MmuINT0089758 @ mm10
Intron Retention
Gene
ENSMUSG00000026479 | Lamc2
Description
laminin, gamma 2 [Source:MGI Symbol;Acc:MGI:99913]
Coordinates
chr1:153148928-153150866:-
Coord C1 exon
chr1:153150744-153150866
Coord A exon
chr1:153149118-153150743
Coord C2 exon
chr1:153148928-153149117
Length
1626 bp
Sequences
Splice sites
5' ss Seq
CTGGTATGT
5' ss Score
8.14
3' ss Seq
TTCAAAAATCCATTTCACAGCCA
3' ss Score
4.78
Exon sequences
Seq C1 exon
ATGTGGATGGTTGGAAGGCGGTTCAGAGAAACGGGGCACCTGCAAAACTCCACTGGTCACAGCGCCATCGGGACGTGTTTAGTTCTGCCCGAAGATCAGACCCCGTCTATTTCGTGGCCCCTG
Seq A exon
GTATGTGAGGGGTGATTTCTGCAGAAGCCAATTGGTGGTAGGACTGCAGAGTCAGGAGAGAAAAACTAAGTTGAAAGACGTGATGTGCGACCCGTCCCTGTCACTGGGGCTGCAGCAGCTCCAGTAGACACCCGGAGCTTAGGCCCAGTCTGATAAGGCAATATTCCATGACACTGTAGAGCCATCCAGGCATCCTAGAGCTCAGCTCTGCTGGGATTCCCTCCATACCCACCGATTAGCCAAATGAGCAGTTACTAGATTCCCATCGGAGCATGAAACCAAACTTAATGGGTCAATTAAGAAGCAGACACAAAGCATGTCTTTTTGAAAAGCTAAAACATTTAGTTAATGTGTATGTATGTCTGCACATAGGAATGCACACATGTGTGCAGGGTCCCTCAGAGGCCAGAAGAGGGTGTTGGGTCCCCTGGAGCCGTAGCTATAGGAGGCTGTGAGCCGCACAATATGTGTGCTAGGAAACTGAACTCAGGTCCCCTGGAAAAGCAGGAAGAACTCTTTAACTGCTGATCCATCTCTCCAGCCCCAAAGCACGTGTTAAAACTTTAAAACTGGGCTGGTGAGATGGCTCAGCGGTTAAGAGCGCCGACTGCTCTTCCAAAGGTCCTGAGTTCAAATCCCAGCAACCACATGGTGGCTCACAACCATCCAAAACGAAATCTGATGCCCTCTTCTGGAGTGTCTGAAGACAGGTTACAGTGTTCTTACATATAATAAATAAATAAATAAATAAATATTTTTAAAAACTTTAAAACTATTGTTAGTGATCTGAGTGGCAAAGGTCTGGCTGGAATTTGAATCCTAGTTCATAACCTTAGCTAATGAGCACTTCCCAAGCAAGTGGTTCTTTTTAACATCTCTGAACTTTAGTCCTCTCAACTATTAAATGAGAGAGGGCATGCCAATAGTCAAGAATTATTGTCATCAGACATGGGCAGAGCTGGGGAGATGGCTTAGCCGGTAAAGAATGTGTGGTACAAGCATGACGACCTGCGTTTGAATGCTAAGAACTCACAGGAAAAGCTGGTGATTGTGGCACATGCCTGTAACCCCAGCCCTACAACAGTAGAGACATGAGAATCCCTGGGGCTTGCTAACCAGAGACACTTGCCTAATCAGTGGGTTCCAGGTTCAGTGAGAGACTGTTTAAAAAAAAAAGGTGTCAAGTGATTGAGGAGGACACTCAACATGATATCCAGCCTCCACATGCTTGTTCACATCCCTGCACACACATTCATGCTCATCTGTTACACACGGAAGTACACACACAAATATAATATCTGCTAAGGGTTCGCTAAAATGAAAGACACTTATATATAACGAGTGGCACCCCAGCTGTTTTGCCTTGGATCTTTGTCCATCAGGCTGTCTATAATAGTCATGTCATGAGCTATCTGATAAGTAGAATTATCTTTGGAGCTACTTACACAGCCAAAATATCACACTCACATCCCATGACATGATTGACCCTTCCGTCAGGGTAGCTTGGGATAGAAGGATGGGTGGGTCACACAAGACTCCAGTAGAAACTGACAATATTAATTTAATTTGGTCATGCATTTGTCTTCTCAGCAGTACCACTGATCTTTTCAAAAATCCATTTCACAG
Seq C2 exon
CCAAATTCCTCGGTAACCAGCAAGTGAGTTACGGGCAGAGCCTGTCTTTTGACTACCGCGTGGACAGAGGAGGTAGACAGCCGTCTGCCTACGATGTGATCCTGGAAGGTGCTGGTCTACAGATCAGAGCTCCTCTGATGGCTCCAGGCAAGACACTTCCCTGTGGGATCACAAAGACTTACACATTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026479:ENSMUST00000185356:6
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:
PF0005213=Laminin_B=PU(3.8=11.9)
A:
NA
C2:
PF0005213=Laminin_B=FE(48.1=100)
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:
ATGTGGATGGTTGGAAGGCG
R:
TGAATGTGTAAGTCTTTGTGATCCCA
Band lengths:
312-1938
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