HsaINT0022388 @ hg19
Intron Retention
Gene
ENSG00000249087 | C1orf213
Description
chromosome 1 open reading frame 213 [Source:HGNC Symbol;Acc:25122]
Coordinates
chr1:23697632-23698330:+
Coord C1 exon
chr1:23697632-23697702
Coord A exon
chr1:23697703-23698005
Coord C2 exon
chr1:23698006-23698330
Length
303 bp
Sequences
Splice sites
5' ss Seq
TCTGTAAGT
5' ss Score
7.96
3' ss Seq
TATTTGTTCCCATGATTCAGCAA
3' ss Score
4.31
Exon sequences
Seq C1 exon
GCCTGCGGGGCGGGGGCGGGGTGGCGCCCAGGACGACTCCCCGGGCTCAGCTTGGCTGCCTGCCTCCTTCT
Seq A exon
GTAAGTGCTTTTTTTTTCTTCACCTGGGACCCTCTAGAGGTTGGAAAGAGAAGAGAGGCTGGGAGCGGATGGAAAGCATGACTGCATCTGGAGCCCCTGGGGGGAGTGGGGAAGAGGGAGTGGAAGGACAGTGGCTGAGGGGCTTCCTGTTGCAGCCTTCAGCTGGACTCAGGGTTGGGGTCACTGGAGGAGGAGGTGGCTTCCTGCCCCATTGTTCTGGACTGCAGTGTTTCTTGGGAATACTTACTGTATGTGGATTTTCAGTAACCAACTTGGAAAGCTGTATTTGTTCCCATGATTCAG
Seq C2 exon
CAAACAATGAGTACCTACTGTGTGTAGAAGCAGCAGGACAGCCTGTCATCACTGGGAAAGAGGCCAGAAGAGCCGTTTGGCCAGGGTCTCCAATTTAGGCTTTCAACATTATCTCTAAAGAAGGTTATACATTATGTCGGCTCCACTGGCTGATGGGATCAAAGACCCTCCTTGTATATCCTTAAACCTGTACTCTATTACCAGGCCACTGTGCCTGTGGAGCACTGTAAGTTCCTACCTTTTAATAAATTTTATAATTATCTTGTGAGCAGCACAATTGTCATAGTTTTTTGTATCAGAAACATTAATTTGTTAAACATTTTAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000249087-C1orf213:NR_033691:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.254 A=0.000 C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NO
C2:
NO
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
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:
CTCCCCGGGCTCAGCTTG
R:
AAAAACTATGACAATTGTGCTGCTCA
Band lengths:
326-629
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)