MmuINT0078173 @ mm9
Intron Retention
Gene
ENSMUSG00000066842 | Hmcn1
Description
hemicentin 1 [Source:MGI Symbol;Acc:MGI:2685047]
Coordinates
chr1:152474503-152477502:-
Coord C1 exon
chr1:152477346-152477502
Coord A exon
chr1:152474625-152477345
Coord C2 exon
chr1:152474503-152474624
Length
2721 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGA
5' ss Score
10.77
3' ss Seq
GTGTTTGGACTCTCCTCTAGGCT
3' ss Score
8.88
Exon sequences
Seq C1 exon
TCCCTCCATCGATTGCTATGGGTCCTACCAACGTAACAGTAACAGTGAATGTCCAAACTACTTTGGCTTGTGAAGCTACTGGGATACCAAAACCATCAGTCACCTGGAGAAAAAATGGACATCTTCTTAATGTAGATCAAAATCAAAATTCATACAG
Seq A exon
GTAAGAATAAGTCATTTCTTTTAAATATTTAAAATTTTTTTTAAATTAGGTATTTTCCTCGTTTACATTTTCAATGCTATCCCAAAGGTCCCCCATACCCACCCCCCCAATCCTCTACCCACCCACTCCCCCTTTTTGGCCCTGGCGTTCCCCTGTACTGGGACATATAAAGTTTGCAAGTCCAATGGGCCTCTCTTTGCAGTGATGGCCGACTAGGCCATCTTTTGATACATATGCAGCTAAAGACAAGAGCTCCCGGGTACTGGTTAGTTCATATTGTTGTTCCACCTATAGGGTTGCAGTTCCCTTTAGCTCCTTGGGTAATTTCTCTAGCTCCTCCATTGGGGGCCGTGTGACCCATCCAATAGCTGACTGTGAGCATCCACTTCTGTGTTTGCTAGGCCCCGGCATAGTCTCACAAGAGAGAGCTATATCTGGGTCCTTTCAGCAAAATCTTGCTAGTGTATGCAATGGTGTCAGCGTTTGGAAGCTGATTATGGGATGGATTCCTGTGACACAATTGTATATAGTTATTGGTACTATATGATTTCAATACATTGAAATATAATATATTTCATGTATAATATCATGATGTATAATGATTAGATTAGGATAATAGGCAGAGGCAGAGGCAGAGAGGCAGAGGCAGAGGCAGAGGCAGAGGCAGAGGAGGCAGGCAGATTTCTGAGTTCGAGGACAGCCTGGTCTACAAAGTGAGTTCCAGGACAGCCAGAGAAACCCTGTCTTGAAAAACAAAACAAAACAAAAACATTAAAATTTTTTTCAGCTGGTGCTGGCACACATCTTTAATCCCATCAATCAAGAGGCAGAGGCAGGCAGATCTCTGTGAGTTAGTGGCCAGCCTGGTCTACAGAGTTCCAGGACAACCAGGACTGCATAGAGAAACCCTGCCTTAGTACCCTTCCCACCAAAACAAACAAACAAACAAAAAAAAAACATTAAAACCCCCTTTCTAGCGGCTATTGTGAAATGTTCAGTGGTTACCCAGACACTCCTCTGTGCAACTGCGCTTCCATGCTGCTGTCATTGCACACCATCCCAAGACCTGGGAACTGAGTCACGTCTTTACTCCTGTTAGCTCATATTTTTATCTTCCATATATAATGAGTGCAAGTAGATCCTTTTCTGTACCTGGATAATTTCACTTAACATAATGAAGTAAAGATAATTCCATTGGAAAAACTATCCCACCGAACATTTAGAAAGTTTTTTAAAATAACTAGCATTTTAACCCTATCAAAAGGAGCATCAAATACATTTTTTAAATGAAGAATTAGCTAGCCAGTTGTTAGAAAATACTCCCTTAGTATGAAATTTGATCTCCAACCTATTTTTAATTAAAGATGCAGTTTTTCTATATACAACAAACCTATGATGGCTATTGTTGAGGTCTACAGGCATGTTTAACCTAGTTTGTTTAGTGTCTTCTATAATTTCCTAATGACAATGGCTGTAAACACCTTTTCACATAAAAGACAAAATGTTCTGTGGGAATCAATACAAGCTTTAGTTGTAAAATAAAAAATGAAATCTAACACCTTGAACTCTAATGTAGCTACTTGGCCCCTTAGGTAGGTAGAAACAAAAGCAGTTTCTCCAGGTCTTACCCTCCTCCAGCTTCCCTGCTAGATCTTCCTCTATGGCAGTGTAGCTGTCTTGAAGGCTGAACTTTGAGTCATTGAGAATTTCTGCTAGTTTAACACCCCTTCACCTCGGTTCAGTTAACAGCCCATTATCCCATCAAATTATCTGCCGGGGTGCTAACATCAAATACAGTCGTAGTGAAACTTTGACAAGAGGTAATTCTGACTTACAGGAAATATGAAACCAAGAATGATTCCACTGAAAGTCTATCAGCTCCATTTCTCTCATCCTTTAATGTTTGGCATTGGACTCAGTGATTGAAAAGTAAACTTTGTGCGGAGAAGGCGTAGACAGTGTGTCAAAGACACTTCTATTAAACCAAACCCACGTCGCTTTTCTTTTTCCATTTTTAATTGTGCAGCATACATGCATACACATGTAATTACATGTGTGTGGGTACTTGTGGGAAGGTAGCAGGACTGCACATATGTGTGCATATGGATGCCCGAGGCAGATGTTAGGAATTATCCTCAACTGCTCTTCTATCTTATTCACGGTATCAGGATCTCTCCATCATATGCATATACATACAGGCGTGGATATGTATACACATGGTACATCTCCAAAATAGCCATGAGCCACAACATAGAAAGAAGCATATATAAAGCACGGGGCAGGGGCAGTGAAACAGATAGACCTCTACTCACTTACATGGCATAGATGGAATCAAATATCCACCCTCAAAGTCACTGATAAATTTGAGATGCTTTATGAGAATCGTGTCAAATGGAGCCTGGGATACATACTGTTATTAAATAGTAGCTGTCAATATACTTCATCTACTAAGAGAAGTTTGATTATGATGCACGTATTCAGAAAATGTAAGATTCGGTGTTCAGGCAATTCTTCCAGGCAGCTGTTTCTCGTTATTAGGAAGTTTAGATCCTTTACTGTATAAAGTTACATTTTGATGTGCAAACTTTGCATCAGATGAATGACGCTCACTTGACATGAAGGAGGAGCTCTTTCCCTCAGCTTATCTCAGCTCCTTCAAACACCAACTGCAAAATATGTGGAAACTAACGTACAGAATCTCGTGTTTGGACTCTCCTCTAG
Seq C2 exon
GCTCCTTTCCTCTGGTTCACTTGTAATCATTTCCCCCTCTGTGGATGACACTGCCAGTTACGAGTGCACTGTGACAAGCGATGCTGGAGAGGACAAGAGAGCAGTGGACCTCACTGTCCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000066842-Hmcn1:NM_001024720:75
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.057 A=NA C2=0.357
Domain overlap (PFAM):
C1:
PF0767911=I-set=PU(55.6=94.3)
A:
NA
C2:
PF0767911=I-set=PD(43.3=92.9)
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:
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: