MmuINT0032437 @ mm9
Intron Retention
Gene
ENSMUSG00000015854 | Cd5l
Description
CD5 antigen-like [Source:MGI Symbol;Acc:MGI:1334419]
Coordinates
chr3:87169712-87171801:+
Coord C1 exon
chr3:87169712-87170032
Coord A exon
chr3:87170033-87171462
Coord C2 exon
chr3:87171463-87171801
Length
1430 bp
Sequences
Splice sites
5' ss Seq
AGAGTAAGT
5' ss Score
9.35
3' ss Seq
GCCTCTCCTTTTCTTTCCAGACC
3' ss Score
11.1
Exon sequences
Seq C1 exon
AGTCTCCAACCAAAGTGCAGCTAGTGGGAGGTGCCCACCGCTGTGAAGGGCGAGTGGAGGTGGAACACAATGGCCAGTGGGGGACTGTGTGTGATGATGGCTGGGACCGGCGTGATGTGGCTGTGGTGTGCCGAGAGCTCAATTGTGGAGCAGTCATCCAAACCCCGCGTGGCGCATCATATCAGCCACCAGCATCAGAGCAAAGAGTTCTTATTCAAGGGGTTGACTGCAACGGAACGGAAGACACGTTGGCTCAATGTGAGCTAAATTACGATGTTTTTGACTGCTCACATGAAGAAGATGCTGGGGCACAGTGTGAGA
Seq A exon
GTAAGTATGAGAGACTCAAGGGCCATTTTCTAGTATCCTATGCCCCAGATGGTCATTTTGCTAGTCTTTGGTTCCTGCCGTGGACTTTCACACAGTTCTACGATGACAGCAACACCATCCTTTCCCTTTACATGTTACACGTTCTTGATTGCAAGACTTGGATATAATAATAGCTACGATTATTACCTGTATTGCTTCTTCCTTTCTTTCCAGGTATACATGAGATTCAATTTCTCTTATTCGTGGACATGCAAAAAAATCAGCACAGATATGTCAGCCACTGAACATTTGTTCAATGTGTCTGTGTGGGGCTGAGATGGGGTTATGGGAGAACTCATGAGGTTTAATAAGTGCTTTTGTGAACATTTCAGTTCTCAAGTTCTATCAGCTTAATTGAAGAGGGGGAAGATACTGGTGGGAAGTCAAAGCAAGCTCGCAGATAGATGGACACAGGCATATAAATGTGCAATCAATGCAGACACACAAATAGATGGACACACAGACATGTTCCTTCACTGTCCTACATAATTAGCTCCCTATGAATTAATGTGATGTGTGTGTTTTCTCTAAAGGCTGCGATTTAACTACAAGGCTGCCTCTGTCCCCTTCTTTTTGTGTCCCTGCAGGATTTATCATTAGAGAAAAGATGAGCTCTCCCAATGTTAAAGTCTCCCAATGTTGTCATTAGAGACAGATGAGCTCTTCCAGTGTTGAAGTCTCCGATTTTTTAGAAAAGTCAAGGTTTGGGAACATTAGTAAGGGATACTTGATTTTTGCCAACATAGAGCCAAAAATATATTTTGACATTTCTGTTAATATGTGTATTTACTAATATTTGGTGCTTTTTCAACATTAATTTATATATAATATAATTCCATATAATATACATAGATTAATATAATCTATATTATATAAATTACATATAACATATTTTATATTAATTTGTAGTGCCTTTAACTGTCTCTTGTGAGGAGAAATTAGAAGTTGAATAGCGGTTCACACTGTTAATCCCAGCACTTGGGAAGCAGAGGCAGGTGGATCTCTGTGAGTTCAAGGCCAGTCTGGTATACAGAATGAGTTCCAGGACAGCCAGGGCATAGAAAAACCCTGTCTAAAACACACACACACACACACACACACACACACACACACACACACACACACACACACACAAATAGAAAAAGAAAAAGAAAAAGAAAAAGAAAAAGAAAAAGAAAAAGAAAAAGAAAAAGAAAAGGAAAAGGAAAAAAAGAGAAAAAGAAAAGTCGCTACGGAAGTGAGTATGATTCTGGTGGGGGCCTAACCACCGTGTACTATGTGGTACTTACAACCATAACAGCCAAGAACTGAGCCATGTGTAATCAGACTCCCTTTTCTGAAAAGACCATGTTCTGGCATGGAACAAACATTGCCTCTCCTTTTCTTTCCAG
Seq C2 exon
ACCCAGACAGTGACCTCCTCTTCATTCCAGAGGATGTGCGTCTAGTAGATGGCCCGGGGCACTGCCAGGGTCGAGTGGAGGTGCTCCACCAGTCCCAGTGGAGCACTGTGTGTAAAGCAGGCTGGAACTTACAGGTCTCAAAGGTGGTGTGCAGGCAGCTCGGGTGTGGGCGGGCATTACTGACCTACGGAAGCTGCAACAAGAATACTCAGGGCAAAGGACCCATCTGGATGGGCAAGATGTCGTGTTCTGGACAAGAAGCAAACCTTCGGTCTTGCCTTTTGAGTCGTTTGGAGAACAACTGTACCCATGGCGAGGACACATGGATGGAATGTGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000015854-Cd5l:NM_009690:3
Average complexity
IR-S
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:
PF0053013=SRCR=WD(100=91.7)
A:
NA
C2:
PF0053013=SRCR=WD(100=86.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTCTCCAACCAAAGTGCAGCT
R:
AAGAGGAGGTCACTGTCTGGG
Band lengths:
342-1772
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: