MmuINT0143084 @ mm9
Intron Retention
Gene
ENSMUSG00000028082 | Sh3d19
Description
SH3 domain protein D19 [Source:MGI Symbol;Acc:MGI:1350923]
Coordinates
chr3:85918709-85920799:+
Coord C1 exon
chr3:85918709-85918839
Coord A exon
chr3:85918840-85920740
Coord C2 exon
chr3:85920741-85920799
Length
1901 bp
Sequences
Splice sites
5' ss Seq
ATTGTAAGT
5' ss Score
8.54
3' ss Seq
CACAATTTTGTCTTTGCTAGGTT
3' ss Score
9.27
Exon sequences
Seq C1 exon
AGCAAGCTGACGATCTGAGTCTCACATCTGGAGAGATTGTTTATCTTCTCGAAAAAATAGATGCAGAGTGGTACAGAGGGAAATGTAGGAACCAGACTGGCGTGTTTCCTGCCAATTACGTCAAAGTCATT
Seq A exon
GTAAGTGGGTTTGTTTATTTTATTTGGCCACACATTCAGTGAGTCTCACACGCAGATGGGAAAGAGAAACTAGAAGCCTACAGTCTTGAATTTGCCTTTTCTGTCTTCTCTGGATCATTTGACACTTGGACATTTTTTAAGTGAATATTTTCTCACACAGACTGGCTCTGTCAGCATTCAGTTATGAAGGAGTAAGATCTCAGCAGTGACCCTGTTACTGCTGACCGATTGGCTATTGCCAGAGTTTGGGAGTGGAGGACTCACTGTCTTCCGTTAGGTACACATTGCTGGAACCACCATGCTCCAACGAAACAGTATCAGTTGTCAGTCACCCGTCCTCGGAGAGCTCTTCAGCACTTAAGAATGTGTGTTAGTGCTTGGAGACATTTAGTGAACATGAGTTAGTGCTACAGACAGTTTCGAAGGGATGCTCTTTGGGCGTGTGGCACCACGTCATTTTGAGAACCAGAACACCTGAGGGAGTAGTCCATTGTTTTCACATAATATTTTCAAGTCAGACTGGAGAAAATTATATTGAAGTGTCAAAATTGTATGGCCCTTAATAGCTTAACTTGTGAACACACTCCAGTATGCTGAAGGCTTTCCTGCTAAGCCTGAGTAGCTGTGAAACATAGGGACAAAACAAGACTGCTCTTTGAACACATGTATTAATAGGAAAAATATGATTCACTCCCTAATATAACCTATGGATACTATGAAATAGCACTAAAACTAACTTAAACGTTAACAGCTTATTTTGGAGGGGGAAAAAAAAACAATAATTTTCCATTACATCAGAAACTTTTAAAATCTAGGTATTACAGAAAATCTGTATTTTTCAAGTAGAAAGAGTCTGAGCCTCTTGGATTATGAAATGTAAGTCTTAAAAATATTGCCCAGTGCAGATGCGGCCTGGTCCTTCCCAGGCCTGCAGCCACGTTCTCTAAATTAATATTAAGAGTAATGTAAGTTTGAACACCCCTCCTCATTTCTCTTCTGCTCAGTGGAGCGGTGCTCTAAAAAGCACATTTCCCACACTGAAATCAATCACCCCCAGTCGGCCACATTATTGGTATAAATGTTATTCCTAAGCGCACAAGTTTAAAAAATTGTTTTAAAACACCAAACTTAGAGGATTTATCAGAAAGGGCACTGATCTGATACAGACCTCACAATCTTAAGTAGTTTTCAACTGCGTGGTTGTGGCTGAGGATTTCATCCCAACACAGCTTTCCTGGTTGCTTTCTACTAAGCAACCAGATGAAATGCCTGGCGCTTAGTAGACGGTCATTTAGCACAAATTGCCTTCTTCTTGCCCTGTGGATATGAAGAGGCAAAGTGCCCTTCAATTCATGGAGAGGATCCACCAGTCTGATCAAACGCTTCATTTGGGGACCAGGGAAGTGTTGCAGCATCCTGCCCTCCGTTTGAACAGGGCGACAGCATTACCGCCCACTGCCTGATGTCTGATGTCTTACACTCCTTGGATGAAGTGTAGAGAACTCTCAGGGATAGAATGTGTGATGTGCTCGTGGAAGCACGGAAGGCGAGAGGTAACTGGTTGATCAAGGAGGACTCCATCGAGAGCTAGTCTCCCTCCATGCCTTCTAGACAGGGGCTCACTGCTGTAGCCATGGCGAGCCTCTTTCTCATGATCCTCCTGCCTCAGCCTCCTGTGTGCTGATGTTACACAAGTATGTAACCACAACCCGCTGAATCTGTATATTTTTTCCAAAACCCCATTTTTGTTTTTTAGTGTTTAGCAACTGTAGCTCCAGTAACTTCAACAGCCAGCTTCACTGTTTAATTTTAGTCACGCATCTCCTAAGTACTTGATGTTAAATGTAGCTTAACCAAATTATGAGAAAAAGGAAGTGTTACCACAATTTTGTCTTTGCTAG
Seq C2 exon
GTTGATATTCCAGAAGGAAGAAGTGGAAAAAGAGAATCCTTTTCATCTCACTGTGCTAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000028082-Sh3d19:NM_001082414:9
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=0.200
Domain overlap (PFAM):
C1:
PF0001823=SH3_1=PD(80.4=84.1)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGCAAGCTGACGATCTGAGTC
R:
TTAGCACAGTGAGATGAAAAGGA
Band lengths:
190-2091
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: