HsaINT0028659 @ hg38
Intron Retention
Gene
ENSG00000183287 | CCBE1
Description
collagen and calcium binding EGF domains 1 [Source:HGNC Symbol;Acc:HGNC:29426]
Coordinates
chr18:59439543-59439816:-
Coord C1 exon
chr18:59439677-59439816
Coord A exon
chr18:59439579-59439676
Coord C2 exon
chr18:59439543-59439578
Length
98 bp
Sequences
Splice sites
5' ss Seq
GTGGTCAGT
5' ss Score
4.85
3' ss Seq
CAGATCCTTTTGTATTACAGGGT
3' ss Score
7.04
Exon sequences
Seq C1 exon
GCTCACCAGGACCAAAGGGAAGCCCAGGCTTCCCCGGTATGCCAGGCCCTCCTGGGCAGCCCGGCCCACGGGGCTCAATGGGACCCATGGGACCATCTCCTGATCTGTCCCACATTAAGCAAGGCCGGAGGGGCCCTGTG
Seq A exon
GTCAGTATCTTATCAGAGATCCACTTCCTTTTTGGGGGAAAATGTGTTTTTGTCCCATGCTTTTGCCTGTGGTTAAACCAGATCCTTTTGTATTACAG
Seq C2 exon
GGTCCACCAGGGGCACCAGGAAGAGATGGTTCTAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000183287:ENST00000439986:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(69.4=72.3),PF0139113=Collagen=PU(20.5=17.0)
A:
NA
C2:
PF0139113=Collagen=FE(28.2=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:
CTCACCAGGACCAAAGGGAAG
R:
GAACCATCTCTTCCTGGTGCC
Band lengths:
171-269
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