MmuINT0106196 @ mm9
Intron Retention
Gene
ENSMUSG00000002341 | Ncan
Description
neurocan [Source:MGI Symbol;Acc:MGI:104694]
Coordinates
chr8:72626309-72627959:-
Coord C1 exon
chr8:72627843-72627959
Coord A exon
chr8:72626423-72627842
Coord C2 exon
chr8:72626309-72626422
Length
1420 bp
Sequences
Splice sites
5' ss Seq
TTGGTGAGT
5' ss Score
9.27
3' ss Seq
ACCCATTGCCTGCCTCCCAGACA
3' ss Score
6.22
Exon sequences
Seq C1 exon
ATCCCACAGATCCCTGCGAGAACAACCCCTGCCTGCATGGGGGCACCTGCCACACCAACGGCACCGTGTATGGCTGTAGTTGTGACCAGGGCTATGCTGGGGAGAATTGTGAAATTG
Seq A exon
GTGAGTGTCCCAGCTCAGAGCACTGTCCTGTCCCTGGGAGTCCAGGTGACACAACTGAAGTTATCTGAGTTCAAACTAGATCACTGAGCTGCTCAGGAGGGAGAGCCATTTCCTACCATGAATATTAGGGGTTGTGGGGAGGACAAGGAAAGGGTTGGATGCTCTCCAGCAAGCAAAGGGCTATGGGGAGACCACCCTCATCCAGGTGCACAGCCGAGTGGGTACCACTCACATTGCTAAATAGGAGATTACATTAAATAGAAATGGCATAGAATAAAAATAAATACATCGAATTTGGGTTCAGCTCATTCCAGTTGCATGAGAGCCAATGCCTTCTGGCCTCTGCAGGCAATGCACACAGATGGTGCCACAAACATATATGCAACCAAACATAGCCAACTATGTCTGCTGAGAATTAAACCTGGGTCCTCTGGATCTTAACCTCTGTACCATCTCTCCAGCCCCTATGGTGTAATTTCTTGATCACTGTGCATCCTTTGCTTGATTTCACAATCATGCTGGGAGTTATAGAGTCATAGCTGACAATAGAAATGAGGGCAAGGCATGGCAGCACACGCCTTAAACCCCAGTGCTCAGGAGGCAGAGGCTTGTGGATCTCTGTGAGTTTGAGGCCAGCCTGGTCAACATAGCATGTTCCAAGACAGCCAGGGCTACATATAAAGAGATTCTTTCTCCAAAACAAATAAACTCACACAATATAAATAAATATCATTTTAAAATATTGTATTTTAAAAATCCAAATGAGTGACAGCTGAGTAACAACACCCAAGATTGACTTTTGGCCTCCCACAGATGCATCATGTGGATACACACACACACTCATACACACACACTCACACACATACATACTCACTTAACACACTCACATACACACGCACACACATACACATATGCATATACACACTCACACACACACACACTCATACACACACTTATACACACATACACTTATACATATACACACTCATACACATGCACACACATACACGTGCATATACACACATACACACTCATATACATATACACTCACACTCAATCACATATACACACACACTCATACATACACATTCACACACTCACATAAACACTCATACACAATCACACATACACACACACTCATATGGGAGGATTGTTTTAGGGGGCAAAGCGTCTGGTTCTGTTTACAAATACTGCCAGTGGAGCCCTTGTGAGTAAACTTTTGGGCTGCTGTACCCCAAGTGCCTGAGTCCCACTCTTCTACCCCATGGCACTTGCTGTCACTCCACTCATGTTCACCAGTGTCACAGCTGCAGAGCAATCCCTGTGGGTATCCAGGGGATGGTGAGAAAGACCTTGACCCTGTGGGTTGGGAAATGAGTAGAGGCTGACCTCTGACCTCTACCCATTGCCTGCCTCCCAG
Seq C2 exon
ACATTGATGACTGCTTATGCAGCCCTTGCGAGAATGGGGGCACCTGCATCGACGAGGTGAATGGTTTCATCTGCCTCTGCCTCCCCAGCTATGGGGGCAGCCTGTGTGAGAAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000002341-Ncan:NM_007789:9
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.050 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0000822=EGF=WD(100=77.5),PF0000822=EGF=PU(7.9=7.5)
A:
NA
C2:
PF0000822=EGF=PD(89.5=87.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATCCCACAGATCCCTGCGAG
R:
CTTCTCACACAGGCTGCCC
Band lengths:
230-1650
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: