HsaINT0138488 @ hg19
Intron Retention
Gene
ENSG00000102317 | RBM3
Description
RNA binding motif (RNP1, RRM) protein 3 [Source:HGNC Symbol;Acc:9900]
Coordinates
chrX:48433556-48434055:+
Coord C1 exon
chrX:48433556-48433671
Coord A exon
chrX:48433672-48433948
Coord C2 exon
chrX:48433949-48434055
Length
277 bp
Sequences
Splice sites
5' ss Seq
AGGGTGAGA
5' ss Score
6.65
3' ss Seq
ATCTTCTCTCCCTCTCACAGTGG
3' ss Score
10.38
Exon sequences
Seq C1 exon
GACTTGAACTGCCATGTCCTCTGAAGAAGGAAAGCTCTTCGTGGGAGGGCTCAACTTTAACACCGACGAGCAGGCACTGGAAGACCACTTCAGCAGTTTCGGACCTATCTCTGAGG
Seq A exon
GTGAGACGGGCCATACTCACAATGGGGGTTGGTGAGAGAAAGTCTGGGATCCTTGCATTTCAAGGAGTATTAACTGAAAAGTTAGGACCCACGCCTCCAAATTCTTTTTCTTCCTAAGCCTATGGTGTAGACTAAGGATGAGGGGAAGCGTCTTTGGGATTAGTGGGAGCGCTCCGTTTTCCCTACCTATGCCATCTCCTTTTCCGGCCACCCTTTGCTACTTAACCTTTGGGGTACTGACTGGTCCACATTGCTCCATCTTCTCTCCCTCTCACAG
Seq C2 exon
TGGTCGTTGTCAAGGACCGGGAGACTCAGCGGTCCAGGGGTTTTGGTTTCATCACCTTCACCAACCCAGAGCATGCTTCAGTTGCCATGAGAGCCATGAACGGAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000102317-RBM3:NM_006743:2
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=0.057 A=NA C2=0.329
Domain overlap (PFAM):
C1:
PF0007617=RRM_1=PU(38.0=77.1)
A:
NA
C2:
PF0007617=RRM_1=FE(50.7=100),PF093415=Pcc1=PU(51.4=52.8)
Main Inclusion Isoform:
NA
Other Inclusion 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:
ACTTGAACTGCCATGTCCTCTG
R:
CTCTCCGTTCATGGCTCTCAT
Band lengths:
222-499
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- 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)