MmuINT0078109 @ mm10
Intron Retention
Gene
ENSMUSG00000066842 | Hmcn1
Description
hemicentin 1 [Source:MGI Symbol;Acc:MGI:2685047]
Coordinates
chr1:150755256-150756618:-
Coord C1 exon
chr1:150756523-150756618
Coord A exon
chr1:150755384-150756522
Coord C2 exon
chr1:150755256-150755383
Length
1139 bp
Sequences
Splice sites
5' ss Seq
TCGGTAAGA
5' ss Score
10.53
3' ss Seq
GTACTCTTTCTCTGATGTAGTTG
3' ss Score
7.2
Exon sequences
Seq C1 exon
ATTTATGGGCAAGTGATAAAGGAACGTACATCTGTGAAGCTGAGAACCAGTTTGGAAAAATACAGTCGCAGACAACAGTAACGGTGACAGGACTCG
Seq A exon
GTAAGATTAACTTTCTAGAGGCGACATTCTCCACAAACCTCAGACCTCTTGGGTGATGTCACCCTTTACAGTGACAATTTCCCTCAATTCTACAGCCAGGGAGAGGTTTGGGTTCCTAAGCTATATTTCATACAGTGTTACAACTATAAATAACTTAGAGAGCACCTGCTCAGACTCCTCATCTTCTATTTGACTATTGGTCAGTTTAAATAGGTTGAAGCCTAAACACACACACACACACACACACACACACACACACACACACACACACACACACACACAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGTGCTTTTGATGGCTTTTACTTCAGCCCTCATATGATTATATTCATGAGTTGTGAAGTAGATCTAGAATACAAATTATTTCCAAGTTGTGGGACTTTTGCTTCAGTATATTTTACTGACTAGACATGTCTGACTGATGAAACTGTTAATTTACTCTCATTTTTAATTTATGTCTCCATTTATTCTTTGGAATTTTATCCCAGTACTATAGAATACAAATTGTTATAGTATTAAATGTGGCTTAAAGTACTTAACTGCATGTATCTGATTAATGTTGGTTTACAGAATTTTCTGTATGTACAACTCCATTTGTCTTTCTACCACCTACACTTTTAGATAATATCTCTTAAGGAATTTGCGCTCATTTGTGGTGTATATTTTTGTTAATTTCCAGAAAAGAACAGGTTAGCCACACTTCTTTGCTCTTCTGTCTCAGCAAACTCATCTCTGTTTAGGCTCCTGATGAATCCTAGTCTATTCTGTTTCTGGCTATTTCCCTGATAGTGGGTTCTGATAATTCCAGGCTTCCGCTCACAAGCACCCTCACACACTCTCCGTTCTAACGTATATGCTGTGAACATCTGGCCCTGACATTGCTCTTCTGTGTAGGTTCTCCTCTTTCCTCTTGATATTTCTGCAGGATCACCTGTACTCCTCCCAGATCTACTTTCACCCCTTACATCCACATTCAAGTTTGTGTTCTACTTTAAGCCCTATTCCTGAAAACTCCAGTTTTAAACAACATAATTCTCAATTATCCTTCTTACAATAATATTCTCCTCTAGTCTTCATGAAGTTGAGTACTCTTTCTCTGATGTAG
Seq C2 exon
TTGCCCCACTTATTGGAATCAGCCCTTCCATGGCCAGCGTTATTGAAGGACAGCCTCTAACTCTGCCTTGTACTCTGTTGGCTGGAAATCCCATTCCAGAACGGCGGTGGATGAAGAACTCAGCCATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000066842:ENSMUST00000074783:17
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0767911=I-set=PD(30.4=84.8)
A:
NA
C2:
PF0767911=I-set=PU(45.5=93.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATTTATGGGCAAGTGATAAAGGAACG
R:
TGGCTGAGTTCTTCATCCACC
Band lengths:
222-1361
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- 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