MmuINT1020678 @ mm10
Intron Retention
Gene
ENSMUSG00000055632 | Hmcn2
Description
hemicentin 2 [Source:MGI Symbol;Acc:MGI:2677838]
Coordinates
chr2:31459081-31460738:+
Coord C1 exon
chr2:31459081-31459207
Coord A exon
chr2:31459208-31460049
Coord C2 exon
chr2:31460050-31460738
Length
842 bp
Sequences
Splice sites
5' ss Seq
CGGGTAAGG
5' ss Score
10.17
3' ss Seq
CTTGTCTGTGTCACCCTCAGGAC
3' ss Score
11.03
Exon sequences
Seq C1 exon
ACATCAACGAGTGTGAGGAAGATGGCATCGAGTGTGGGCCTGGCCAGATGTGCTTCAACACCCGAGGCAGCTTCCAGTGTGTAGACACGCCCTGTCCTACCACCTACCGGCAGGGCTCCAGCCCCGG
Seq A exon
GTAAGGAGGGGCCAAGCTGTCGGAGGTACAGGGGCGGGCACATGAGTACAGGGCTTTTTCTCCAGCTTGCCCATGCCTGGACACCCACACACACACACACACACACCCACACACACACACACACACACACACACACACACACACACACACATTCAGGAAGGCACCTCAAGGCAAGGGGAAGTTGCCCTGCCAGACATCCTGGGCCAGAGCTACGTGCTGGGACACCTGGGACACCTGTACCCAAGCAGGGACAAACTTGGCTCCATGCCACTACATGGTGTGTGCTCTCTGGGACACCCCTCCCCTGTACAAACATAACCTCAGACAGAAAGCACCTCCAAACATAGGAATTGGGGAACTCTCACAAACTCCAGGACTCAGCACACTATGTTCATTAAGAGGCACCAGGACCTCAGGACCTAGGGAAGGCTTCTGGACCAGACCTTACAAAGGGGAGTGAAGCAGGCGGTGGGGGAGACTCTGACAAGGCTGAACAAGAGTCTTTGAACCTCTCCTGCCCCTGGGAGTGCAGACATATGACTCAGTCCCTAGGCTCCTCACTTCTAGGCCCCTCTCAGTGAACCTAAGCGTCTGAGTTTTATCGTGTTGTGTGTTTGCTGAGCTACCCTGGGCTTTGGGCAAGGAAAGGAAAAGAGGTGGGGGGCGGGGGGAAGACATGCTAAAGGGGAGGAAAACCTCTGTTTGGCTTCTCTGGGCCTCAGTTTGTGGATCTCTGAAATGAACTAACAGGGGCATATGCAGGCAAGGTATTTGGGGAGCTTGGGGATGAGCTGGGGGTGCACCGGATGGCGGCCCAACGAGCTTGTCTGTGTCACCCTCAG
Seq C2 exon
GACCTGCTTCCGCCGCTGCTCTCAGGACTGCAGCGCCAGCGGCCCGTCTACACTGCAGTACCGCCTGCTGCCGCTGCCCCTCGGCGTGCGCGCCCACCACGACGTGGCCCGCCTGGCCGCCTTCTCCGAGGCTGGCATCCCTGCCAACCGCACGGAGCTCACCGTGCTGGAGCCCGACCCACGCAGCCCCTTCGCTCTCCGCCAGCTACGCGCTGGACAAGGCGCGGTCTACACCCGCAGAGCGCTCACCCGCGCCGGGCTCTACCGCTTGACTGTGCGCGCAGCGGCACCCCGCCACCAGAGCGTCTACATCCTGCTAATCGCAGTGTCGCCTTACCCGTACTGAGGCCAGAGCTGCAGATCCACCCTGACCTCGCAGAGAGGAACAGAGTGGCCCTTGCCCATGACACCTACAGTGACAGAGAACATCCTCTTCTCCCGCCCCCGTGCGTCAGTGAGATCTTTGGTAAACACTGCTGTGCGCAGAGCCTTGACCCCAGGGCAGAGACCGCTGCCCCTTTGATGGCAAAGCCAATGGGTCAGGCCTGAGTCCCGTCTTTCCTCAGATCTCAGCGGGGAGCTGGGCAAGATCTCAGTGGTCCAGGACAGACCCAGTAGGGGTGGAAGCGACTGGCACTGTCCTGACCACATGGAATGTGTATAGTATAAAAAAAATTTTTTTTTACTGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000055632:ENSMUST00000113532:97
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.026
Domain overlap (PFAM):
C1:
PF126622=cEGF=PD(12.5=7.0)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCTGTCCTACCACCTACCGG
R:
AGGATGTAGACGCTCTGGTGG
Band lengths:
352-1194
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