MmuINT1020671 @ mm10
Intron Retention
Gene
ENSMUSG00000055632 | Hmcn2
Description
hemicentin 2 [Source:MGI Symbol;Acc:MGI:2677838]
Coordinates
chr2:31453383-31454690:+
Coord C1 exon
chr2:31453383-31453620
Coord A exon
chr2:31453621-31454627
Coord C2 exon
chr2:31454628-31454690
Length
1007 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGG
5' ss Score
10.07
3' ss Seq
TCTTCATGCTTCCATTACAGAGG
3' ss Score
8.19
Exon sequences
Seq C1 exon
GACTTCCAGGAGCACTACGTGCAGACAGGGCCTGGCCAGCTATTTGCGGGCTCCACACAGCGTTTCCTCCACGACAGCCTCCCAGCCTCCCTGCGCTGCAATCACAGCATCCAGTATGATGAGACCCGGGGCCTCCAGCCCCAGCTGGTGCAGCATCTTCGGGCCTCTTCTATCAGCTCGGCCTTTGACCCTGAGGCAGAGGCCCTGAACTTCCAGCTTACCACAGCCCTGCAAACAG
Seq A exon
GTGAGGCCCCACTGTCCCACTTCCACCCTACCAGCGAAGACGGCCAGAGTCCCAAATTCTGGCCATTCACACCGAGCACAGGCTAGGGAGCAGTCTATCTCCTCTGGCCCCGCCCATTCCAGCCTGGCTCCGCCCACTCTAGCAGGGCCAGTTCAGCTCCTCGGGCCACTCCTGCCCAGACCTCTGAAGCCTTTTCCTAGGCAGGAGAAATACTCCACACTCCAAGTCTAAACCACACCCACTCCCTTCTCCCAAGGTGCCTGCACCAAAGGCCCCGTGGGTGCAAGCTCTGGTGACCCACCTGAACACATCATAGAGTCACAGCTGAGGAATGCTTTAAAAGTATCTTTTCATTGCTTAAGATCCAGAGAGGAATGCTGGAAGGAGCAAGGCTCTAAAGGCAAGGCACACCCTAATTCAGAGCCTATCTGTGCTGCTTTCCGGCTACGGACCTGGTGGGAATCCCATGGTTCCTAGCTGCACAGTGGTCATGAACTCCTAGCTTCCCCGAGGCTCCAGGCCAGCAGTAAAGACTCTGCCTCTACAACCCTAACTGGCCCCCAGAGTCCACCTTGCTAAGGGTGACTGTCCCTGCAATTGCTGAGGCAGTCCCATCTCCCTTTCTTGCTGGCCGTTGACCAGCAATCACAACCCCCTGTACATGACTGTTGGGCTCTGCTGAGCACAGTTTTGCGCTCGTGATCTCAAACAGTCTACTTCTCTCTAGTGGTCTCTCTTGAGTTCTCCTGGCCTTAAGAGCCTCCCCACCCCCACCCCCCACCCCCACCCCACCCCCCGGGCACAGCTACAAGACCAGGCATGTCCCCACAACTACCACCTCCCACAAGCCTGGGCCCGGAGCCAGCTGGTTGTCTCGCTGTCACATGTCTGGTTCAAAGCTGAGGCTGAGCTCCCAGCCAGGGCCTACTGCCTGGCCCAGCCCAAAGAACAAGCCCGGGATGCCCTGGGGAATTGGCTCCCTCAGGGTCTTCATGCTTCCATTACAG
Seq C2 exon
AGGAAAATGAAGTTGGCTGTCCCGAGGGCTTTGAGCCGGATGTGCAGGGAGCATTTTGTGTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000055632:ENSMUST00000113532:90
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.050 A=NA C2=0.182
Domain overlap (PFAM):
C1:
PF074747=G2F=PD(26.1=61.2)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GACTTCCAGGAGCACTACGTG
R:
CCACACAAAATGCTCCCTGC
Band lengths:
301-1308
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Ribosome-engaged transcriptomes of neuronal types
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types