HsaINT0024065 @ hg19
Intron Retention
Gene
ENSG00000138658 | C4orf21
Description
chromosome 4 open reading frame 21 [Source:HGNC Symbol;Acc:25654]
Coordinates
chr4:113460489-113461280:-
Coord C1 exon
chr4:113461019-113461280
Coord A exon
chr4:113460846-113461018
Coord C2 exon
chr4:113460489-113460845
Length
173 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAAA
5' ss Score
8.38
3' ss Seq
ATGTCGTATGTTTTTTTAAGGAA
3' ss Score
8.08
Exon sequences
Seq C1 exon
CTTTGTCATTTACTCAGTGCTGTGGACTTTCACCATCCTGATATTAAAACTGTGCAGGTGTCCACAGTAGATGCTTTTCAGGGAGCTGAAAAGGAGATCATTATTCTGTCCTGTGTAAGGACAAGACAAGTAGGATTCATTGATTCAGAAAAAAGAATGAATGTTGCATTGACTAGAGGAAAGAGGCATTTGTTGATTGTGGGAAATTTAGCCTGTTTGAGGAAAAATCAACTTTGGGGACGAGTGATCCAACACTGCGAAG
Seq A exon
GTAAAATAAAAATGGGTTTAATTCATGCATTTCAAGTTCAAACTGACTTTTATGGGTTAATGCTTGGGGTGCTTCAAGCAGGAACAGCTCTGCTGGGGGAAGTAACTGACATGATAATATTGGGACCTCTGTAAAATAAAGAATAGTTGTCTCATGTCGTATGTTTTTTTAAG
Seq C2 exon
GAAGGGAAGATGGATTGCAACATGCAAACCAGTATGAACCACAGCTGAACCATCTCCTTAAAGATTATTTTGAAAAACAAGTGGAAGAAAAACAGAAGAAAAAGAGTGAAAAAGAGAAATCTAAAGATAAATCTCATTCATAAAAAGACATGGTGTAAATATTTTGTATTTATGTAAATTCAGACTCATTTTACATGATATATTTTTTATATTTTTATTACTCTAAACCCTCTTATTAAAAATATGATATTTAAATAACATAGTAAACACATGTAAAAATTTTGTTCTTCAAAAAAGTGTACAAAAGGTAGTATAAAATCCTACTAATAAAAATAAGCTTTTTTCTAAGAAGAATGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000138658-C4orf21:NM_018392:27
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.404
Domain overlap (PFAM):
C1:
PF130871=AAA_12=PD(37.4=79.5)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCAGGTGTCCACAGTAGATGC
R:
GCTGTGGTTCATACTGGTTTGC
Band lengths:
254-427
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)