MmuINT0005546 @ mm10
Intron Retention
Gene
ENSMUSG00000015488 | Cacfd1
Description
calcium channel flower domain containing 1 [Source:MGI Symbol;Acc:MGI:1924317]
Coordinates
chr2:27009926-27014165:+
Coord C1 exon
chr2:27009926-27010105
Coord A exon
chr2:27010106-27014092
Coord C2 exon
chr2:27014093-27014165
Length
3987 bp
Sequences
Splice sites
5' ss Seq
TGTGTGAGT
5' ss Score
5.84
3' ss Seq
CATTGTCTCTTGTTTTGAAGCCT
3' ss Score
7.07
Exon sequences
Seq C1 exon
AAGGCCGCGCGCGGGTGGACACGTCTCTTTGTGCGCGCCTGGGGCTGCGCGCAGCGTTTAGCATGAGCGGCTCGGGCGCCGCCGGAGCGGCCGCGGGCCCAGCCCCGCCGGCACAGGAAGAGGGCATGACTTGGTGGTACCGCTGGCTGTGCCGCCTGGCGGGAGTGCTAGGAGCGGTGT
Seq A exon
GTGAGTATCGGGTCCAGGGAGCGGGCGTCCCCGGGGTTGCCATGGCTCCCGGCCTCAGGCCTGCAGTCCACCGCCGGAACTCGATGGCTTACTGCCCAGTTGTTGCGGCCCTGATCAGAGGAAATGAGACTCACAGAGGACGCGCGTCTGCCCCTTCCCGGCCCTGCCTCGGCCTGGTGATGCTTACCTGGGCTGGGGTGGGACTGCCAAGTTCCCAGCCTTTGGACAAAACTTGTTCATAAATGGGGGGCAGCTCTCCACAGGCTGGGAAGTTTGCTTGGGGGTCAGATGGTGCCAGGAGAAGAGTGGCCCCTCAGGGTGGCTGGGCAGTGATCGGAGTTCTCCTCGGGTTCCTACTGTCCACACTCTCCTAATGCTTCTCGTCGGCCTAGTATCCTCCACACCAGCAAGCTTTCTCTGCTCTTGTAAAGAGGAAGGCAGGTCCGCCTCTTCAGTGCAGCTATGTTGCTGGCCTTCCAAACAGTGTGTTTGCTAAATCCTGGGTGTCCCTTTCATTGTGAATTCCTAGAAGTCCAGGTGAGTGCTGGGAAGGCCCGAGGATCCATTGCCTACCTGGTACCAGAGCAGGAACTGTGTGGGTAGGGGAAGACTCATCCGTTTTCCTGTCTGGAGGAATACCTTGGAGCCCCATCTGTCCAGACGATCTTGCTAGTCAGATGGATAGGGTAGAGTTAGGTATGTGCTGCCCTGGTAAGGCAGCTCTGGAAGAAGTCTGCTGAGGTTGATCAAATCCTCTTCAGTGCAGTTAGCTAGTTCAAGGTGGTATTAAGGGGTGAGGGACAAGGAAGGGCCTGACCATGACCTGTAGGCGGCTATCCTCCCTCCGTCATGGTGATTCAGTCAGTGACCAGGTGATTTCTAGATTAGATTGACTTTGGAAATCCCACCCAGTCCCATACTTCCTGTGGGTACCTGTGCTACTCCCGAAGGCCTCCCTAATCCTCCTGCCGAGCCAAGCTATCAGTGAAACCTTACTGGAGACCTGTGGCCGTAGCTTAAATTGTTCCCTGAACCTGATCATTGGGATCAGGGGGGTGGACATCAAGGTTTTGAATACTGGCATATCATAGGAGGGAAGGATATCGTGTATTTGCTTTAAAAACTCAATAGGGGTTTGGCAGGAGCTATGGCTTAGCCGGTCACTTTGACATAGGGCTATCCTCTCTTGGAATGGAGGATATTCTAAGGGGCTTATTATTTATTGGAGGGATTTATTCTGGTCCCAAAGACCTCTGTAGACAGAGGAAGAAAGGATTATAGGGACATCTCCTTTATATGGAAGACATGAGCATTATTAGCACCCCAAGTGAGTGGATGTATTTGAGTCCTTGGTTGTCAAAGGACTCCTGTTCGTCTGAGTTGCGACCTGGTCCTCCCAAAGGTGGCTCTGTAGGACAGCATGGTGGAGTAGCTCTGTAGATGGAATGCTGAGGACAGGAGTGCAGGCCTTTCAGGTGAGACCAGGCCTAGCTCCACACAGGCAGGGGGCCGACAGTCTTTCACTTCTGTGGCCCTGGAAGCTTTGCTGCGTGAATGAGTGCTGCGTTGAGTTCTTTATTAGAGGAGACTTTGTGACATAGAAGCTGTGCCACTCATTTGGTCCATTCTCCTGCATCAGTTCCCATTTGGATAATGTAACACAGGAAAGTGGAAAATGGTGGAATTCCAGGCCCAGTGGAGGGATCCGGTGACCCAGGCCTGCTGCAAGTTTAATAAGTTGGTGCTAATTGCAGCCTCAGAGGGCCAACACTCTGCCCTCCCTTAGCTTGTGTCCTGCCAGAATGGGCAGCTCTCAGCAATGTCCTCAGAGGCTCCCAGAGTTCCTGGTGAGGGACTTCTTGGTGAAGCCTGGGTGGCTGGGGCAGACTGTAACCTGAAGGTGCAGTCAGAGGGGAGGGGCCTCGCTGGGCTTCCACACTGGAGAAGAGCACACACACTGTCCCCTCTTGGTGTCCTGCTATTCAGGTATTGGGGCACAACCTGCTCATGTGTAGGAGAGAAAAATGAATTAGGAAAGCAACATGTTCAGGGTCACGTGGCTAATGTTTTAGATGGGATTGTCATTTGAATCTTCCCTGGTGTATCATAAGAGGCATCCCTGTCCTGACCCAAATTCAAGATGTGGCCAGACGTAGTGAAACATGCTTGGAAGTCCCCAGGAGGCTGAGAGAGAGAGAGCAAGATAGTTTGAGGTCAGCTTGAGCTATAGAGCAGGACTCTGCCTCAAAGGAAAACCAAACCAAACACCCTCACCAAGCAAGCATAAAGAACAACCCCAAATAAGTCGGAGTGGCCTTTACCAAGTTAGAAGACATTTTTGAGTAGTTTACCTGGTGGCTGCAGACTGATAGGCTAAGATTCCCACTGAAGTCGGAACAGGCCTGACTTTTTAATTTTTTAATTTTTATTTTTTAAAGATTTATTTATTTTATATATGTGAGTACACTGTCTTCAGGCACGCCAGAAGAGGGCATCAGAACCCATCATAGTGGTTGTGAGCCACCATGTGGTTGCTGGGAATTGAACTTAGGACCTCTGGAAGAGCAGTCAGTGCTCTTAAACCTCTGAGCCATCTCTCCAGCCCCCCAGGCCCTACTACTACTTCCTCTTCCTCTTCCTCCTCTTCCTCCTCTTCCTCCTCCTCCTCCTTCTTCTTCTCTCCTTCTTCTTTGAAAAGATATCTCTCTTTATTCAGTTGAGATTGGATACATATTAGTGTATTCAGACTCATTAATGGGCATACAAGAGCTGAAAAACCTGGAAGCCATACTATATCATGGATTTTTTTTTTAAATGTTACAAAAGTCAAAGGATTGGCATATATTCTCAGAAAAAAAAAGGAGTTGACATACTTTTGTGAAAATCAGACTATATATAACGTGTTGTTTTTTGTTTTGTTTTAGTAGACGAAGCTTTAGTAGACTTCTCATTTTATAAGTAACACTAGTCAGCACAGCCCAGCCCAGCAGCAACCAGTGAGAGCCAGGCTTGAGGGCTCAGAACAGTCTACCTACACCAGAGTAGACCAGTTAGAACTCTAGTCTCATCTGGTGGTCTCAATATGAGAGGAAAAAAGACAAAAAACAAAAGAACAAAAAACTATGGAGCTAACAGAAGAAAATCAAAGTTTCTTAAACTAGGTTAGAAATCCGAAAGTATCAAGCCTGAGATTCTCCACCAAAGCCCATCCCACTCTGGAAGCTCTTTTCTATTTTCCCTTAAAAACAAAACAAAATTTCCTAACAAAAGCCAGCTGTCTACATTAAAATTAAGAATGTCTGTTTGGTGAAAACCCCCTAGATACACAAAGTGCTATTTTGAGGGGTTTTGCAGTGGCCAGAACACAAGCAACTCCTCAAGGAAAAGAGACGCACGCAAGAGGAAGCCACCTCCCGAGAAAACAGCCGCTGACAAAGAAAAACCAGAAGGTGGCCGTGCATAAGAAATGGTCTTCAGATAAAGGGATATTAAGATATGTGGTGCTTTATATACATTGACTACCAAAATCAGGATTTACAGCGACAGATGCTGGTAAAGATAAGGAAAGAGAAGCCCCAAGAAAGGCCAGTTTGCGTTCTAAAGAAAACTATGGAGAAACCAGGAAAATGAGCCTGTATAACCCACAGTCCCAGCCTGGACAGGTACACCAAAGAATGACCCACCCCGGCCCAGAGGGGACACATTAAAGATGTTCGCTGTCAGGCCTGACTTCTTGAGAGGGTTTGATAATAACCTGGAACCAAGGGGCAGCTCATCAGAGCCTTAAGCCTTTATATCCTCCAGGTATGAAAGTAGCTAGACTTGAGCTCAAACGTAAACTTACTACTCTCTGCTGTCTCAGGTGATGGTGGTTGCTGAGGGAAGCCCTAGTGCTGAGCGTCTAAAGGGAGCCTCATGTGTTCTCAGTGCCTTCTGCACACTCTGCCATACTCTGCTAACCCCTGCCCATTGTCTCTTGTTTTGAAG
Seq C2 exon
CCTGTGCCATCTCTGGACTCTTCAACTGCGTCACTATCCACCCTCTGAACATCGCAGCTGGCGTGTGGATGAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000015488:ENSMUST00000114006:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF102334=Cg6151-P=PU(9.5=17.5)
A:
NA
C2:
PF102334=Cg6151-P=PU(35.3=96.0)
Main Inclusion Isoform:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
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