCCCAGAGTGGGAAAAATTAGAAGAATGGCAAAAGGAACTTTACAAGAATATCATGAAGGGCAACTACGAGTCTCTCATCTCCATGG
Seq A exon
GTGAGGCTGAGTGAGCACCTATTGAATGAGGTGCCACAGTCCCATGAGGACTCAAACACTTTCTTTTTTCCCCCAGTGTCCTCATTCTCGCTGTTCTCATACACTGTAGAATCTGGTTTCAAGCTGAAGAAGGACAGAACTAACTTATTATGTGCATTTCCTATACATTCCATTTCTTTTACCTGCTTCCTTGAGTAGCTGTTGTAAATAGTTGGAAGTGGATAGATGGTAAGAAGTGATGCAGGATCTAAAAGAAATTAATACCCTGACTGTGGACCTCAAACATTCAGCTGCCTTGAGGGCAGGTGTTGTCATACTCATTTATCTCTTTGTCATGCCTGCTTTCCACTTTTCCTCTTCTAG
Seq C2 exon
ATTATGCCATGAATCAACCTGATGTTTTATCTCAGATTCAACCAGAAGGAGAACACAGTACAGATGACCAGCCAAGGCCAGAAGCAAGTGAGATTCCTGCAGACCCCAGTGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000062519-Zfp398:NM_027477:3
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.821
Domain overlap (PFAM):
C1:
PF0135222=KRAB=WD(100=95.3)
A:
NA
C2:
PF0135222=KRAB=PD(0.1=0.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCCTGTGGCCTTCGATGAC
R:
TTCACTGGGGTCTGCAGGAAT
Band lengths:
238-601
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: