MmuINT0078195 @ mm9
Intron Retention
Gene
ENSMUSG00000066842 | Hmcn1
Description
hemicentin 1 [Source:MGI Symbol;Acc:MGI:2685047]
Coordinates
chr1:152441042-152442386:-
Coord C1 exon
chr1:152442249-152442386
Coord A exon
chr1:152441164-152442248
Coord C2 exon
chr1:152441042-152441163
Length
1085 bp
Sequences
Splice sites
5' ss Seq
CTGGTTAGT
5' ss Score
6.32
3' ss Seq
GAATGCAATGTCATTCCCAGGAG
3' ss Score
4.46
Exon sequences
Seq C1 exon
GTCCAGCAATGAGAAAGATCATTTCTATCCTAAATCCCATTTACTGGACCACAGCAAAGGAAATAGGGGAAGCAGTTAATGGCTTTACCCTCACTAACGCAGTCTTCAAAAGAGAGACGCAAGTGGAATTTGCAACTG
Seq A exon
GTTAGTATCAGGTGAACGTAATTTTCTACTATATAGTTACATACATATAGACAGAGAAGTCCGACAGACAGAAAGGCAGGAGACAGACATAGGTATAGAAAAATTGCTATAAATCTTGGCGACTAAGAAAAATATGGTGTATGCTCTCACAGAAAGTTATTATGAGTTTTTTGGTGCACTCTAACACACATAATGGAAAACAGTTTTATATTTTCCTGTCAATGAATGCTAGCACAAGGTCTGTAAGACACCACTTACACCACTGTGTCCTCAGGCAGAATAGTAATTTTTATGTCCCAAAGACTCCTTCCTCTTCTGTGCCTTTTTTTTTCTTAAACCTTAGAGAGGATTAAAAGCATGAATAAGGAAGGAAGATATATCCTTCTTGTTAAAGCTTTGTCTTTAATCGTGAATCAGCTCTTTTGCCTTACGGTGATTATCGATCTAACAGATGGAAGCAAAGCCAAGCACACTAACACTTTCCCCCTCTGCTTCTGCCCTAATCATTGGGCGTTACCTCGTTGGGGCCCTTGCTGTGTCCACAAAAGTGCTCACAAAGCTCCATTTCAGCCTCCTTGGAATGAGCCAGCCTTGGTGGGATTGACCTTTGGTGAAGAATGATGAGGGTGGACGTCTCCTTAACCAGTGTTCAGTCAGCACAGAAAGCAAGTGGGCCTCTTGCTATCCATCCGCATACGAAGATGCCCTTTTGATAATAATGACAAAACCCCGTAGCCAGGTCTGTAGGTATTGCCGGTCCCTGGTAAAGTTGCCTGGCCCATCTCACAAGCAATAATTTTGTAGAAATGCTTAATTGTTCCGTGTGAGACTAAAATATGGAGACTTCTGCAAAATCGAAAGCTACACTTTGGCCACATGGAAAGACTTTTTGGAAGACAATTCAAGTGGTTTGCCTTTTCTTAACGGGGAATCTTTCTGCTTAGTTCTCTGACATATTTATCCATGTTTGAAATAACATCATGGTATTAGATCAATCTTCTCTGTGCTCCCACAGACCATAGGCATAATAGTAATAATAACTGTTATTATCGTTGCTGAGGAAATGAATGCAATGTCATTCCCAG
Seq C2 exon
GAGAGGTCTTGCGGATGACACACGTGGCTCGGGGCTTAGACTCCGACGGCGCCTTGCTGCTTGATGTCATTGTGAGTGGCCAGGTCCTACAGCTCCACTCACCTGCTGAAGTCGGTGTGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000066842-Hmcn1:NM_001024720:95
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:
PF074747=G2F=FE(24.5=100)
A:
NA
C2:
PF074747=G2F=FE(21.3=100)
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:
GTCCAGCAATGAGAAAGATCATTT
R:
CTTCACACCGACTTCAGCAGG
Band lengths:
260-1345
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: