MmuINT0110267 @ mm10
Intron Retention
Gene
ENSMUSG00000040998 | Npnt
Description
nephronectin [Source:MGI Symbol;Acc:MGI:2148811]
Coordinates
chr3:132906695-132908462:-
Coord C1 exon
chr3:132908343-132908462
Coord A exon
chr3:132906830-132908342
Coord C2 exon
chr3:132906695-132906829
Length
1513 bp
Sequences
Splice sites
5' ss Seq
TGGGTGAGT
5' ss Score
8.73
3' ss Seq
TGATTAACATGTGTTTCTAGATA
3' ss Score
7.39
Exon sequences
Seq C1 exon
GTGCCCTATCGTGTTCCATGGCAAACTGTCAGTATGGCTGTGACGTGGTCAAAGGACAGGTCCGATGTCAGTGTCCATCCCCTGGCCTGCAGCTAGCTCCCGATGGGAGGACCTGTGTGG
Seq A exon
GTGAGTGCACTCGGGAAGCATTCTGAGGAGATGCTGTGGGGTGAGGAAGGCAGCCAAAGGGATAAGGAAGAAGGCAGTTACTTAGTCAGGCGTGTAGCTGCCTTCCTGGAGATATCTGGTATTTTAGACGAGGATTCCTGTGAATGGACCAACACAATCTTATTTTTGAAATCCGAAGGTCAGGAAGAAGCATGAGACAGAGGAAACCATCCAAATGTGCAAAAACCCTGCAGGAAACAGAGCACTGGGTTCAGGAAAACTGGATCTCAGTTTCTGTAGCCCAGAGGGAAGAGAGCAATGGAGCTGAGCAGGTCACCAAGGCTACGGCATTACATGGGTTGCATCACGCATCACAGGGCATAGCATTTTCCCACAACATTGAGATGGCAGTTTAGATCATGGCAGAGTTTGGACTCTCTCAACCTGGCTGAGCTGCAGACTAGCTATGCAACCTTAGTTAGGAAAAGAACTTCTTTTCTTTGAGCTTGGGCCTCCCTTTCTTTAGAATGTGATTAACACAAGACCATTGCAAGTGGCGAGTGAGCTCATGTGTTCCAAAAGTTCAAAAGAGCTCAGTAGAGTCTCCTGCAAGGAGCTAGTCACTAATTAAGAGCCATTTACTAAGCAGCTGCTGTATTCAAGACACTGTGCTATGCTGGCTGCATAGCCTCGGGCAAAGCTCATGAGGTTTTGGTCCTTAAAGAAGTGACTTCCTACCGGGGAAGACAGAACGTTAATAATACTCAATAAAATTACTGGCCCTGCCAAGTGCTAGCAGAAGATCGTAAGAGAAACAAAAGGGCCTGTCTTAGAAAATCATCCATAGGGGATTCCTAAAGTTAGACCTGGGCCATTAGCTACAGAAAGAACATGCCAAGGGACTGGAAAGGCAACTGGCTAAGAGCACACGGGCTAATCTTCCAGGATTCCCAGTACTCACAATGCAGCTTACAACCATCTGTAACTTCAGTCCCAGGGCATCCAACTGTCTCTGGCTTCCATAGGCATGGGCGATGCACATGGTACACACATCTACATGCAGTCAAAACAGTATACATAGAAAATAAAATTTAAAATAAATTTAAAGAGCCTGTAGAGAGGTGAAATGACTGGAGGAGATAAGATTGGCAGTCCAATTTCCAGACTTCTTTGTCTCAGTCTAAAGCGAGGGATGCTGGGTAGGAATGAGGTGGTTGACAGTGCTAGGCAGGTTCCAGCAGTCTTTTAGAAGTAGAAATAACAGGATTTGGTGGTGGTTTAGGAGTTGTAAGCGAAAGGTTTAGCGTGCATGCTTAGTTGAAGCAACTAAGTAGATGGTGTCGTATCTACTGCTGTTGGTTGTGAGCGCAGAAGAATTCAGTTTAAGAGGATGAGGGGAAACCTGGAGATGTGCAATTTTTTGTTTTGGGGATGTTTCGATGTGGAGTGTGATGCCAGGGTAACCAGGGGGATACCAGTTATAACAGGCTCCCATCTTTGCTCTTTCTAAGACGTGATTAACATGTGTTTCTAG
Seq C2 exon
ATATTGATGAATGTGCGACTGGAAGAGTCTCCTGCCCTCGATTTAGGCAGTGTGTCAACACGTTTGGGAGCTACATCTGCAAGTGTCACACTGGTTTCGACCTCATGTACATTGGAGGCAAATATCAGTGCCATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000040998:ENSMUST00000042744:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0764510=EGF_CA=PD(18.0=22.0),PF146701=FXa_inhibition=PD(92.7=92.7),PF0764510=EGF_CA=PU(0.1=0.0)
A:
NA
C2:
PF0764510=EGF_CA=WD(100=95.7),PF0764510=EGF_CA=PU(0.1=0.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTGCCCTATCGTGTTCCATGG
R:
GCACTGATATTTGCCTCCAATGT
Band lengths:
251-1764
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