MmuINT0075929 @ mm10
Intron Retention
Gene
ENSMUSG00000030606 | Hapln3
Description
hyaluronan and proteoglycan link protein 3 [Source:MGI Symbol;Acc:MGI:1914916]
Coordinates
chr7:79115102-79118151:-
Coord C1 exon
chr7:79117849-79118151
Coord A exon
chr7:79117494-79117848
Coord C2 exon
chr7:79115102-79117493
Length
355 bp
Sequences
Splice sites
5' ss Seq
AGGGTGAGT
5' ss Score
9.25
3' ss Seq
GATGGTCCACATTCCCACAGGGC
3' ss Score
8.56
Exon sequences
Seq C1 exon
GTGTGGTTTTTCCCTACCAGTCCCGCGAAGGGCGCTACCAGCTCAACTTCCACGAGGCCCAACAGGCCTGCCAGGAGCAGGGTGCTATGGTAGCCACTTTTGAGCAGCTTTTCCGAGCCTGGGAGGAAGGCCTAGACTGGTGCAATGCAGGCTGGCTGCAGGATGCCTCCGTGCAGTACCCAATAGTGCTGCCCCGGCAGCCCTGTGGAGGCCTGGGTCTGGCACCTGGTGTTCGCAGCTATGGCCAGCGCCACCACCGCCTGCATCGTTATGATGTGTTCTGCTTTGCTGCTGCCCTCAAGG
Seq A exon
GTGAGTGAAATGGCCAGGCACAGGTCTGCCCTGCTTGGTGGTTACCTGAGGGAGGGCCTGTGGAGCCTTGGCTACTTGGTTTAAAAAGCATCTGCTGGCATGTGGTAGGTGCTCAGTAAAAGTCAGGTGAGCGACTGGTTCAGCCTGGGTGGGTGCTCACTCAGAATGCAATTGGGGCATACAGAAATGACTAGAGCAACCCCAGCCCTATGGCAGTATGGTAGTGGGATGAGGCCTGTACAGGTGGCCCTTCAAAGTGTCTAATACAGATTCCCATAAGGCAATTTCTCCCTGCCATGGCAGGCTCTTTCCCTTTCTATGCTGGATAGCACTTAGATGGTCCACATTCCCACAG
Seq C2 exon
GGCGGGTGTACTACCTGGAGAACCCCAAGAAGCTGACGCTGCTGGAGGCCCGGGAGGCCTGTCAGGAAGATGGTGCACAGATCTCCACGGTGGGCCAGCTCTTTGCGGCTTGGAAGTTCCGTGGCCTGGATCGTTGTGATGCTGGCTGGCTGGCAGACGGAAGTGCCCGCTACCCTATAGTTCACCCTCGACTCAACTGTGGCCCCCCTGAGCCTGGAGTACGGACCTTTGGCTTCCCAGACCCCCACACCCGCTATGGTGTCTACTGCTATGTCCAGCATTAGCAGGGTGGCTAGCTGTACATCTGCTCTGCCCCTGACTTCCTGGGCTGAGTGTTTATCAGGTGGACCATTGTCCCTTGTGGGTTGGGGGATTGCTTGGATAGTTTTTATACTTCCCAACTTAAACATTTAAAGGTATTATTATTATGATTATTATTTAAAAGTATTATTATTATTTTATTTTACAGACCCAACTCTTAATTCTCCTGGCATCCTTCTCTGGGGCACTTGGGGTCCATTGGCTTAAAAAGGCTCTGCCATGTTCTGGTACAGCTGCCATCCCTACTTGAGGAAACTGGCACTCACAATGGGCAATAGCTATGACTAGCTCCCTTTCCTCAGCTTATACGTGGCAAAGGCTGAGTGTTGACTCTTTACATTTCTGCACAGGGTCCTCAGACTTGTGGGGGGGACTTAGGCAAGGGAGAATTTCCCTTCTTCTCCTGGTTCCAAAGAGTCTAGGTCTCCTCCCCATGTCCCCTGCTTAGCAGTGACTCTCTGGCTGTGTGTACCTTATTTGGCCAACAAAGGATGCTATGATTCCCTTCCTTCCTTTCCAACTGATCCCTGTATCTGACCCTTTGTCTCCTTCAGTCTCAGGGACTAGGGATCCCAGCCCTGGGTAAGCATGGAATAACTCCTGTCCTCCATCTTCCACTGGGCTGCCCCTGCATGCTGGTTTGGTTTGACCTTGTCTAACCTACAGCATCCCTGCCTCATGTTGCTGGTTAGCCACTGGGGATCTGGTTCCCTTCTTCACCATCTCCACCCCAGGATGGCCCAGCTGTGAGGGCCTTAGGAGAAGAGTAGGAGGTGCCTTTCATGAAACAGGGGCTCCTGTGCTTTCTAAAGGGTCTCAGAGGCTGAGGACCAGGGAGTGTCTTTGTTCCTCACCCTAACAATGCTTCAGGGAACCAGAGCTGTATTTCATCCAGTTGTCTCCTGGTGCTTAGCAATCAGGTGTTTAGTCAGTTTTTCTTTTCTTTAAAAAAAAATGTGTGTGTGCACGTGTGTGTGTGTGTCTTTGTGTGTATATGTATGTGTCTCTGTATGTGTATGTATATGTGTGTCTCTTTGTGTATGTGTGTCTCTGTGTGTGTATGTGTGCATATGTTTGTGTGTATGGGCAAGTGTGTATAGAAGCCTGCAGAGGTCAGTTAGGGCACTTGATCCCCTGGAACTAGAATTATGTATGGGTTGTGAGCCACCTGACATGGATGCTCTGCAGGAACACCAAGCCCTCTTAACCCCTTAGCCATCTAAGTCAACCCCAACCTCCTAAGATGGCTTCCTTTTGGAGGAAGGGAGATGAGCAGGGATTGAGACAGTCTCACATAACCAGAGCTGGTCTTGAGCTTTCTGTATAGCTGAGGATGGCCTTAGACTCCAATCCTCTTGTTCCCCAGTGCTGGGACTACATCTATGGCACCATCACACATGACTAACAGCCTCTGGGAATGTGTTAAAAATTCAAGTTCCCCTGCCTCACTCCAGTGTGTTGTCCCAGCCCTTCAGGTGACATGCTACCCTGTTTTGCTAGTGGAGATGGAACCCAAGGTCTTACATGTCTGTTAGTCAGGTGCTCGTACACCAAGTATTCAGGCTATCTCATCATGCAAGTAGCTGGGATTGTAGGCTATGCTACCAAGTCTGGTGCATTTAGTCTCTCTTGAGTGCTTCTTTTGTTGTTTCGAGACAGGGTCCTACTATGTAGCCCAGGCTGGCTCCTGTCTCAGCTCACTGAGACATCATGCCTTGTCTTAAGTTCCCATTGAGCCCACCTGCAAAGCTGCACTCAGAACCACAGAATGGCACAGGGGGATGAGTGCATTCAGGCATACACACACAAATAGGTTCTATGTGTTCGCACAAACACGCTGTATTCACACACTCTCAGGGACCGTGACAGGGTCCATCAAACGTAGTGTCATTCTGACAAGGCAACTAGCTGTTACTGAACACACAGGACTCACACACCATCTTAGAGTCATGTGATCAAAGTGTGACTCCATAGAGGTCCCAGATCATGGTCACAGTCATCTTTTACTTAAATAAGACTTAGAATAGATTTTTAAAAATAAAAAATAAAAAAAATAAAGAAAAAGAAAAGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000030606:ENSMUST00000206092:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.039 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0019312=Xlink=WD(100=94.1),PF0019312=Xlink=PU(0.1=0.0)
A:
NA
C2:
PF0019312=Xlink=WD(100=95.8)
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:
CCTAGACTGGTGCAATGCAGG
R:
TATAGGGTAGCGGGCACTTCC
Band lengths:
352-707
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