MmuINT0118691 @ mm10
Intron Retention
Gene
ENSMUSG00000037791 | Phf12
Description
PHD finger protein 12 [Source:MGI Symbol;Acc:MGI:1924057]
Coordinates
chr11:78028843-78030539:+
Coord C1 exon
chr11:78028843-78028981
Coord A exon
chr11:78028982-78029316
Coord C2 exon
chr11:78029317-78030539
Length
335 bp
Sequences
Splice sites
5' ss Seq
TCAGTAAGT
5' ss Score
9.14
3' ss Seq
ATCATGCCCCTTTTTCCCAGGGC
3' ss Score
8.2
Exon sequences
Seq C1 exon
AATACCAAACATTATGAGCTGTTAAACTACAGTGAGCATGGGACAACGGTGGACAATGTGCTGTATTCATGTGACTTCTCTGAGAAGACCCCGCCAACCCCCCCAAGCAGTATTGTTGCCAAAGTACAGAGTGTCATCA
Seq A exon
GTAAGTTGGAGCAGAGGCCTGTGGCCACACAGCTAAGGCCCCCCGTCACCTTGGTTCTACCATGCTGTCAGTGACCTACAGTTTCTTGCCTTCCCAGTCCCCTTGGCCAAGCTCATTGATGGTGGGCCTGGAAAAAGCCACCGAAAATCAAGTGCTGAACACCCACATATGTATCAGACCTGGGCAGGGACTTGAGACTCCAGCCCCGTCTGAGCATCCTCAGCCCTGATCATGTAGCATAGAATGGGGAGACGCAGGGGGCCAGTACTGCCAGTCACCCCAGACAGGTCAGCCATTCACTCTTCCCCTCCTATGATCATGCCCCTTTTTCCCAG
Seq C2 exon
GGCGCCGCCGACACCAGAAACAGGATGAAGAGCCAAGTGAGGAGGCAGCCATGATGAGTTCCCAGGCCCAGGGGCCACAGCGGAGACCCTGCAATTGCAAAGCCAGCAGCTCAAGCTTGATTGGGGGCAGTGGGGCCGGCTGGGAGGGCACAGCCTTACTCCACCATGGCAGCTACATCAAGCTGGGCTGCCTGCAGTTTGTCTTCAGCATCACTGAGTTTGCGACCAAACAGCCCAAAGGCGATGCCAGCCTGCTGCAGGATGGGGTCTTGGCTGAGAAACTCTCTCTCAAGCCCCATCAGGGCCCTGTGCTGCGCTCCAACTCCGTTCCCTAGGCCATTGGCCTGGACGCCCACCCAAGACTCCTGCAATGCAAAAATGTACACGAACCAAGCCTGGGTGTTTTCTATACCAGAAACCCTCAACTACAATCTTTGCATGAAATGAAGAAAACCTTTTGACTGTTTTTTAAGACTTTTTTTCTTTTCTCAAGTTCTAGGGGGCATTTGCACATATATTTGTACTCAACATTTCATGGGAAAGCGGCAGATCCGCGCTGAGGAGCAGCGAGGGCAGGGACAGGAGGCCCTGGTCTGGACACTTCCTCCAGCACAATCCCTTCCCCCGCCTCCTGCTCCTCCCCCTCGACCGCCTGCCCACTGTTGTAAAATAATCAGAAACTTGTTCTATTTTGTGGCAGTGACAATAGTTTTATATTAAAAGAAAAAAATACAGTTTTCATACAGCAAAATCTATACAATATCATTGTTTTATTTAATATAAAGATCGCTACCCACTCCTTTCCATGGTTCCCACCCTACAAGGACTTCCCCTCTCTGCAGCAGTTGCACTACAGGTAGCTACTGTGTATATGGACAAATGAGAAATGAATCCTTTTTTCTGGCTGTCCATCTATTTTATTTCAAATAAGGAAAAGTGTATTTGGATTTTGTGTAAATACATCTAGTGATGGCATTTTTTCAATGTTTTTAAAAGCTGTGTACAGTACATGTGGTAGAGTGTTTCTCAAATTGTCTATTGTAGCAAAGGCGTTTTTGTCGTAAACCTGTTCTGTGTCCTTTTTTGTTCTTACCACTTCTCTTCCTCCTCACCCCAGATACTTCCTCTTCCCCACAACCAATGTACATAGTAATTGTAATGTTTTAGACTTGACAGAAACTTTCCTGTATTCTGTATATAAAAACCAAAAATACTTCAAATTA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000037791:ENSMUST00000049167:14
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.170 A=NA C2=0.351
Domain overlap (PFAM):
C1:
PF0049821=FHA=PD(47.7=66.0)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCCCAAGCAGTATTGTTGCCA
R:
CCTGATGGGGCTTGAGAGAGA
Band lengths:
342-677
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