MmuINT0078098 @ mm9
Intron Retention
Gene
ENSMUSG00000066842 | Hmcn1
Description
hemicentin 1 [Source:MGI Symbol;Acc:MGI:2685047]
Coordinates
chr1:152427358-152429478:-
Coord C1 exon
chr1:152429353-152429478
Coord A exon
chr1:152427487-152429352
Coord C2 exon
chr1:152427358-152427486
Length
1866 bp
Sequences
Splice sites
5' ss Seq
TTGGTGAGT
5' ss Score
9.27
3' ss Seq
TATTGTCTCCATATCTGTAGACA
3' ss Score
6.85
Exon sequences
Seq C1 exon
ATGTGAATGAATGTAGACAGAATGTGTGCAGACCAGACCAGCATTGTAAGAACACCCGCGGTGGCTACAAGTGCATTGATCTTTGTCCAAGTGGAATGACCAAGGCTGAAAATGGGACCTGCATTG
Seq A exon
GTGAGTGCCAGGCTGTTTCCCTGGCAAAGAACTCTTTCCTACCCACAAGTTAAAGAAGGACTCTATTCTAGAATAGGACAGTACTGTAAACCTAGATAGCAAGAGAGTCCTTCTCCATCCATCAGTTCCTCTAAGTCCTTCTAAGCTTGAGCTCTAGAACCCTAGCCTAATGGTGTACAAGGAAACAGAAGCACACATGGAGTTATGACCATTCTGCGCTCCCATCCATCCTACGCTTTTTGCAAAGTTTAATAACCACATGAATTAGTATTTGTGAATCATGTCATTTCTAACTTGAAATTTAGTATATCTGCTAAAGTTCACAGCAAGGTCAAGAAAAAAATATATTTGTAGATATTTATTCCAAAGATGTAATATTCTACAATTGCTTTAAATATTAAATCAAAGAGAAAAATAGGTTAATTGTATCTACAACTATATTCTTTATAGTCTATTCTGTAGCAGCTACAAAGGTCACCAGATGTCATTGGTTGCATCTTAAAATATCAGATAAGTTATATTTCTTCTAGGTTTATTCTTTGTATACCTATTCTGTACAAGCTTGCATGAGTTGGGAAAGGTAGAAACTGCAGACACATAGTTAATAAAACAAATGGACTGAATAAGATGGATCAACAGATCAGGTAGCCAAGCCTGACCACCTGAGCACACTGTAGAAGGAGAGATCTGTCTCTCAGAAGTTGTCCTCTGGCTGCTGCATGTGTGGTGGCATGCAAGTGCCCTCCACACACACAATAAGAAAATGTAATAGTAAGTAAAAACAGATTAATTTGGCTTACTCTCCTGTCAAAAGTAAGGGGGAAAACTCTACTATTCAAGGTAAAAGGAAACACCATAAAAGATATGAATAAAATTGATCAGTGCCCAAGAAAGTACTCATATGTAAGAAGAATGGCTATCAAAAACATTGTAGAAATGATCACATTTAAGTTTAGGTATAACTGCACTATTAACTGTGTTGATGGCAGGAAGGAGAAGGCAAAAAAGTCTTGTATTCAGAAGGATTAGGAAGGCTTATTGATTTTAAGGTCCATTAAAGCTTTCTATACCTAAGAACTTCTAGAGGCAAGTATTGGACTATCACCTTTGAAACACTTTTTAACTCTGTTTTTCTTAAGGGAGTAGCAAGCAACACTGAACACCACATACTGTGGCTCGCAGTTGTGTTTGTTTTTTAGGAATATTGATTCTATAATTTGATCTCAGACAATTAGAAATGGCATGAATTGAAATACTAGACTAAAAAGCAACAGAAGTCCAGCCCAATCAGACTGTAAACGTAGAGATTTATGGCTTCAGTTGAAGGTTACAGAACTACCCAACTACAAAAATAACTCAAAGATGACCCTGATATTAACAGCCACGGTGACTAGGAAGGAGTGCTGTTGCTATAAATAAGGAAGTAAGGGTAGGCTTGGAGCATGCTGGCTTCACAGTGCAGGTCAGAAGCTGAAGTGGGTGCCAATCCTGCCGGCAGCTGCAACTGTGATACTGGGCATCAGAAACAGGGTAGCACTCTGGCTGCAAATCCGCATACACACTGACCTTTCCGACAAATGGATAGTGAGAAGAACTATAGAGAAGTACGAAGACAAAGCAAAACCCAAAGATAAGAGCAAAACTCTTTCCGCCATGGGAAACAAGCAGGTAGGGCGGGCCAGTTTATAGTGGCGGGGCTGAGATTTAAACCCAAGTTTACTGCTGCCAAGTCCTAAATCCTAGTTTAATATAATCTCAATGACCGGGTAAGAATCACAAATTTCAGTGAACAGCAGAATGTGTGTTTCATGTATGATGACTTCAAGTCTGAAGAAAGGTTGCTTTTTATTGTCTCCATATCTGTAG
Seq C2 exon
ACATAGATGAGTGCAAAGATGGGACCCATCAGTGCAGATATAACCAAATATGTGAGAACACGAGAGGCAGCTACCGGTGTGCATGCCCAAGGGGTTATCGGTCCCAAGGTGTTGGAAGACCCTGTATTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000066842-Hmcn1:NM_001024720:102
Average complexity
IR-S
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=WD(100=95.3),PF0764510=EGF_CA=PU(0.1=0.0)
A:
NA
C2:
PF0764510=EGF_CA=WD(100=95.5),PF0764510=EGF_CA=PU(0.1=0.0)
Main Inclusion Isoform:
NA
Other Inclusion 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:
TGTGAATGAATGTAGACAGAATGTGT
R:
CAATACAGGGTCTTCCAACACCT
Band lengths:
254-2120
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: