MmuINT0106193 @ mm10
Intron Retention
Gene
ENSMUSG00000002341 | Ncan
Description
neurocan [Source:MGI Symbol;Acc:MGI:104694]
Coordinates
chr8:70109941-70112187:-
Coord C1 exon
chr8:70111894-70112187
Coord A exon
chr8:70110538-70111893
Coord C2 exon
chr8:70109941-70110537
Length
1356 bp
Sequences
Splice sites
5' ss Seq
GAGGTGCGT
5' ss Score
8.42
3' ss Seq
CTTTTCTGCTTTTTCTATAGCTC
3' ss Score
10.41
Exon sequences
Seq C1 exon
GTGAAGTCTTTTACGTGGGCCCGGCCCGCCGACTGACCCTGGCGGGCGCGCGGGCACAATGTCAGCGGCAGGGTGCAGCGCTGGCCTCGGTGGGGCAGTTGCACCTGGCCTGGCACGAGGGCCTGGACCAGTGCGACCCGGGCTGGCTGGCAGACGGCAGCGTGCGCTACCCCATCCAGACTCCGCGCCGGCGTTGCGGGGGCCCCGCCCCAGGTGTGCGCACTGTGTACCGCTTCGCCAACCGCACCGGCTTTCCTGCGCCAGGAGCACGCTTCGACGCCTACTGCTTCCGAG
Seq A exon
GTGCGTTAGGAAGTGTCCCTGCAGATCACGCCCCAGAGCAGTTGTCTTGGCCACTCCTCGTGGGTGTGCATCATCCAAACAGGTCAACAGCCCAGGGTGTCTGACTAAGCCGTGACCCTAGGAGTGGTCCTTGCCTGACTACACACGGTTTAACCTCTGCAGCTACTAGTTGTGCGTGCGTACGTGCGTGTGTGCGTGTGCGTGTGCATGTGTGTGTGTGTTTTCCCTTGCGATCACAACCCCAGCCGGAAAACTTGGTTTATGGCTATGCCTCACGTCACAAGACCCCTGAAAGTGTATGATGAAAGCCACGCCTCCATGGGCGTTTCTCCTTCCAGACCACATCCCATAATCTGCATTGGGCGGAACAAACCACATCCCACTATTGGGTTCCCTGGAATTAGGAGCATATGAAGACCACATGCCCTGCCAGTAGGTCCTCTCCGAATCACGTCCCTCGCCAGGATCCTTGTTGAGGGCCACATCTTATGCCTTAAACCCGTAAGCCCCACGGGGACCATTGATGAGCATGGTGGCCATGCTTCTAGACACAGGCAAGCGAAGGCCACAGCCCTACCAGCATTTATTTACTTATTTATGTTTTGCTCGAGACAGGGTCTCACTAGCAAGCGCGAAGGCCTGAGTCCCATGCCAATCACCAAATAAAGCCAGGTGTGGGCTGAGAGCCTGGGGGGAGGAGGAGGCGAAAGAAATCAGAAGTGTTGAGGTCATTCTGGACTACAGAGCTCAAAGCCAGCCTGTGCTACAGGAGATTCTGTCTTGAAAAGCCATAAACAAAGCAATAGATCATTCCTAAACTGGGTGGAAACCATGTGACTAGCCACACTCTCTAGGAGAGAATTCACCCCCTGAGATGGGTCTTTCCTTAGATGTGTACCCAACATTTGGAAGGCTGAGCTGGGAGAATCTCTGAGGGTTCGAAGCAAGCCTGAGCTACACATTGAGTTCCAGGTTAGCTTGGGTTGCAGACAGACAGAAGTCAGATTACTCTGGTGAAGGTTGCATCCTCCCCTGTGGGCTCTGCCCTGGGTGGGGCCTGTCTGTCTACCTGTCTACCTGTCCCCACACCGTAGGCCCAGCCCAGTAGAGATGTAGCAAGAGCTCCGCCAGTGAACCAAGCTGCCCTGATGCTCATGTAACTAGCTGACCCTGACCTTGACCTGCACATTCTGGTGCAGCAGGAATGGTGCACTTCCTCTTCTCAGGCTGGGGAAGCTGAGAAACCACCCAGAAAGACAGACAGGTGCCCAGATGCAGCAGGCTAGAATTTGCATAGACATCATGCAGGAATTTCCCAGCATGCATGGGCCCACACCTTTTCTGCTTTTTCTATAG
Seq C2 exon
CTCATCACCATACAGCACAACATGGAGATTCTGAGATCCCCTCATCTGGAGATGAGGGGGAGATTGTGTCAGCAGAGGGGCCTCCAGGCCGAGAACTAAAGCCCAGCTTGGGGGAACAGGAGGTGATAGCACCTGACTTCCAGGAACCTCTCATGTCCAGTGGAGAAGGCGAACCCCCAGACTTGACTTGGACACAAGCACCTGAGGAGACCCTTGGTTCTACTCCAGGGGGTCCCACGCTGGCCTCATGGCCCTCTTCAGAAAAGTGGCTCTTTACGGGTGCCCCAAGCTCCATGGGTGTCTCCAGTCCCAGCGACATGGGAGTAGATATGGAAGCGACAACACCCTTGGGCACACAGGTAGCACCCACCCCCACGATGAGGAGGGGCCGCTTTAAAGGGTTGAATGGTCGACACTTCCAGCAGCAGGGCCCAGAAGACCAGCTGCCTGAGGTAGCAGAGCCCAGTGCCCAGCCTCCCACCCTGGGAGCTACTGCCAACCACATGAGGCCTTCTGCAGCCACAGAGGCTTCAGAGAGTGACCAGAGCCACAGTCCTTGGGCCATTCTGACCAACGAAGTGGATGAGCCAGGAGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000002341:ENSMUST00000002412:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.056 A=NA C2=0.980
Domain overlap (PFAM):
C1:
PF0019312=Xlink=WD(100=98.0)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTTCGACGCCTACTGCTTCC
R:
ATCTACTCCCATGTCGCTGGG
Band lengths:
352-1708
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