MmuINT0024351 @ mm9
Intron Retention
Gene
ENSMUSG00000028121 | Bcar3
Description
breast cancer anti-estrogen resistance 3 [Source:MGI Symbol;Acc:MGI:1352501]
Coordinates
chr3:122226087-122227953:+
Coord C1 exon
chr3:122226087-122226258
Coord A exon
chr3:122226259-122227841
Coord C2 exon
chr3:122227842-122227953
Length
1583 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGA
5' ss Score
9.22
3' ss Seq
ATAACCTTTCCTTCTTGCAGATC
3' ss Score
12.3
Exon sequences
Seq C1 exon
GCACAACACCATGGCCATTGGCATTGCTGTGGACATTCTGGGCTGCACAGGCACACTGGAGAACCGAGCGGGTACCCTCAATAAGATCATCCAGGTGGCGGTGGAACTGAAGGATGCCATGGGAGACCTCTATGCTTTCTCTGCCATCATGAAAGCCCTGGAGATGCCTCAG
Seq A exon
GTGAGATGCTGGCTTTGTGCAGCCTCCCACACAAGCATGCATTCAACACTCGTCAAAGAGTTCTATACGTCTCCACCATGCACGTCTGACTGCTCTGGCCAACCTCTAAAGATAAACGTTAGTGAAAGCCACGCCAGGGACAGGCAACCGAGAGCACTGTCCTTAGCATTTTGATTCTGTTTCTAAAAACACTGGTAATTGATCATAGTTCAATATCTCATCTTTGATGCAAAATAACAAGAGTTAGCCTCACTGCTAACAAGCAGTATTCCTGAAGAACCAGTCAGGGCAAGACACCATGCTGGAGTCTGTGGTATGACAGAGGCTGCATCCACTTGGGTCACCAGGGATGTGGCTATTTGGGGTAATGACTGGGGAAACCGAGGCATTTAAGGAACTTGTATCAGAGATTCCCTAGACCAGCGGTCCTCAATCTGTGGGTCCCGACTTCTTTGGGCGTCAAAGGGGTCACATGCCAGACATGTTACATATCAGACATGTACATTACAATCTGTAACAATAGCAAAGTGATAGTTATGAAGTGGTATTTTATGGTTTGGGGGGGTCACTGTGACAGGAGGAACTGTATTACAGGGCATTGTAGCATGAGGAAGGTTGAGAACCTCTGCGCTAGACTCGATTTGTCTCAAAGCATCTTCCCCAAGGTACTTCATTTAGGAAGTTGTCTCGCTGTCTCACTGATGATGTAGCTCCTCGGCTAGAATATCTCAGGCAGGGTCTCTGCCTTTGTGTGCACTGGCGGATGCTTTCAGAAGCCTGTCAAACACAATGGGCCTCCACTGTGAAGGAAGGGAGGTCTGCTGTCTCTGCTGCTCAGGTCCGCTTTCCCTCACGTAGGTGCTTAAAGAACTCTGAGTGGTAGAGTCAGTCAGTCAAGCCAGGTTCGGCCAGCAGCGTCAACACTGCTGGGTCTTTTATCTTGGCTGTTACCTACACACAGATTAGCTCCGAAATCCTGCCAGGTGCTCATAAATAGCCATCCTTCCCACAGAGGGATACAGCTCAGTCATATGTCCTAGAAGTCAGAGTATAATTGGCACATACTTTTCTTCATTAAAAACAAACAAACAACAACAAAGAATGACCACCTTAAAAGCAAGATGCTGAACAGATTAAGGGCCCTTACCAGAAATTTCTTGGAGAACCGTGTGATGTCACTAGCCGTCCTCTGATCTGCACATGAAATAACTACAATGAGATAGTTACTTTTAGGCATTTTTTTTTAAAAGTATGTATAGAAACACACATGAAGCATTGTGGGATGGGTCACCAGGGCAGTGTAGACTTATAGGCTGCGCCTCTTCTCCCTCACAGCGTAGACTAAGGTAGAGGCTGCGCCTCCTCTCCCTTACAGTGTAGACTAGGGTAGGGGCTGCGCCTCCTCTTCCTCACAGTGTAGACTAGGGTAGGGGCTGCGCCTTTTCTCCCTCACAGCTGCTCTGACAGCTTCATGATCATCTGTCACCTGTTCCAAAACTTTAGCAGAAAGGTTTTTTTTTTGTTGTTGTTTTGTTTTTTTTTAAAAAGAGACTTTCTGAAACAATAACCTTTCCTTCTTGCAG
Seq C2 exon
ATCACAAGGTTAGAGAAAACATGGACGGCTCTGAGGCACCACTACACGCAGACAGCCATCCTCTATGAGAAGCAGTTGAAGCCCTTTAGCAAAATCCTGCATGAAGGCAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000028121-Bcar3:NM_013867:9
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:
PF0061714=RasGEF=FE(28.8=100)
A:
NA
C2:
PF0061714=RasGEF=FE(18.7=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCACAACACCATGGCCATTG
R:
TGCCTTCATGCAGGATTTTGC
Band lengths:
281-1864
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: