MmuINT0089741 @ mm9
Intron Retention
Gene
ENSMUSG00000026479 | Lamc2
Description
laminin, gamma 2 [Source:MGI Symbol;Acc:MGI:99913]
Coordinates
chr1:154986856-154988901:-
Coord C1 exon
chr1:154988656-154988901
Coord A exon
chr1:154987002-154988655
Coord C2 exon
chr1:154986856-154987001
Length
1654 bp
Sequences
Splice sites
5' ss Seq
GAGGTAGTA
5' ss Score
4.45
3' ss Seq
TATCTGCCTCTTATCTCTAGCTT
3' ss Score
8.32
Exon sequences
Seq C1 exon
GTGCCCGCTGTGAGCTCTGTGCTGATGGCTTCTTTGGGGATCCCTTTGGGGAACGTGGCCCAGTGAGGCCTTGTCAACGCTGCCAATGCAACAACAACGTGGACCCCAATGCCTCTGGGAACTGTGACCAGTTGACAGGCAGATGCTTGAAATGTATCTACAACACGGCCGGTGTCTACTGTGACCAGTGCAAAGCAGGTTACTTTGGAGACCCATTGGCTCCCAACCCAGCAGACAAGTGTCGAG
Seq A exon
GTAGTACTATACCCTTAGACAAATTATGCACCCCTATCTTTTCATCTCTGTATATGTATGTGTGTGCATGCGTGTGTGTGTGTGTACACATGCACATATGTAAGGACATATGAGCTTGCTTTAATCTATACATGGAAGCAAAGGCAAGGACGGCTAATATCACGAGGCAACTAGTTCCATGACCAGACCGGCTCCTGAACAATCTGCACTATTCATTCGCATGTCACATAAGACCAGCCTCCCCTGCACCAGCTTCTGAAAGCAGCATTAGAAACTCTCAAATGGTTAAACCTGGGTGGGAAAAGTAAAAAAAAAAAAAAAAAAAAAAAAAGTCAGGTTTACATTCCTGAGTGAAAGAGCAGATAAGTGGGGGCACATCCTGCCCAACCCCAAGGCAGGTAGGCAGAAAGGAAGCTGCCAGACCTGTCACCAGAGAGCAATAAATGACTCACCACTGAGCCGGAACAAACCCAGGAGGGGAGGAGTCTGGTTGTAAAGCCGTTGAAGAGACCCTCTCAGGATGTCAGTGTGATTACGAAGGTAACCACAGAAGGTTCTCCCGAGGAGATTCGGCTTCAAAGAGGCTTTCGTAGGGGGGCTGCTAAGGGCTCAGATCAGAGCCCAAGTGTGCAGGTGTGTCCCCTCAGCTCAGCCTGAGAGTGCAGGGCTACCGTCAGCCCCTAAACAGGGACACACTGAGGCCCCAGATGACTCTGGTGTGTGGCTGCTATCAGGTCCTGACACCAGAATGTCTACCTAGAGATGCTTCGAGGTCCCCTGTGACCAGGTGGGGTGGTTCATGCCTGCAATCCCAGCACTCCTGAGGCTAAGGCAGGATAATCCTGAGTTAGAGGCTAGCCTGAGCAACTGAGCGAAACCTTTTTTTTTTTATTAAAGTAAACAAACACATAGTACATAAATGAAAACTCTTTCGTTGTTTAGATTTCATTAAAATTAGACAAGGTCCTTTACTCTGCTATGAGCAGCTGCCGTTGCCTGCAGTTGGCGCCTCAGGACTAAAGTAGCGGTGCTGACTAAGTCTTAGCTCCTGCGGAGTTCATACACTAAAAAGGAGAGGCGTGGGAACTATGTGCAGGTAACGGCAGAGTACTCAGCTCCGAGAGCAGCGTGGCATCTCTCCCACTGGTACATCCTTGTCTCCGGAACAGAACCTGGCACACAGGAGGGCCACTGCCTCCTCTCCTTACCTTCCCTGCAGTGGGAAGAAAGGAACCCTGGCTCTTCTGAGTTCTCATGGCAGCTTCCTTTCATTTGGTCTAGGATCTGAGCAAACCCTCTGAGCTTACATTCCTCAGCTAGAAAACAGAAGACGCTGTTTACAGCTGGCTTAAAATAGGCCGAAAAAAAAAATGCACCTTATAAGCAAAATCAGGGTGCCAGCAAAGTACCCAGTAGGCTTTTGGCATGATGAGAGGAGAAAGATGATAAGTTTCCTGGCACCTCTGCATTCGAGCGCACACACATGGATCACGCTTGTGAGGTTCCCTGAGCTGGCTTCAATAAGAATGTGCTCAAGGCTACAGCCAAGGGATGATGGATCTGACACAGCCTCAGGGTTCTCTTCCCTAGCTGTACCTCCCATTCTGGGTCAAGTTGGGTGGGAATACACCATTTATCTGCCTCTTATCTCTAG
Seq C2 exon
CTTGCAACTGCAGCCCCATGGGCTCGGAGCCTGGAGAGTGTCGAGGTGATGGCAGCTGTGTTTGCAAGCCAGGCTTTGGCGGCCTCAACTGTGATCACGCAGCCCTAACCAGTTGTCCTGCTTGCTACAATCAAGTGAAGATTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026479-Lamc2:NM_008485:12
Average complexity
IR-S
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:
PF0005319=Laminin_EGF=PD(45.3=28.9),PF0005319=Laminin_EGF=WD(100=65.1)
A:
NA
C2:
PF0005319=Laminin_EGF=WD(100=89.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCTCTGTGCTGATGGCTTCTT
R:
GTTAGGGCTGCGTGATCACAG
Band lengths:
342-1996
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: