MmuINT1020613 @ mm10
Intron Retention
Gene
ENSMUSG00000055632 | Hmcn2
Description
hemicentin 2 [Source:MGI Symbol;Acc:MGI:2677838]
Coordinates
chr2:31392962-31394846:+
Coord C1 exon
chr2:31392962-31393138
Coord A exon
chr2:31393139-31394688
Coord C2 exon
chr2:31394689-31394846
Length
1550 bp
Sequences
Splice sites
5' ss Seq
ATGGTGAGT
5' ss Score
10.13
3' ss Seq
TCCTTGCCACCACTTTTCAGTGC
3' ss Score
6.91
Exon sequences
Seq C1 exon
ACGTCTCCTGGTTCAAGGGTCGCCAGCCCATCTCTACCCAGAGACGGGTGATAGTGTCAGCTGATGGAAGAGTTCTTCATATTGAGCGAGTCCAGCTTTCTGATGCAGGGAGCTACCGCTGTGTGGCGACCAATGTGGCGGGCAGTGCAGGGCTGAAGTATGGCCTACGGGTCAATG
Seq A exon
GTGAGTGGCTAAGACTACAGGGCCTTCCCAAAGTGCTTAGTTTCTTCCCATTTGTGTAGCCTTCTGTCTCTTGTCCACTTGCTTTTCAGTTTATCTACCGTTCGTTCATCTGCCCATTCCCCATCTATACATCTGTCCATCTGCCCACCTACTATTCACACACCTATCTTTACATTCACCCACCACCCACCTATGTATCCATACATTCACCCATATATCTACTTATCTACCATCTACTTTTCCATCTATCCATTTATTTACAGTCTACCCCCACCCACCCACCGATCTACCTGCCCATTCACCCACTGAACATCCATGCACTCAACTATCCATCCACTCATCCATCCATCCATCCATCCATTCATCCATCTACCCGCCCATTCACCACTAGCAATCTAGACTTTCACTCATTCATATAAACAATTATTGCCCATACATTGAGCCAACCATCTATGTATTCTAAACTTCTGTTCATCCATTTACTCAGCCATCCAGCCTTCTATCTATGTACACAAATATGTGCCTATCCATGACTGATCCACTATCCATCCATCCAATCCTGTGCCCATCCATCTCATCTCTATTCCCCCATCTAAACTATAGAGACATAGGGAACATGAGAAACTGAATGGAGACTGGGTGTTGAACAACTTTCCCTGACAGCTTGTGAACAAATGCTAATACATCCTGCCTAGGGTCCCAGTGGCAAACCAAAGACACCATTCCACCCAATTCCAGCTTGGGGAGCCAATGGGTTTACTGGGCTCCCTTACAGGAGTATGGGTGAGGGTTTTCTTCTAGGAGTATGAATGCACCCCAAACAAGAACATTACTAAAAACCCCCATCTCAGCATCTCAAAGGCTGCATGGATAAAGTCTCCTTCGGTCAATCTCCCACCTCCCATAGCACCTCTAGCATCCTCCAGCACTCCCCAATATCATGTGCAGCTGGAGAAGAGGGAGCAGCCCTCCCCACCTTCTCTTTCAGTGACAGAATCCCAGCAGGCTCAATCTTGTGAGGATCTCAAACAATAAGTCTTAGCTGCTCCGGTGAGGATAATAGTCACGGCATGCGTGGAGGCCAACCTTGCCCCACACTGGGCATGTGTGGAGCATACAAATTAAGGGGCACTGGATGATGGTGGTAGCCATCTGGAGCTGTCAGCTTGGGTCTCATGGGCTGTGAGAGAGGATAGCTTTTGTTCTCCTCTTGGCTACAGTGAGATCTTTTGGCTGTGGTTTTCCCAGGATGACAGTGTTACATCTGAGACCCCACAGTGTCCCCATAATAAATCCCCAAGACCTGAGTTCAAGCGTGGGGTCTGCCACGTTTTAGCTGATTAGCCTCGGCCAGGTGACCCTCCTCTCTCAGCCTCAGTCTCTCATTAGAAGCCTCTGGTGTGTTGACACAATGCCTACTGCGTGGCTGCCTGAGTTGCAATGTCACATTCTGCTTTTGTTTGTGACTTGTGCTCCTGAGGGTATACTAGACCATGTCACATGCAATGGGGCTCAACTCTGTTCCCTGTTTCCTTGCCACCACTTTTCAG
Seq C2 exon
TGCCACCCCGAATTACCCTGCCACCCAACCTACCAGGCCCAGTACTGCTTGGCACACCCTTCCGCCTGACCTGTAATGCCACTGGCACCCCCCGCCCCACCCTGATATGGCTGAAGGATGGAAACCCTGTGTCTCCTGAAGGAATCCCTGGCCTCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000055632:ENSMUST00000113532:38
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=0.113
Domain overlap (PFAM):
C1:
PF0767911=I-set=PD(64.8=95.0)
A:
NA
C2:
PF0767911=I-set=PU(54.9=94.3)
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:
ACGTCTCCTGGTTCAAGGGTC
R:
TTGAGGCCAGGGATTCCTTCA
Band lengths:
334-1884
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