MmuINT0037398 @ mm9
Intron Retention
Gene
ENSMUSG00000026034 | Clk1
Description
CDC-like kinase 1 [Source:MGI Symbol;Acc:MGI:107403]
Coordinates
chr1:58478618-58480932:-
Coord C1 exon
chr1:58480764-58480932
Coord A exon
chr1:58478779-58480763
Coord C2 exon
chr1:58478618-58478778
Length
1985 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGA
5' ss Score
10.57
3' ss Seq
GTAAAATTTGTCTTTCATAGATG
3' ss Score
7.78
Exon sequences
Seq C1 exon
GGTATAGGCCCCGCCCATCTACGTCACCAGTTTTTCCGAGAAGAAGCTCGCACTGCGTCTGTCCGCACCATTTTGTGTTGGGAGATCGTCGTAATCGTTTGCAGACTTCTCGCCGTCGCCTTGTAAGCTTTGTCTTCGCCTTGCAAGCTTTGTCTTCAGGGTTGGAAAG
Seq A exon
GTAAGACGCGGTGTCTGTCAGGGCCTTTCCTTGTATCTTCCCGCCGCCTCCAAGGACCCCGCTGCGGCTCTTCACGGCGGAGCCACGCGAAGGGGCTCTGTGCCCCGGCTGCGGAGCTCTGGCCGCTGGCTTCTGCGTAGGCGGGGACGATGCCCGCAGGCTCCGCGTCCCGAGGAGGGCCGGCCGACTGCAAGAGCCCGAGCTGCCGCGGCGGGACCTAAGATGGCGGTAGGGGGAAGGCCGCGCTCGTCCTTCGCCATGGCGGCGCCAGGGCGCGGCCTTCGCTTGGACTCGGTCGGTCCTGGTTTTGCTCTCGGCGGTGGCACGGCGCAGGTTTTGGTGCTGTTTTTCTTTATATTTGAAGCGAAAGGTCTTGGTAACCAGGCCGGCCCCACACGCTGCGGTCGCTGATCTTGTTAGAGATGGGCGCTGCGGGGACAGCGTCACAGCAGGCTGTCACCTCAGTTCTGTGTAGTTTCCGCCTTCGACGAAGAAAAGAATTTCAGAGGCGGTCGATAGATAGCGAAGTCGAGCATAATGAAAACGAGGCACACCGGGACAGCGCTTGTGAGAGCGAGGAACAAGTGATTTTTAAGAAGGTTTAGGATTTACTTAGGTTTTGTAACATTAAAACTCAAGACGGCCGGGCTGTACTGCCTGTCGCTCGCCTTTTAATCCCCTTTGAGCCTGTCTCAAAAAAAAAAAAGTTATAGAAAATTTCCTTTGTAAACAAAGTTGTAACGGGGGAGTTGTTTACCTTTAGGAAACAGGAGGGGAACACCCTAAGATTGTACGTCACTTCCGCTCTGAACAGCTTTATTTTCAACATCATGGCCTGTCCTGTACAGTTAAGTAGAGTGGCTTTATTGGTGGAGCCCGAATTTTGTTGACTCGGCATAAAAGGCGCGCCTGTTACCTTCTCAGGCTTTCCTCCCATATTTTCATAATTTTCCCAGTCTCCCTCTGCTAGCAGTAAGAGTGTCAGCGGGGACCGTGGGCATTTACTTGACGGTGAATTGGGAATTGAGGTCATCTGCTGAGCAGCTTTTTTTTTTTTTTTTTTTTTTTTTTAATAGCTGTAAACAAACACTTCATAACATCCAAACTGGTATTTTACCAAAAACAAACAAAACACTTTGGGGGCGGGGGCTGTTCCAGACAGGGTTTCTCTGTATAGCTCTGGCTGTCCTGGAACTCATTTTATAGACCAGGCTGGCCTCTTACTCAGAAGTCCGCCTGCCTCTGCCTCCCGAGTGCTGAGATTAAAGGTGTGCACCACCACGCCCAGTTAAAAAAAAACTTCTTAATTAGGGTCACTTGTGGTTACGTTGGTCGGAGACTTGGTTTGGGTAGAAATTGAACCTTGTGAACCTGTAAGTTGAACTTCTGAAAGAGCTGTCATACATTTTTCTTAAGTTTTAACCTTTTTCACTTAAGGTTTTAAACCTTTTTCACTTAATATGAATTTGGGCATTGTGAAAACAAGGTGAAAAAAAATCTGGCCGGGCATGGTGGCGCACACCTTTAATCTCAGCATTTGGGAGGCAGAGGCAGGTGGATTTCTGAGTTTGAGGTCAGCCTGGTCTACAAAGTGAGTTCCAGGACAGCCAGGGCTACACAGAGAAACCCTGTCTCGAAAAACCAAAAAAAAAAAAAAAAAAAATCTGTGAATAAAGTTTACATTGCAGAATCTGAGGCAATGCAATAATTTTTATGATTGCAGACAGTTGACTAAAATTTTAGAACTTTGATTTTAAACAAAACGTTAATGCTGGGGGTCACATGCATTTTATCCCAGTACTCCAGAGGCAAGAGGCAGGTGGCTCTTTGAATTCAAGGGCAACTTGGTGCACATAGTTAGAGCTACTCTATATTGAGGCTGTCTGGGGAGGGGAAAGATGGAAACTAATGGGAGTTTGCAAAGAAACATTTACTACTGAACATCACAGAACTACAGTTTAACTGGTAAAATTTGTCTTTCATAG
Seq C2 exon
ATGAGACATTCAAAGAGAACTTACTGTCCTGACTGGGATGAAAGAGACTGGGATTATGGAACATGGAGAAGCAGCAGCAGTCACAAAAGAAAGAAGAGATCACATAGCAGCGCCCGTGAGCAAAAGCGCTGCAGGTACGATCACTCCAAAACGACAGACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026034-Clk1:NM_001042634:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=0.500
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
PF105774=UPF0560=PU(26.0=85.2)
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCCCATCTACGTCACCAGTTT
R:
CTGTCTGTCGTTTTGGAGTGA
Band lengths:
318-2303
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: