MmuINT1022137 @ mm10
Intron Retention
Gene
ENSMUSG00000026943 | Lcn12
Description
lipocalin 12 [Source:MGI Symbol;Acc:MGI:1924951]
Coordinates
chr2:25490845-25492109:-
Coord C1 exon
chr2:25492008-25492109
Coord A exon
chr2:25490953-25492007
Coord C2 exon
chr2:25490845-25490952
Length
1055 bp
Sequences
Splice sites
5' ss Seq
GTGGTAATG
5' ss Score
4.46
3' ss Seq
TACTGTCTCCTCCCCATTAGACT
3' ss Score
5.77
Exon sequences
Seq C1 exon
GTAGAAACTGGAGACTTTCTCATAAGACAATAGACAAGTTCATCTGCCTGACCAGGACCCAAAACCTCACAAAGGATAACTTCCTCTTTCCTGATTTGAGTG
Seq A exon
GTAATGGTTTGCATGCAGTGGGTGATGGGGTCTGGAGAACCTGGACTATGGTGGCACCTCCCTTGGCCTTCACAAGTCCCATAGCCACTCTCCAGGCAGGCACTGCAGATCTTCTGGGGATGTGTGTGGGGTCTTACAGTCCCAGGCAGTCTGAACCAAATGCTTGTTCACAGAGTTTAGCCTGAGCCAGAAGGGAGGTACTCATGGCTTATGGTCCTATCTGAGTCCTAGGCCATTTTGTTCCAATCCTGTGTCCCTGTCACAAGCTGCCCTCTCCCCACACAGATTCTCCAGTTCTGGGACACTTCTCTCTACTCTGGTTCCCTGTTCACAGGACACTGGAGTTCCTCCATAGAAGTCTCTGAATGCAGACAGTGTATTCCTAGTAGGAAAGTCTTGGAGATCCTAAGGCCTAGAGGCTTCAGGGTTGAGCCCTGTCTTCAGCCTCATGCCTCTTATCACTGGCGTTAGGACCTCTCCCCAATCTCCACCCAGTCCGGGGCCATTTCCCATCATGCTGCCTCCGGTACAAAACTGTCCAGCCACATTTGAACATGTTCTACAAGCATGTTCTACAAGCGCTCAGACAGGCATATGCTTGCACACATCTGCTCACACATGCACCTTCACCTCTCACCCTTGTCATTTCTAGATAGGTTCTTGTTGCATAGCCCAGGCTGTTCTGGGATTCATGATTCTCTTGCTTTAGCCTCCTGGGTGCTGGTATTTTTGGCCTGTGCCACCACACCCGGGTCACATCTCATACATTCACATGTGATTACATGTGTGTTTGTACTAACCTTAGCACTCACAGTATCATACTACTATCATGTACCACAAGTCTAGGATCCTGTGGGGACAGGCAGTGCTATGCAGGGGCTTCTGGAAGAGCCTGGTGCCACTCTACAGGGCATGTCTCCTAAACCCCTCCCTGCAGCCGCTTCTGGTCTCATCTCCCTGCCTAACTTCCAGTTTGTCTGCCTGTTGTCCCTCCTAATTCACTCCCTGGATCCTCCTCCTTATCCACCATCCCAATACTGTCTCCTCCCCATTAG
Seq C2 exon
ACTGGTTACCGGATCCACAAGTCTGCTGAAGAAGGAACAGGTTCCTGCCAGTAGAGCCTCACCCTGCCTCTGCTCTCAACACAAATAAACACACTGCCTATGACTCCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026943:ENSMUST00000028312:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0006118=Lipocalin=FE(23.3=100)
A:
NA
C2:
PF0006118=Lipocalin=PD(0.1=0.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AATAGACAAGTTCATCTGCCTGACC
R:
TGGAGTCATAGGCAGTGTGTT
Band lengths:
182-1237
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- 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