MmuINT1020654 @ mm10
Intron Retention
Gene
ENSMUSG00000055632 | Hmcn2
Description
hemicentin 2 [Source:MGI Symbol;Acc:MGI:2677838]
Coordinates
chr2:31426797-31428309:+
Coord C1 exon
chr2:31426797-31426953
Coord A exon
chr2:31426954-31428187
Coord C2 exon
chr2:31428188-31428309
Length
1234 bp
Sequences
Splice sites
5' ss Seq
CCGGTAACG
5' ss Score
7.34
3' ss Seq
CATCCCTCTGTCCATCCCAGGCT
3' ss Score
8.49
Exon sequences
Seq C1 exon
AGCCCCCGGCCATTGCTCCTGGCCCCTCCAACCTGACCCTGACGGCCTACAGCCCAGCCTCGCTGCCCTGTGAAGCCAGAGGCTCTCCCAAGCCCTTGGTGACCTGGTGGAAGGATGGGCAGAAGCTGGACCTCCGCCTACAGCAAGGCGCCTACCG
Seq A exon
GTAACGAACGGTCCATCTACGGTGTAGACATATGAGAGATTGGGGCCCATCACACCGAGTGTGGCAGGGTTAGTGAGGAGGGTCCAGGACCCCAGGTGCCAGGGGAAATTGTGACATGGAGGCAGAGGGATCCCCCTGGCAGGAGAGAAGGTGCTTGAATACATGGCCCCATGGAAAAAACATGCATGACTTATTCAGCACATTGAAAACAGAACATGGGGGGACTAGAGGAGCTTAGTGGCAGGTCAGTTGCTAGGCATACAGGAGGCCTGTAGTGGTAAATAATTAAAGTCTGCTCTATGCTCCCAATGGCTCTGCACCCGCCCAAGGGCTCTGGATTCACTAATGAAAGACACGCACATGAAACCTTTATATTTAATATGCCCTGGCTAGGTCAATGGCTGGGCCACTCTTGAACCTCCATATGGCTAACACACTCCCCTCAGTTATTCCTGAGTTAATACTTGCTAAATCTATATAGCATCTCTGCTACCCTGACCCAATCGGGGGAGTGGCCCCTGGGGCCGCTTTCTCCGACTCTTACATGTTGGTGGGCTCTCCCTCCCACACTTTTTCCTGTGTGGTATGCCCTCCTAATGGCAGAATCCCTCTCCTCTGCGGTTCTTGCCTGGGAATCCTAAAAGCCCCTCCTCTGTTCATCTGCCCAACAATTAGCCACTGGCTCTTTATTGACCAGTCGAAAAACCAACTGTTGACAGGGACCTGCAGCAGATGTGGGAATTCCCATGCAAGCACAAGTCAAATCCCCATCAGAAGCCTGCGGTTACTTCTGAGAGCTTCGAGTGTTGCCCATGTATCATATGTGGCCAGTGGGAAGTGACCATCAGATGTATTTGTTATGTATCTCATCGATGACACACTGTCCCCAACACCACACAGGAAGAGGAACAGAATCAATGCACACGAAAGTCCACAAGCCCAATAGCTGAGACTTCTAGGACTAGAAAGTTCTAGAAGATACTTCTTTTTCGTGCACGATGTTTGTCTGTGTTGAGTATATCTCATGTGTGTTCAGCAGCTCAAGAGGCCCGAAGAGTCTCAGATCCCCTGGAGCTGGAGTTACTGCCTGGAAGTGTGGCAGGGCCTCTGAGCCTCTGAGGCCCTAGAAGATCTGAGTCATGTCTAGAGATAGATGCAGGGCAGGCCTGGAGTGGGGACACAGCTGTGGCTCACCCCAGGCCCCTCACTTCAGCCATCCCTCTGTCCATCCCAG
Seq C2 exon
GCTTCTGCCTTCCAATGCCCTGTTCCTCACCGCTCCCAGCCCTCAGGACTCAGCCCAGTTTGAGTGTGTCGTGAGCAATGAGGTGGGAGAGTCCCGCAGGCGCTACCAGGTGACCGTCCATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000055632:ENSMUST00000113532:75
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.038 A=NA C2=0.214
Domain overlap (PFAM):
C1:
PF138951=Ig_2=PU(55.3=98.1)
A:
NA
C2:
PF138951=Ig_2=FE(43.6=100)
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:
CCATTGCTCCTGGCCCCTC
R:
CATGGACGGTCACCTGGTAGC
Band lengths:
270-1504
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