MmuINT0078100 @ mm9
Intron Retention
Gene
ENSMUSG00000066842 | Hmcn1
Description
hemicentin 1 [Source:MGI Symbol;Acc:MGI:2685047]
Coordinates
chr1:152420606-152424752:-
Coord C1 exon
chr1:152424402-152424752
Coord A exon
chr1:152420726-152424401
Coord C2 exon
chr1:152420606-152420725
Length
3676 bp
Sequences
Splice sites
5' ss Seq
TAGGTAAAT
5' ss Score
6.62
3' ss Seq
TCTGTTCTCTTTCTAAACAGATA
3' ss Score
11.8
Exon sequences
Seq C1 exon
ACATTAATGAATGTGAGCAAGTACCTAAGCCTTGTGCACATCAGTGCTCCAACAGCCCCGGCAGCTTCAAGTGTATCTGTCTGCCAGGACAGCAGTTGTTAGGGGATGGGAAATCTTGCGCTGGATTGGAGAGGCTGTCGAATTATGGCACTCAGTACAGTAGCTATACCCTTGAGCGGTTCTCCCCTGTGAGAAGCGACTATCAACCTTCGCAGCATTACAGACAGTACTCACAACTCTACAGCTCCTACTCAGAGTATAGGAACAGCAGAGCATCTTTCTCCAGGAATAGAAGGACTATTAGGAAAACTTGCCCTGAAGGCTCTGAGGCAAACCATGAGACATGTGTAG
Seq A exon
GTAAATGTCAGCCATATTGCATTCCTTTCTGTGCGCTCACTTCCTGTCTGGAGTCTAAGCATGTATATAGCACCTGTGTTTGGTGCACTGAACTCAAGGCTGGACTGACTCAAAGGATTTTGACAGTTATTTGGGCACCTACGATAATTACAAACTATCCAAATAAATGATGTATTTGCATGTGTGCATTTTAATAATTGTGTTACTCTTTCTGAAATGTTACTGAATTAAATTCGACATTGACGTAAATGATGTGAGTTTTTAGGAATATACACACATTGTCACATAATATGATACTGTCTGCACCATAGCTTTGTTTGATGCAGAAGTAGTGGCTTAGAAATGAGTTTTAATGACCCAACCAACTGGTCTATGCAACAACCCACATTCTGTTGACTATTGTTCTTAGTCTTACCGTGAAATTTCTCAGTCAGGTTATTTTGTATGTTTATGGACAGAAATAATGTGATCCAGAGCAACTTGGTCCCATTGCTTCGAAATATGTGTGCTCGATATCTTTATCTAAACTCATAAGCCAGTAACTTAATTTTGCAAAACTTAACTATAATTTCCCACTGAACTGAGTCCTTGTTTTCAGCTAAGTTGTAAACATTGCCATCTGCCATAGATTTAAGTCAATTTTGGTCGGTATCTACAGTTTGCGTGTCATTGAGCTAGACAACAAGAAGAATTAGCAAACAGCAATTAGCCCCAGTATTTTGTTAGATGGCAAAAGAAAGCTCACAGGAAAGGAGGGAGTCAAGACAGAACTCCTATTAATATTCAAAGACCATTAGACCAGACCATTCGTCCATCCTTAAAGCTCTCCTCAGAGGCCATTAGACCACTTCAGTCTTACAGTGTCCTACATGTTGCTTATCCTTAGTGATATAAGCTTTCTGCTTAAACTTCTTTAGTCTCTTGAGGTTTACTTTATCCTCTGACTTGATTTTTTTTTCATTTATTTTTCCACTCCTTTCCATCCCATTATCTTTTCTGACATGCTTCCATGGTCACCTCTAGGTGGACCCAGATTCTCCTATTCTACAGTCTTAGCTGTGTCCACCAGACTTCCTGAAAATTTGAGCTTCATACTTTACTATTACATTCATATGTATCCAGTGTTTTTCTTTCTAGTCATCCCAGTGTAGCTAAAATATATCATTACGAATATGTTAACTTTGCTATGTGGTGAGCTTTCCAGAACTATGGACACTGTCAGTGGCTTATGCTTCAAACGTAATGCATTTGTTAGCAGTGCCCTACATTTGGTCCAGTGTGGACAAATACCACGTGATCACTAATTCTCTGCATCTGACTTCGCTCTGAGTGTTTAACAGCTTTCCCTGCCTACAGTTTTGATCTGGGTCTTCGCTTATCAAAACGTTCACTATTCATTTAGTAACACGCTGTCTTTAAAGTCGTCTTCTGAACCGTTATTCTGACTGTAGTGCTTTGTAGCCTGCCATTCTCCCACTTCTGCCTTCTTTTTGGGCAAACTCATTATTTCTAGCCTAGTTTCATTCTCTTGCCTCAGAATCGTTGCTTATTTCCACACTCCAACTGCACTAAGCCACACCCTCGTGCCAGGCATCAACTAAGCCACGCCCTCTCGCCAGGCATCACCTGACTGCTGTGCTTTAAGATTGAAGGCGGACAGCAGCTTTAGAAAGATTCTCTTACCAACAACCCAACTCCCTATTTTCATTATTGCTCACATCTGTTGCTCCACCATACTGGAGTCTAATAAAGTTTTTCTTTCTTGATGTTTCTAATATACCAATGCGTGGTGCATCGAAATAATCTTCCTTTGATAGGCATGCATTGTTCAAGACTATTTTAGAGTATCAATCATATATGGATCTTTGCATTTACTGGGGAAACACTGAGGCATCTTCGATATTTCTTAAAATATGGTGGATATTTTATTGGGGCTAATAAAGATATTCACACTAAGGTTGCAGACAGCTCTGGAATCATCTAACAGAAGTAACTTACAACAAACATTGGCTGCCTTTAATTAACCATCTGGGACAGACAAGTTACAAAAGGATTAAATTGACATTGTGGAATCTTGTTAGATTTGGGCAAATTTTAGTTTTTAACGAGTTGATCGCAGGGTTTAGCAGAAATAATGAACTTTGCTTCAGTTCTGAAAGCAGAAGGCACACTTTGCCATTTTAAAATTCATATGCTGTGAAGCTCCGCGTTAATGACTTCAAGTTCAAAATCATTTGAATGTCTGTTGTTGTTTTAGATTAAAGCAAATATTTAAAGAGAAAAGACAAAAATAACTCATGAAAATTATGAGATGAATACTTTGGCTAGATAAAATGATGCATAAACATGGGAAGTGAATATTTGCTGGATATTATCATTAACAGATTTTGACAAATTACAATTACGTTTTCAGCATGTGCTGAGCAGATCCCTTTACTCTGAGTCGTCTCCCAGACTCACTCTGTCCATGCTTTGCTCCTACCCTTCCTCCTCCTGCTCCCCCTTCATGTCATAGTCTCTGTTATCTCACTGGTTAGTGTATTCTCAGGGACCATGAGAGAGCTGATCAAAAAAAAAAAAAATGACCATTAGACTCTAAAAGCAAACACTGAGTTTGAATTTACTGTACTTGAGTGGATGTGATTTTTTTTTCACTTTAATGATAGTAGACAACCCTCCCCCTGCCCCCTTTGTGGTTTATAAAGTGTTTTCTCATTTACTGCAGTATATGGATCTCCCAACAAACCCATGAAGTAGAATAGATGGTTTCCACGCTTCCGTTTAGCAGAAAAATTGACTGAGATCTTGAGAAATTAGATGAGTCCCCCAACTTAGTACAGCTATAGACATGTATTTGCCACAAGTAGTTTGCCATTATATAAAGAGATTGAGAAATATTTCTCACAAATAAGAAAACATTTCTACTTGAAAATATCTGTGTATGGGAAAGCTTTGTATAGATATTGTATGGAGGAGAGAGGTGGGGGGAGGGAGAGGGAGAGAGAGATCTGAGCTCACATGAATTAAAGTGAAGATTAAAGAGATGGCTAAGTGGTTATGCATACTGGCTACTTCTTCAAAGGAGCTGGGTTTAATTTCCAGCACCCACACAGTTTGTAACTCCTGTCCCAGGAGATTCAATGCCCTCTTCTGGCCTCTATATGCAGTACACAGCCATGGTACACAGACACACATGTAGGCAAATTACTCATGCACACTAAATAATAAAATAATTTTTTAAAAGTAGATACATCCATTTCCAATTAACATCAAAAGAAATTTTAAGGTAAATTTTACCATTTTAGCAAAAGGTTAGGGTTTTGGTGGTTTCAGATCTAACACAGATCTGTTCCCCCCATCCTCTGTCATTTTAATGTAATTTAGCAACACAGAAAAAGAAAAAAAAAAAACAAAGTTGAGGCTTCAGGTCATATATATGCATGTAAAATAATAGATAACGGTTCATATATTATAAAGTAGTATAGTGCATCTTGTAATATAGTTAATATTTATGTCACTAAAATCAGACTTGATGTACAGTAAGCACTTTTAAGAGCATGAATGTAAATCCAGTCATGAACATTTCTATCGTATGCCTGTGACTTGTACTGATAGCTGTGTAACAGATCCTGCTCGCATCTGGCATGACTATATACTCTGTTCTCTTTCTAAACAG
Seq C2 exon
ATATTGATGAATGTCAAAACAGAGACACTTGCCAACACGAGTGTAAAAACACGATCGGGAGCTACCAGTGCGTCTGCCCACCAGGTTATCGACTCATGCTCAATGGGAAAACGTGCCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000066842-Hmcn1:NM_001024720:104
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.008 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0764510=EGF_CA=WD(100=33.9)
A:
NA
C2:
PF0764510=EGF_CA=WD(100=95.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
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: