HsaINT0035483 @ hg19
Intron Retention
Gene
ENSG00000099622 | CIRBP
Description
cold inducible RNA binding protein [Source:HGNC Symbol;Acc:1982]
Coordinates
chr19:1270927-1271245:+
Coord C1 exon
chr19:1270927-1271035
Coord A exon
chr19:1271036-1271138
Coord C2 exon
chr19:1271139-1271245
Length
103 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGG
5' ss Score
9.16
3' ss Seq
GACCTCTCTCCCCTGCACAGTGG
3' ss Score
7.91
Exon sequences
Seq C1 exon
GCCGCCATGGCATCAGATGAAGGCAAACTTTTTGTTGGAGGGCTGAGTTTTGACACCAATGAGCAGTCGCTGGAGCAGGTCTTCTCAAAGTACGGACAGATCTCTGAAG
Seq A exon
GTGAGGCTGCTGCTGGGCCCGCGGCCCTGGGCGGGGGGGCTTGTGCTCCTCCTACCTGGAAGTACAGCTGGGTGCTGACTGCAGACCTCTCTCCCCTGCACAG
Seq C2 exon
TGGTGGTTGTGAAAGACAGGGAGACCCAGAGATCTCGGGGATTTGGGTTTGTCACCTTTGAGAACATTGACGACGCTAAGGATGCCATGATGGCCATGAATGGGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000099622-CIRBP:NM_001280:2
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.139 A=NA C2=0.243
Domain overlap (PFAM):
C1:
PF0007617=RRM_1=PU(38.0=77.1)
A:
NA
C2:
PF0007617=RRM_1=PD(56.9=48.7)
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
ENSP00000322887, ENSP00000412831, ENSP00000464906, ENSP00000465334, ENSP00000465338, ENSP00000465558, ENSP00000465779, ENSP00000466025, ENSP00000466110, ENSP00000466207, ENSP00000466216, ENSP00000466238, ENSP00000466712, ENSP00000466897, ENSP00000467138, ENSP00000467307, ENSP00000467449, ENSP00000467734, ENSP00000467848, ENSP00000467948, ENSP00000468016, ENSP00000468097, ENSP00000468224, ENSP00000468645, ENSP00000468788
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGCCATGGCATCAGATGAAGG
R:
CTTCCCATTCATGGCCATCAT
Band lengths:
214-317
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)