MmuINT0037122 @ mm10
Intron Retention
Gene
ENSMUSG00000030158 | Clec12b
Description
C-type lectin domain family 12, member B [Source:MGI Symbol;Acc:MGI:1918433]
Coordinates
chr6:129380488-129382478:-
Coord C1 exon
chr6:129382380-129382478
Coord A exon
chr6:129380704-129382379
Coord C2 exon
chr6:129380488-129380703
Length
1676 bp
Sequences
Splice sites
5' ss Seq
TGTGTAAGT
5' ss Score
7.65
3' ss Seq
TGCCTCATTGTGTCTTGCAGTTT
3' ss Score
8.87
Exon sequences
Seq C1 exon
GACACCCAGCTCAATCCTCACTTTGGCGAGGCGCTGCCTTGAGTTTGATGACCCTCTGTTTGGTGCTGGTAACAGGACTGGTGACCTTGGCAACTATGT
Seq A exon
GTAAGTATATGTGTATTAGACAAAAGAACGTCATTTAGAAAACACTTAGTGTGCTAATTCAGGAAGGATAAGGTACCAACACACAGAATCCTCAAATCACTTCTGCTACTCCAGATCATTCTACAGCACACTTTCAAAGCAAACTAACCATGGGCCTATTTCACTGCTATGTGAATTCTACCCCACAGCCATTCTTCCTTTTTGATGAAACTTATCATACTATGAGAATTCTTCTTGTGTTAGTTATTGGTTGGAATGAACAGGCTCTCTTCTGACCACAAACATATTTGTTATTCTTAGTGAAAAACATGAGAACAAGGGGGAGATGGATTTGCAGAGAGGCATGGCAATTTGTTTATCTTGAAACTTAGTAGAAGATTAACTCAATCTGTTCACCAATGACCTTGCTAGGGTAAAGAAAATATTTGAGTGGCAGCAACAACCTGACTTTTGTGAATGAGGAAAGTCACATAGATAAGAAAAAGAAGAGGTGGGAGTTATGTCACACCTGGCTGACAGAGTGAAACTATTCACGTGTCTTACAGTGGAAGCCACTCCCTAGAAGACCCTAAGAGAATATTCTCTTCATTCTGGGTAGGGCATTTTATATTATGGTAGTGGAAAGCCTAAGGATATGTATGTTATAAAATGTTAAGTATGTGAAATAGAGTATTAATTTGATCAGTACTCACTCTCTGGAGACTTGTAATAAAAATTTATTAAAATATTAGAAGACACTGTATGAATCAGCATTTCTTGTTGATGTGACTAAACCAAACAAAAAACAAACAACAGCAAAAAAGAAAAAAATCAAAACAAAAAACCCAAAGCAGAGATTAAAGTAGGAAGGTTTTATTTTGGTCCATGGTTTAATTAAGAAGGAATATAGTCCCTCATGATGGGAAGTCATGAAGACAGACTTGTAGAGCGGTTGATCATATTGCATCAGAAGTCAGATAGCAAAGAGAAATGAATGCAATGATCTGCTTGCTTCCTCCTTTATACTCAGCCTAGGTCCATAGCCTAGGGGATGGTGCTGCCCACACTCAGGGTGGGTCTTCATATTTCAGAGAAACCTCTCTGGAAATGCCCACACAGGCACATCCAGAGGTTTTTCGGCTAGGTGAGCAATACTCATCAACATGATCAATCATCACAGACACTAATGTCTTCTCTGCTCTATTCATTTATTTCTTATATAAAAGCTATGATTGATATATTGATATATTGTTAGCTATGATTTGGACATTGGAAAGCTTAATAAAAATTAGAGTTTTTTAAAATAGATGCATGGATCCAGAACTAGGAATGGTTAGAATGGTCCAAGACAAGTCTGGGATTATTATCAAGGATGAAAGAAATGAGGCAGAAGTGTGAGTAGGAAAGCAACATGAAGTCAACAAGAGAGAGAGAGAAAAGGGGAGGAGGGAAAGAGAAAGGGAGGGTAGAAGGAAGAATGAGAAAAAGAAAGAAGTAAGTGGAGAGGAAAGAAAGGAGGGAGAGAGTGGAGGTAGGAGAAGAAAATAGAGGAGGAGGAGGGGGAGGGGAGGGGGAGGGGGAGGAGGGGGAAGGGGAGGAGGAGAATCCCTGGTGGCCGGGGGACTACACTCTTGAGTCAGCCTGGCAGCCTTGTAAGAGCAGCGGCTCCCATATGCTTGCCTCATTGTGTCTTGCAG
Seq C2 exon
TTTTGCAGGTGTCTAATGACATTAACTCTGATTCAGAGAAGTTGAGTCAGCTTCAGAAAAGCATCCATCCACAGCAGGACAATCTGTCTGAATCACTGAACAGCTCCAGAAAGAGTCTGACGGAGGAGTCTCTCCAGTCCCAGATCTCTGCCCTACTGGAGAGGCAGGAGCAGATGGCTACCAAACTCTGCAAGGAATTCCTCATCCACGCTTCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000030158:ENSMUST00000112082:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.088 A=NA C2=0.233
Domain overlap (PFAM):
C1:
PF086266=TRAPPC9-Trs120=PU(31.6=91.2),PF083915=Ly49=PU(23.1=82.4)
A:
NA
C2:
PF086266=TRAPPC9-Trs120=PD(67.3=90.4),PF083915=Ly49=FE(59.5=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
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:
ACACCCAGCTCAATCCTCACT
R:
AGAAGCGTGGATGAGGAATTCC
Band lengths:
313-1989
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