MmuINT0075933 @ mm9
Intron Retention
Gene
ENSMUSG00000007594 | Hapln4
Description
hyaluronan and proteoglycan link protein 4 [Source:MGI Symbol;Acc:MGI:2679531]
Coordinates
chr8:72610707-72614761:+
Coord C1 exon
chr8:72610707-72611030
Coord A exon
chr8:72611031-72612028
Coord C2 exon
chr8:72612029-72614761
Length
998 bp
Sequences
Splice sites
5' ss Seq
CGGGTGAGA
5' ss Score
7.62
3' ss Seq
CACACTCTCGGGTCCCACAGGCC
3' ss Score
8.86
Exon sequences
Seq C1 exon
GGGTGGTCTTCCCCTATCACCCGCGCGGAGGTCGCTACAAGATGACTTTCGTGGAAGCGCAGCGTGCTTGTGCCGAACAGGATGGCATTTTGGCGTCCGCGGAGCAGCTGCACGCGGCCTGGCGCGATGGCCTGGACTGGTGCAACGCGGGATGGTTACGCGATGGCTCGGTGCAGTACCCAGTGAGCCATGCCCGGGAGCCCTGTGGCGGGACTGGGAGCACTGGAGCTGGTGGCGGCACCAACGGGGGCGTGCGCAACTATGGATATCGTCATAACGCTGAGGAACGCTACGATGCCTTCTGCTTCACGTCCAACCTCCCGG
Seq A exon
GTGAGATAAGTCTTTTCCAAAGAAGCGGGTCTCCAGCACTTATTTCCCGCCTTCTTGAAAGAGACCTGTCCCAAGGACCTAGGCCCCCTAAATACATAGGCTTCTCCCTGAAGGGGACCCTTCTTCCCTCTCTCCTTCCTCTTAATCATTATGTCCTCTCCCAGGAAAGGAGGCCCTCTCCTCCAGTTCAAAAGCTCTCTCCCTGGAGGGACACCTGCCCCACATGCACAGGCTCTGACCCATGGAGCCTGGCCGCTGATTGCATAGTCCCAGTCCCCTAGAATGAGGTCCGCCCCAGGCGCATATGCCCCGCCCCTTAGGGAGAAACCCGCCCCAAGTGCCTAGTCTCCAACCCTTTGAGGAAGACAGCCCTAACCGCCTAACCCTAGGGCCTGGCAGGTGGAGGGAAGTCTGTCTCAGAAACATAGACTCCATCCCTCAGGGTATAGGCTTTTTCTCTCTTGAGGAAAGACTTCCTCCATGGGCTCCGCCCCAAAGAGATAGGCACAAATTAAGCCCAAAGCCCCCATCCCCGCCTCCCTGAGGAAGACCTGTCCGAAAGACATAGAGCCTACACCGTGGTTGAAGGTCCATTTCAAGAGTGTGGACTCTGCCCACAAGAACACAAGAACACAAATCCTATGCCTAAGGACACAGACACTACGCTAAGGCATAAGGACACTAGAGAAAACCTTTCCCAAACATAGGTCGCGCCCCAAATAAGAGCCCTGCCCAATGGACAGAAATCTCCCTGAAGTGCATAGACCCTCCCTCCAAGACCATTGTCCCCCACCAAAGTGAGCAGGCCCCGCTCCTCCGCCTTGCCTCCGCTTTCCAGGCTGCCACAGGGGGGCAGTGAAATGCCACATGGTACCAGCATCGCACTGGCGGTCCCAGGTTGCAGTGAATGGGATGGACTAGGCTCAGGAAGCCCTAGGACGCTAGAGCCTGGCGGGCCTATCCCTGGCCGGGGTCTAACACACTCTCGGGTCCCACAG
Seq C2 exon
GCCGCGTGTTTTTCCTGAAACCGCTGCGACCTGTGGCCTTGGCCGGGGCAGTGCGCGCGTGCGCTGCGCGGGGTGCCACAGTGGCCAAGGTCGGGCAGCTGTTCGCTGCGTGGAAGCTGCAGCTGTTGGACCGCTGCACTGCAGGCTGGCTGGCGGATGGCAGCGCGCGCTATCCCATCGTGAATCCGCGAACTCGCTGTGGAGGTCCTCGGCCCGGCGTGCGCAGCCTGGGTTTCCCTGACGCCTCCCGACGTCTCTTCGGTGTCTACTGCTACCGCGCTCCAGGTGCCCCAGATCCGGCTCCAGGCGGCTGGGGCTGGGGCTGGGCCGGCGGAGGAGGTTGGGCTGGAGGGTCGAGGGATCCGGCTGCCTGGACCCCGCTGCGTGTATAGATCTGGAAGGATGCGTGTTTGGGGGTGTTAGTGGCTGATCCAGTGGCCTCATGCACCCCCTGGATACCGATCACGTCTCAGAGTCTCAGAGATTCCTTGGACATATGACACACCCCTGCGGTGCACTGCAGACTGATCTAGCTACCTGTGGTCTTTGGACATTGACCATACCTAAGGTCTCCTGGATAAGCGACCTACCCCTGCGGTGAGCTGCAGGCTGACCCACTTGTTGTGGTTCTTGGTCGCTGACTATGTTGCCCTCTGAGGATCCCCTTTGGATAGTGGATATTTCATCTTTTAGACTTTGCCCAGAAGAGTCATACTCTCCCTAATCCCCGGGACCCCAGTAGACCAGCAGGACTCTACGGTTTCCAAAAGATGAACCTTCTATGGCCTTCTGAAAAACAGGTGGACACCCCCCTCAGTCACCTGGAGGCTGGACCCCCAGGATTAACTGGAGACCTGCCCCCAAACCTTCTGTATTTCCCGGGAGCTGGAAAACTGGTCTTGGATCGTCAGCTGTACACTGACTCCATCACCTGGTGAAGAAACAGAAAACCACAGGTCACAAGATGATCGTGCCCTGTACGAGCAAGTGACCCAGATTCCCACTCTTTCAGAGAGTCTCTTTACGTTTTCAAGGTAGCATACTTTGTCCCTGGGTCAATATGGAGGACAGACCCAACACCTCTGGTGTCACAGGAGAGTCTCCTCAGCTGGCTCCTGGAACAGCGGCCATGCCTATCCCTCAGGTTTTCCTCTGACCAGAGAGTAGACTCGCTTGAATGTCCCGTCCCCGGGCTCCTTGGGGGATGTCACCAAAGAGATTCCCTCAGACAAGAAACCCCTAAAAATCTGACTTGCAGAGACAAGCTGCTCGGCTTCTTAAGGTCACATAGGCCACCAATGCAGCCTTACCAGGCTCACCCGCTACACCCACAGAAATGGCACATTCTGCCTTCCTCTGTAACCATGGTTACCACACTTTTCCTTTCTTACTGGCCTAAAGCCTAACACCTACCACTTCATTTTTGTCTGTCCCTGCCCTGGTGGACTGCTGTGGAGACAATCTTCCCCACTGAGTATCCTCAGGGTAACCCAACATTCAGTTCTCCAGGCCTCTCCATGGAAACAGCTGCCCCTTTCCCAAAGAGCATCTTCTGTTTCTCTCAGTTGCCCAAGCCCCGCTCCTAGACAGTTTGAAACACCCAGACTGTTGCCATGGAGTCCAAACCTCTGGTGTCCAAGGTAACAGAATACCTGTCCCTTCAAGGCTTTCCCCTCCAGGGTCCCATCCTGTCCAACTGTTGCCATAGAGAACGTCGGTGTCTCCATGACAACTGACCTGCAGCACTCAGGAACTTCTTGCTATGGGTCCCTCTGACTGGAGCTGCCTGCTGTGTTCCTCAGGCGCCTGACAAATGTCCCTTCTTCAGATGGGCCTATGCAGGACTCTGCTTCTGGAACAGCTATCTGCACCATCCATTTGCATGCTAACTTTACTCCACCCAGCAGCTGAGCAGGAGCCACCACTGCAACCCCCTCCAGCATTTTAAATGTTCACCCTGCAGACTAGGAAACTGAGGCTGTGGTACCGCACAAAGGCCGACCTTTCCTTCTTGGAAATCAAGGAGGGCAGATTCTCCCTGAAACCATCAATTTCAACCCATTTCTGAGGACCCATGTGTGCTCAAGGGTCAAGACCAGCCCAAATGCAGGAGCCTCCAGGTCTCAGATGCTGCTGGAACCAGCAAGTACCCTTGCCCACACACTTTCCTGCCTGCCCCATCTATCTCGGCTAATTCCACCCCTGAGTCTGGAAGCTAAGGGGCTGTGGGCTCCAGTCACACCTTTTGTTCTAAAGTGTGCAGCCAAACACTTATCCAGACTCTTCTCTGGGCTAGGATTGTTCTGAGGTCCCCAGCAGCAGCCTGCAGCCCAAGTTCAATAAACCTTTGTTTTTTCTGGTGAATGTGAAACAAGGCTGCCAGTCCCTGTCAGTGCAGTGGGCTTCTCGGTTCAAAAGTGGCTCCTCTCCCTTTTTTCACTGCTCCAGGATCCTGTGGGATCCTCTCTGACCTCCTCATGTGCCCTGGGGCATGTGTGCATACACATGAATCATAGTAACATGTCATCTAAAAAACGTTAAGTAGGAGCTGGCTGTAGAAATGAGGTAGCCAATCTGTATTTTTATTTATTTGCTTATTTATTTTGTTTTTTTTGAGACAGGGTCTCACTGTTTAGCCTTGGCTGTCATGGAACTTGCTACATAGACCAGGCTTGGCCTTGAGCTCAGTGATCTGCCTGCCCCAAGTGCTGAGATTAAAGGTGTAAGCCACCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000007594-Hapln4:NM_177900:4
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.083 A=NA C2=0.023
Domain overlap (PFAM):
C1:
PF0768612=V-set=PD(0.8=0.9),PF0019312=Xlink=WD(100=94.5),PF0019312=Xlink=PU(0.1=0.0)
A:
NA
C2:
PF0019312=Xlink=WD(100=70.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGTGGTCTTCCCCTATCACCC
R:
GGTTTCAGGAAAAACACGCGG
Band lengths:
345-1343
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: