MmuINT0027931 @ mm10
Intron Retention
Gene
ENSMUSG00000017412 | Cacnb4
Description
calcium channel, voltage-dependent, beta 4 subunit [Source:MGI Symbol;Acc:MGI:103301]
Coordinates
chr2:52449950-52452020:-
Coord C1 exon
chr2:52451869-52452020
Coord A exon
chr2:52450046-52451868
Coord C2 exon
chr2:52449950-52450045
Length
1823 bp
Sequences
Splice sites
5' ss Seq
AAGGTAATC
5' ss Score
7.46
3' ss Seq
GGTTCCTGTCATCTTGTCAGGTT
3' ss Score
7.26
Exon sequences
Seq C1 exon
CGGAAGTACAAAGTGAAATTGAAAGAATTTTTGAGTTGGCAAGATCTTTGCAATTGGTTGTTCTTGATGCAGACACCATCAACCACCCAGCACAGCTGATAAAGACATCCTTAGCACCCATCATCGTCCACGTGAAGGTCTCGTCCCCAAAG
Seq A exon
GTAATCAGCACATCCCTGTCTACACTCTAGAAACTTCCCTCTTGAGGGATGTCTCGGCCCTTTGAGTTTTGGGGGCAGAAGAATGTCTCCAGAGTCTGTTAGTGAGCACATTTTAAAATAGTACTCAAGTTCTAGGGTAGCCGAGAATAATACTACATCTCTTTGAGAAGTTCCTGCCTGCTGTCAGCTTGATAAAATACAAACAGAGCTTAAGGAAGGAAAATTAAAAGTAGACTCTTCATTTTCATAGGCTGCATATTCCCTCTTGGCCAATGTCCTCTTTGATACCAATTCCTAAATCACCTGTATTCTCTGCCCAGTTGGGAGAGGGGATATATAATCCAGAGAGAGGTCTTAAGTAAGGTGAAAGATCGCCATGTAACCATCTCCTACACCAATCCTACAGGCCTTCTCATCTGTGTGTAGCTGGGCTCCTTAAGGAACATAGTTCTGCCTTGGTTAAGCACAACTGGCCATGATGCTACCAAATGACTGGAATAGAGGAAGAAGGCCCCGATTCCACTTTTGATTTTGATGTCCTTTTATTTCTTACATTTACTTAGTTGGTATTTTTGTTTGTTTGTTTTTAAAGTCTGTGTGTGAACTTGTGCTGTCACAGCTTATGTGTGGAGGCCAGAGGACAACTCAAGGAAGTCAATTCCCTCCTTTCACCATGTGGGCTCTGAGGATGGAACTCGGGTCATCAGGCTTGGTAGCATTCACCGTCACCCACTGAGCCTTCTCACTGTCCCCGCTTTTGCTTTGGAACAGTGATGGTGTTCTAAAAATAAATATGAAATAGAAACCCATGAGAGGCGTTGCCTTAATACTTAGCTCCTTTCCAAGGCCTCCTTGAATGAGTTTGGTTTGCCTAAATGCAAATTCAACCCCCTATCCAAACAGCGGTCTCCTTTTGTGGTCAAAGAAAAGCCTAGAGAAGCTGAGACTTGTCACCCTCCCCAAGTTCTCAGCCTCCTGGAGGGCACAGCTCTTCTACAATAAGAGTGGGACTCCCAAACTATGATCAGGTAATTCTGGAGAGTGGGTAGAACAGACCAGCATTCCCTTGACCACTGGAAGTATCCTTGCCCCTAGTCCAAGCATCCTCTGCAGTGAGGCTGTCACCCACACCCCCACAGACACTGCTGGTGTCTGGAAGTCCAGGATCAGGCACTTGCATGGACTCATGCACTAAGGTATCACAGAACTTCATGAAGGAGCATGTTGAAGCGGGGAAAGCCCTGCTAAAGCATAAGCAAAAACTGAAAGGGAGAGTGTATGGCCAAATGCAGCTACAGCTATGTCCAAAGCTGTAGATATGTCTGTCTCTTATCCAGCAATGTTTCAACACAAATGTTTTACCTAGGTTTTCAATCCTGAAATAGTTTGATTAATTTAAATTTAAATCAACTATTTCATTAATTTATTAAAAATATAACATGCATGACCCTGATACCTGGCATGAAGATAATGAACTCAAGTATTACTGGACCAAATAATATCAAAATATTGACTCAACATAAGGAGGAACAGACCAGCTCTTTCTCTTTGACAGGAAGCTTTGAAATCTACAAGAGACATAAAAGTCTAGGTGGGAAGCGAGGCTGTCATCAGGAGCCCACAGGGAGCTAGGGCAGGATAGCTATGTTCAGTCCACTCTAGGCCCGTAGCATAGAGATTCTACGTAGGTGATTTCTCACACTGGAGATCCTTTTTACTAATCCTCAGGGTTACATAAACTGGGAAAAAAAAAATCTGAGCCCAGTGTTTGTGGTTTCCTTTCACCTCGTTGACAATCTCTTGGGTTCCTGTCATCTTGTCAG
Seq C2 exon
GTTTTACAGCGGCTGATTAAGTCCAGAGGAAAGTCCCAAAGCAAACACTTGAATGTTCAACTGGTGGCGGCCGATAAACTGGCCCAGTGCCCGCCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000017412:ENSMUST00000102760:10
Average complexity
IR
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:
PF0062516=Guanylate_kin=FE(27.6=100)
A:
NA
C2:
PF0062516=Guanylate_kin=FE(17.1=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGGAAGTACAAAGTGAAATTGAAAGA
R:
CACTGGGCCAGTTTATCGGC
Band lengths:
241-2064
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