MmuINT0045837 @ mm9
Intron Retention
Gene
ENSMUSG00000013539 | D16H22S680E
Description
DNA segment, Chr 16, human D22S680E, expressed [Source:MGI Symbol;Acc:MGI:101825]
Coordinates
chr16:18300918-18302883:-
Coord C1 exon
chr16:18302779-18302883
Coord A exon
chr16:18301646-18302778
Coord C2 exon
chr16:18300918-18301645
Length
1133 bp
Sequences
Splice sites
5' ss Seq
CAGGTGATC
5' ss Score
4.28
3' ss Seq
TAAAGGATGCTTTCTTTCAGAAC
3' ss Score
5.66
Exon sequences
Seq C1 exon
ACAGCTGCCAGACCCAGCCATTGAGGACCAGGGCCAGGAGTATGTACAGCCAATTCTGAACAAGTATGCAGCTGTGTGTGTCCGCTGTGCCACCTATGGCACCAG
Seq A exon
GTGATCTGGATTGGGACTGCTGGGCACGTTCACTTCCTGTTGGGTATCCCCCACAATACAGCTGGCCATGGCTAGGTACCACCCCTGACTCAGTGCATTCCAGTGTCTCTTCAGACTTAACTGTAGGTTGATCAGATCCTTTAGGTAAGGTGCCCGTGCATAGGTCAGGTGGGTCAGAGCTCTGGCCTCCTGAAGCTGCCAATGTATCCTAGGTGGGGCTTCTGGCTGCCTCACCTGTTCATAGAAGCCAGAGATGGCATTTGGGATGTTTCTGCTGGCAGATATTGGTTGGCAGATGCCCTGGCACTGCTTTTCCAGAGCCTGTGATTTACATGCTGGATGGCAGCTATGAGCTGGTCTTTCCTTTGTGTGCCAGCTCTTTTGAAGGGCAGGAGCTTACACATGAGAACCTACTCAGGATGGGCTGGAAGGAACAAGCAAGGGAGCCAGCTGACTTAGCCTGGGCCCGTGGAGGAAGAAGGAGATACAGGAGAATTCTAGGTGAACAGACCATGCACCTCAAGTCGTTGAGAGCTCAACGTCTTGTTCTTGAACATTCAAACATGGCTAGGTATCTGGGGGCCTGGTGTACTGCCGGTGGGGTCAGATCTGGGACCACCCTGTAAGGAATGTGGTAAATTGGTATTTTTTTTTTTTTTGGCTTTTTGTTGTTGTTGTTTTGTTTTGGTTTTGGTTTTTTTTTTCTTTTTGTTTTTTCGAGAGAGAGTTTCTATATAGGCCTGGCCATCCAGGAACTTGCTATGTAGACCTGGCTGGCCTCCAACTCAGAGATTCACCTGCCTCTGCCTCCTGAATGCTGGGATTAAAGGAGTGCGCTACTACCACCCAACCTGTGAAATGGGTCTTGCTATAGAAAAAGGTCAGGCCAAGCTGAAGTGTTTTAGAGCAGCAGTAGTAGGACTCTCCCACTATGTGCTGGCCAAGGGCCCAGATGCCTCTGGTGAACCCCTCATGTCTTCAAACTTGAGGCTATTATTTTAATAGCCCACCTGATGCCAGAGCTGAGTAGCTAGCTCAGACCTTGGGTATGATGGGTACCCTTCCTACCTCAGGTCTGGTCCCAGCCATGATGCTAAAACACGGGGCTGGGGCTAAAGGATGCTTTCTTTCAG
Seq C2 exon
AACCAACACCATCATCCTTGTGGATGCAAATGGCCACGTGACCTTCACTGAACGGAGCATGCTGGACAAAGACACCTCTCGCTGGGAGACCAACACCTATGAGTTCACACTACAGAGTTAGCCCCTGCCAGGTTCCAAGGATGCTGTTCCTGAAGGGCCAGCGTGGACAGGAACCTTTCACGGCCACTCTGCAGGTCTGTGGCTCAGCCAGCACCCCTAGGACCAGGTTGTTCTGATTTGTGTCCTCATACTCAGCTCAGGGTCTCTCTTTGTACCAATGGAGAACGACAGAGTTAAATACTAGGCGTGAGTCAGGCCTGGGTATGCCGTATGTGAACACACAGACCTGTTTGTTGCTCAACCCCACTGCCACTGTGTGCACCTGACTGATGAGTAGGATCATGCCTCTCACCTCACACGTTTGGGCAGTGGGTCTCATCCATGGACGGGTAACAAAAGCAGACTCTTTACAGAAACTGGAGATCCTGTATTTGTTTGTGTTCATATGTGTTCGGTGGTTCTTCATATACGAGGACCCTGTGTGCATTTTCTCAGTCCTGTAGTGTGGACCCTGGGATCTCTTAGACCCCTGCTTGCCCAGGATTGTGGGTTCTGAGCAAGACATCTTCAACCAGTCCCGTCCATCTCCCATTGCCCTTGTTATGGTATACACCATAGGAATGTGAACTTGAATGTGCACAGTTGATAATAAATCTTTGAAGTTGTAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000013539-D16H22S680E:NM_138583:8
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.194 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF057427=NRDE=FE(12.9=100)
A:
NA
C2:
PF057427=NRDE=PD(12.9=85.4)
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:
ACCAGGGCCAGGAGTATGTAC
R:
ACCCTGAGCTGAGTATGAGGAC
Band lengths:
342-1475
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: