MmuINT0091850 @ mm10
Intron Retention
Gene
ENSMUSG00000000693 | Loxl3
Description
lysyl oxidase-like 3 [Source:MGI Symbol;Acc:MGI:1337004]
Coordinates
chr6:83035455-83037592:+
Coord C1 exon
chr6:83035455-83035797
Coord A exon
chr6:83035798-83037428
Coord C2 exon
chr6:83037429-83037592
Length
1631 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGC
5' ss Score
9.6
3' ss Seq
GCTCATCTCCCTTTCCACAGGCC
3' ss Score
10.86
Exon sequences
Seq C1 exon
TGCCCCCCTCCTTGGGCCCCACCCGCCATGAGAGCTGTCAGTGTGTGGTATTGCTGCCCATGGGGACTACTGCTGCTACACTGTCTGTGCAGCTTCAGTGTGGGGTCTCCGTCTCCTTCTATCAGCCCAGAGAAGAAGGTAGGAAGCCAGGGGCTGAGGTTCCGGCTGGCTGGCTTTCCTAGAAAGCCCTATGAAGGTCGAGTGGAGATACAGCGAGCTGGTGAATGGGGCACCATCTGTGATGATGACTTCACGCTGCAGGCTGCCCATGTCCTCTGCCGGGAGCTGGGCTTCACAGAAGCCACAGGGTGGACCCATAGTGCCAAATATGGCCCTGGAACAG
Seq A exon
GTGAGCGATGCTCTGGACTAGCCCGGACATTATCTAAGTGCAGTTCAAGTACATAGAAAAGAACAAAACACCTTAATGGCACAACCAAAGGGACACGGGACACCAAGAATGGGCAGAATCAAGCAAACCCACAGATTATAAACCATCTAACATACTAATTTCAGGGCCATGTGACCTGAAGCTAGCCAGTACTCTCCAGGAGCCTCCAGTGTTCCATGTGTACAGTGAGAAGGGGGCTATGTTCTCTTCCACAAAGTGAGACTCCATAGAGCTATGCACAAAGACAGCCCAGTGCAGGGGAGCCCTGGGTGATCCAAGTGCAGTCGACTCAGTGATAATATGAGGGCAGGTGAATGGTATCCGAATGTCCCCTAGCCAGAACGGGTCATATACTACAGCTGACAAAATCGGGACCCAGGTCAGAGCTAAAACCAGCAAGCAGGAACTCATGTGGAACAAGTATGACAGTGCGAGGGTTGAAGCACAATTCTCTGGAGCTGAAAGTGCTCAGATTGTATGGGCTCACACTGTGGGTGTGATGGGTGGGCACCTGCTGTTGATCCCCCTCCCCTGTTCCCAGTTGCTCCACTGCTTCAGAGATCAAGTGTCACTTTGGAGATAACAGCCTTGGAGACCAACAGTAGAAAGTGGAGATGCTCAGAAGTACTTTCCTACACTCAGTCCTCCAGAGAGAAGGAGGGAAGGAGGGAGGAAGGTGGAGACAGACAGAGAGAGACAGAGAGGAAACCGCTTTCAGAAAGCCACTTTCAGGAGGAATAGCTAAAGAAACCAAAAGCTTGGCACAGAAACAAACAAGCAAAGCCTCACTTAGCAATTACATGACGGTTGGGTTCAATTCAGGAAGGACAGTCGTGGCTGAAGGGTTTTCTGGGTGGCATCAAAGGACTGAATCAGACCTAGCAGGGGAAAGTTGTAAAGACCCACAAGGACCTTCTGATAGTTACGTGGCCTCCTGGGGCTGAAAGGTAAAAGCCCTGTGAGAATAGGTGAGGTGCCCTGAACACTGGCTGGAACACATAATTTTCGCGAGGTTCCTCCCAGTTTTGAGTGGTCAGTGATAGTCAATATGGCCCAGAAAGTAAAAATAGGGTTTCTGTGGCAGTAGGCCACGTAGGTATACAGAAAAACGCCACAGGGGAGACGCCAGGGTGAAGTGAAAGACTCTAAGATTCCCAAGTCTCAGGGAAAAGTCAGACTCTTAGGCAAGTTACATCATTTTTCGGAGCCCCAGTCTATTTATATAAAGTAATCTTCTGGCAGCTGCAGTCTGAGAATGATTGTGTATATACTATGGCAAAGCATTTGGCCCTAGTAGGGACTTAGTTATAGCTGATAGTGAATGAATCCTGATTGATATTGGTGAGAGCATAAATGTTGATTCTCTGTTGTTGGTTGTTTTGGTTTTAATTCACCCTAATCAGGTCTTCAGCATCCCAGATCACCAGTAACCTTTCATCAACCTCACACCCTCTTTCCTCTCACCCCCCCCAGGGTCCCCTGTCTCTTCCCCATCTTCCTCTCATCAAAGAAGGATTAGCCTCAAGGCCGAGTGAGGCCACCATTACTGTCAGCCATCCTCAAACACTTCTTGCTCATCTCCCTTTCCACAG
Seq C2 exon
GCCGAATCTGGTTGGACAATCTGAGCTGCAGGGGGACTGAAGGAAGTGTGACAGAATGCGCCTCTCGGGGCTGGGGAAACAGTGACTGTACCCATGATGAGGATGCCGGGGTCATCTGCAAGGACCAGCGCCTTCCCGGTTTCTCAGACTCCAACGTCATTGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000000693:ENSMUST00000000707:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.009 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0053013=SRCR=PU(57.3=51.9)
A:
NA
C2:
PF0053013=SRCR=PD(41.7=72.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCCATGAGAGCTGTCAGTGTG
R:
GCAGCTCAGATTGTCCAACCA
Band lengths:
348-1979
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