MmuINT1020605 @ mm10
Intron Retention
Gene
ENSMUSG00000055632 | Hmcn2
Description
hemicentin 2 [Source:MGI Symbol;Acc:MGI:2677838]
Coordinates
chr2:31385150-31386889:+
Coord C1 exon
chr2:31385150-31385304
Coord A exon
chr2:31385305-31386610
Coord C2 exon
chr2:31386611-31386889
Length
1306 bp
Sequences
Splice sites
5' ss Seq
ACTGTGAGT
5' ss Score
7.94
3' ss Seq
ATGTCCCTCTCTGTCCCCAGCAC
3' ss Score
10.84
Exon sequences
Seq C1 exon
GCCTATCCTTCCAGGGGATCCTCACATCCTGCTGCAGGAGGATGGCCAAGTTCTCAGAATTATCAGCAGTCACTTAGGTGACGAAGGGCAGTATCAGTGTGTGGCCTTCAGCCCAGCCGGCCAGCAGGCCAAGGACTTTCAGCTCAGCATTCACT
Seq A exon
GTGAGTCCAGTACCTTCCAGCCCTAGCTGGTCCAGGAACTTGCTTCCCTGCCTCCTGTTGCTGCCTGGGAGGGAGAGCGAGGTCAGAAACGGGGCCTGAGGGTCAATAACAGGAGCCAAGGGCATATGGCCCCTCATCTCCCCAAACTACCAACTTTATACACTCACTACTTCCGATGTGTGTTGAACTTACATTTATCTGAGAACGCCAAATAAGGCAAGTTAGTATTTCAAATGTCAGTGGGAAGCCAGTGTCCATCACATCAGTGGAAGGAACAGGAAAAATTAATACATTCAGGGCTGGGGTGGGGCTCTGCAGTGGAATCCCTTTGCCTGGATGGGAGAAGCCCTAAGTACTATAGGTGATAGCATAGTGGCCTCAGAGGGAGCCTTTCCTCACTGCCACCGGGGACAGGAGAGTTAGGAGGGCATGGGTCTGGGAAGCACCAAGAAACGCATTCAAAGAGATGGAGGCAGTCCTCCTAAGGCCAAGCAATGGGCGCTCGGCCTGCATCTGTGCTCTGTGGTAACAAGGGGGGCTGAGAGCTTAGGGAAAAGGCTCAGTTGGTACAGTGCTCGCTCCACAAGCCTGTGAGCCCGAGTCTGAATCCCCAGAACTCATGTGGCTGCTGGGAAGATCACCTCACCTAGACAGTCACCAGCACTGAGGACACTGAGACAAGTGGACTCTTGGGGTTCTCAGGCCAGCTAGCCTAGCTGAGCTGGTGAGTTCCAGAGCCAGTGTCACAAGCAGTAAGGGACAGGGTCTAATAGAGGAAGACACCAGATGTCGACCTTTGACCTGTGTGTGTATGTGTGCGTGTGCGTGTGCGTGTGCGTGTGTGTGTGTGTGTGTGTGTGTACCCACGTGCACATGTTCTGGGAGGCAGAGTGATGTCCTACTGTACCCATGTACCTCAGCCATTGTCCTGAGTACCAGCTGTAAGTACCCTGCCCTAGGGGAAGCCCTGATCAAGTTCCTCCACAGATGGGGACCCCGAGGCCCAGAGAGGGGAAAGGACTTACCCCAGGTCATACAGTGAGTTAGAAGCCCTGTGGGCTCCAGAACTCAAGCCTGCGGCCCCTCTCCCCATCTGCACCATCCCTACCCATAGTGACTGGACTTGCTCCCCACATTAGCATGTCCCTGAGCTGGCCTCTTCCGTTTGTGTCCCCATATCCCTCCCTTATCCCTCATGCCTGCCAGTCCCTATAGTAGAAGCCTGGGTGTGTGCATGCTACTCACGGGACATCCGCCACCTACTCAGTTTGTCTGTGACCACCCTCATGTCCCTCTCTGTCCCCAG
Seq C2 exon
CACCACCCACCATCTGGGGCTCGAATGAGACAGGTGAGGTGACTGTCCTGGAGGGCCACACCGCACAGCTCCTATGTGAGGCCCGAGGAATGCCATCCCCTGCCATCACCTGGTACAAGGATGGGACCCTGCTGGCCCCCAGCTCAGAAGTGGTTTACAGCAAGGGCGGCCGGCAGCTGCAGCTGGTGAAGGCCCAGCCCTCCGATGCTGGCCTCTACACCTGCCAGGCCAGCAACCCTGCAGGGATTACGAAGAAATCCACCAGTCTGGAGGTTTATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000055632:ENSMUST00000113532:30
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.127 A=NA C2=0.090
Domain overlap (PFAM):
C1:
PF0767911=I-set=PD(59.5=94.3)
A:
NA
C2:
PF0767911=I-set=WD(100=90.4)
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:
GATCCTCACATCCTGCTGCAG
R:
TGTAGAGGCCAGCATCGGAG
Band lengths:
358-1664
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