HsaINT0028651 @ hg38
Intron Retention
Gene
ENSG00000183287 | CCBE1
Description
collagen and calcium binding EGF domains 1 [Source:HGNC Symbol;Acc:HGNC:29426]
Coordinates
chr18:59696629-59697380:-
Coord C1 exon
chr18:59697212-59697380
Coord A exon
chr18:59696710-59697211
Coord C2 exon
chr18:59696629-59696709
Length
502 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGC
5' ss Score
9.88
3' ss Seq
TCCTCTGCACTTTTTCATAGAGA
3' ss Score
7.17
Exon sequences
Seq C1 exon
CGGAGCTCGGCGCTGGGAAGAAGCCGGGAGCTTCCCTGATGGTGCCGCCGCCTCCGAGCCGGGGAGGAGCTGCCAGGGGCCAGCTGGGCAGGAGCCTGGGTCCGCTGCTGCTGCTCCTGGCGTTGGGACACACGTGGACCTACAGAGAGGAGCCGGAGGACGGCGACAG
Seq A exon
GTAAGCGCTGCAAGCCCCAGCGGAGGGCGAGCTCCTGCTTGATGCGCGCCCGGCTCGCGGGGTGCGGGCGGTCCTCCCCGGCGCCCACTCCCACAGCGATCCGCACGCCCTCACTTCTCCGGGGATAAGGAGAGTGCTCAGCTGTCCTGGGCGACACTTCCCTCCGCTCCCGGGTATCAGCCTTTGCGCCCTGCCATCCGTGGGTCGCGTCAGGGATACCCTTCGCCCCGCGTTCCTGCCTCCCCCCGGGTGCCACACTGGCTGGCACAGCTCGTGAACCCCGCTTCCTTTCTCCTGGAGCTGGTTCGCTTCGTCGTGACCCTCGCGTGGCTCGTCCCTGTGGCCGGAGTCTGCCCCGCGTACGCGTTTGGGGACCAGCCCCTGCCCAGAGCGCCGGGACGGGGAGCCTGGCGATCCCCACGCGCCAGGGATTCCCCAGCGCGCGCTGCCCGCCTCCGCTCTCCCGCTGAGAATCGAACATTTCCTCTGCACTTTTTCATAG
Seq C2 exon
AGAAATCTGCTCAGAGAGCAAAATCGCGACGACTAAATACCCGTGTCTGAAGTCTTCAGGCGAGCTCACCACATGCTACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000183287:ENST00000439986:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.318 A=NA C2=0.018
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Cow
(bosTau6)
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:
GCTCGGCGCTGGGAAGAA
R:
CTGTAGCATGTGGTGAGCTCG
Band lengths:
246-748
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