MmuINT0078198 @ mm9
Intron Retention
Gene
ENSMUSG00000066842 | Hmcn1
Description
hemicentin 1 [Source:MGI Symbol;Acc:MGI:2685047]
Coordinates
chr1:152434079-152435404:-
Coord C1 exon
chr1:152435342-152435404
Coord A exon
chr1:152434199-152435341
Coord C2 exon
chr1:152434079-152434198
Length
1143 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGT
5' ss Score
10.86
3' ss Seq
CTTTCTGTTTCTTCTCTCAGATG
3' ss Score
11.99
Exon sequences
Seq C1 exon
GAGATCGCAGTAACCAGTGCCCCTCTGGGTTCATTTTAGACTCGGTTGGACCCTTTTGTGCAG
Seq A exon
GTAAGTATAAGAATGGATAAAATAGTTTCATTTCGTAAACGGTGTCAGCAAGAGTTATCTGTCCTTTATATTTATTTATTCACTGTGCACGGGGGAGTGACATGCTCATGACAAAGCCAAAGAAAAATTTGCAATTGACCCCCTCCACCATTCGATTCCAGGCATCAAACTTTGGTCATGAGGCAAGCAAGCACCTTTACCTGCTGAGCCGTCTCTCCGGCTGGAGTAATGATTATCTTTTAATAGACGTCGGCTGCCATTACCCTAGGTGTTTAATCATTGCAGCTGCCTACAAATGCTCCACTTGATAGCTAAGCAAAGGAGATGGAGAGAAGTCACGTAAACCGCTGAAGGTGGCCTAGTATCGAGTGGCGGGCTGCACTTGAGGTTAAGTGGAATGACAAAGCCCATGTGCCTTCAATTTGGACAAAGGCTAGTGTATCAGAGACTGTGACCAAGTACAGAATAGAGTGAACAGAGACAACTAATTCAGTGGCTCAATGGGAGTGAACACTCAGTGACCCAACACAAACTTGCCTAACCACAGAATTGCTGTCATGGGACAGAACAGGGTAGCTGACCCATAAGGAACCATGAATTCAGCTTGGCCCCAGCAGGCATCCTTGCAAAAGACTCCCTTACAGGAAACCCCAGCCTAGTAAATGACATACATAGAGCCAGCAGGACTTGTTGGCTCTTTCAGTGACCTGTATAATGTGGTGGGCTGGCAAGAGGGGGTGTTTAGACTGTATTGAGGTCTCAGCTCTGGCAGTAAAGGCCTTGGTGACAGAGAGCATTCCCCTTATCTCTGTTCTTCCGATTTGTCATGCAAAGGGAAGATAGTCTCTTAAAAATTCTGTCTTTGCAGAGTGCGTTGCAACTGCATTTAGAGCACGGTAAATGTACATGTAATTTAGCTATCATTTCTGTTTTACAATAAAGTCTTAGCATGTATTCACTAGCAACTCTGAGACCTCAAGTTTTTTTTCTTCAAGGCAACCCCATTCTCTGCCACTTGGAATGTTCTCTGTTATATTTGATCCAATTCCTCGGCATCTATAAATGCTTATTTTCATGGCCTTTAACAGCTCCTAGGAAGCAGGAGTTGTAAACACTGAGGAGCCTTTCTGTTTCTTCTCTCAG
Seq C2 exon
ATGAAGATGAATGCACAGCTGGGAACCCCTGCTCTCATACCTGCCACAATGCCATAGGAGCCTATTACTGCTCCTGCCCCAAAGGCCTCACCATAGCTGCAGATGGGAGAACCTGTCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000066842-Hmcn1:NM_001024720:98
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:
NO
A:
NA
C2:
PF146701=FXa_inhibition=WD(100=90.2),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:
GAGATCGCAGTAACCAGTGCC
R:
TTGACAGGTTCTCCCATCTGC
Band lengths:
182-1325
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: