HsaINT0063209 @ hg19
Intron Retention
Gene
ENSG00000104870 | FCGRT
Description
Fc fragment of IgG, receptor, transporter, alpha [Source:HGNC Symbol;Acc:3621]
Coordinates
chr19:50016644-50017390:+
Coord C1 exon
chr19:50016644-50016730
Coord A exon
chr19:50016731-50017138
Coord C2 exon
chr19:50017139-50017390
Length
408 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGG
5' ss Score
10.07
3' ss Seq
AGCTCTGTTTCTGTCTGCAGAAA
3' ss Score
10.31
Exon sequences
Seq C1 exon
GTCGTCCTCTCAGCATGGGGGTCCCGCGGCCTCAGCCCTGGGCGCTGGGGCTCCTGCTCTTTCTCCTTCCTGGGAGCCTGGGCGCAG
Seq A exon
GTGAGGGCCGCTCCGGGCCAGGGCCCTGCTGCAGGCGGGCGGCGGGAGGCGGCCCCAGGCAGGCAGGGGCGAAGCCAGCGGGACCCGAGTTCCCCGCGAGCCCCTGGCGCTGCCTTCTCCGCTCAATTAACTTTCTCAACGTCTCCTGCTGGGCCTGAGGCTGGGAACCACCTGTCGCCTCTTGTGTCTGTTTCCCTCTCTCTCTCTGGGTCTCTGTCCCCCTCTCTTTCTGGGTCTCTTGTCTCTCTCTCTCTGGGTCTCTGTCCCCCCCCCCCCGGGTTTCTGTCCCCTCTCTCTGAATCTGTCCCCCTCCCTCCATAATAGATTCTTCTCCCTCCCTGGGTATCTGTCCCACTGCAGTCTAGTTCCCCGCCCGTGTGCTCCCTTCAGCTCTGTTTCTGTCTGCAG
Seq C2 exon
AAAGCCACCTCTCCCTCCTGTACCACCTTACCGCGGTGTCCTCGCCTGCCCCGGGGACTCCTGCCTTCTGGGTGTCCGGCTGGCTGGGCCCGCAGCAGTACCTGAGCTACAATAGCCTGCGGGGCGAGGCGGAGCCCTGTGGAGCTTGGGTCTGGGAAAACCAGGTGTCCTGGTATTGGGAGAAAGAGACCACAGATCTGAGGATCAAGGAGAAGCTCTTTCTGGAAGCTTTCAAAGCTTTGGGGGGAAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000104870-FCGRT:NM_001136019:2
Average complexity
IR-S
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:
NO
A:
NA
C2:
PF0012913=MHC_I=PU(48.3=97.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTCGTCCTCTCAGCATGGGG
R:
AAGCTTCCAGAAAGAGCTTCTCC
Band lengths:
318-726
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- Autistic and control brains
- Pre-implantation embryo development
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)