HsaINT0024049 @ hg19
Intron Retention
Gene
ENSG00000138658 | C4orf21
Description
chromosome 4 open reading frame 21 [Source:HGNC Symbol;Acc:25654]
Coordinates
chr4:113507601-113509085:-
Coord C1 exon
chr4:113508436-113509085
Coord A exon
chr4:113507740-113508435
Coord C2 exon
chr4:113507601-113507739
Length
696 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGG
5' ss Score
10.07
3' ss Seq
CTTGAATTATTCCATTGCAGGAG
3' ss Score
6.41
Exon sequences
Seq C1 exon
GGATGAAAAAATCCCGTTCTCTGGAGAATGAGAACCTTCAAAGGCTTTCATTATTAAGTAGAACCCAGGTTCCACTTATTACTTTGCCACGTACTGATGGGCCACCTGACTTAGACTCTCATTCGTATATGATCAACTCTAACACATACGAGTCTTCTGGCTCCCCCATGCTCAATTTGTGTGAAAAGTCAGCAGTTCTTTCGTTTAGCATTGAGCCTGAGGACCAAAATGAAACCTTTTTCTCTGAAGAATCTAGGGAAGTGAATCCAGGGGATGTTTCACTTAATAATATATCTACTCAGAGCAAGTGGCTGAAATATCAAAACACATCCCAATGCAACGTGGCTACTCCAAACAGAGTTGATAAGAGAATAACTGATGGCTTCTTTGCTGAGGCTGTTTCTGGGATGCATTTTAGAGACACAAGTGAAAGACAGAGTGATGCTGTCAATGAAAGCTCTTTAGACTCTGTGCATTTGCAAATGATAAAAGGCATGCTCTATCAACAGCGGCAGGATTTTAGCAGTCAAGATTCGGTTTCCAGAAAGAAAGTACTTTCTCTGAATTTAAAGCAGACTTCTAAGACAGAGGAAATTAAAAATGTATTAGGAGGGTCTACCTGCTACAACTACAGTGTAAAGGATTTACAG
Seq A exon
GTGAGGAAATGTACCGGTCTTGTGGTGCATTTTTCCAATAGTTATTGTCTGAATTTCAACAAAAGAATTACCAAAATATACTGCATAGGAGCAATTTGGACAGATGGCTTTTTTTGATCCTAACTCTGAGCTACAGTTACATCATCCTTTACTTAAAATCTCTCGTAATAGTAGTGAACATTGAATGAAATGATTTATTTGAAAGTATCTGGTGCAGTGTCTGGTAAATTATCAGTACTTAATAAGTGATAGCTCCTACTTTTGTTTCCATCACTACTACCATTACAATTATTGTTTTTACTTTTGACTGTCAATTGTGTTTGCTGATTAAGTCATTAGGGTAAAGGTGCATCTTATTTCACGTTAATTGTGAATAATCCTTATTATAGTCATAACCAGAAATAAAGATACGTAATGATCCATTCACATCAGTTAACTTTTTCCTAGCAAAAAATATATAAAAACTTACTAAGGGGCAGATAAGAAAAGTTACTCTTATATAGGGTTAAAATTGCCATTCGTAGCTATTCTTGCTATATTTGGTTTCTCATTTAAAATTTGAAAGTAATTTTCAAGGATCCTAGAAATCAAAAGAAAAATTAATATTTTTAAAAAATGTCTATGAAAAATAATTTACTCTTTAGTAAACAGTATTTTTCTGGAGTTGCTATGATAACTTGAATTATTCCATTGCAG
Seq C2 exon
GAGATAAGTGGCTCTGAGCTGTGCTTTCCAAGTGGGCAGAAAATAAAATCTGCTTATCTTCCCCAAAGGCAAATTCACATACCAGCTGTTTTTCAGTCTCCTGCTCATTATAAGCAGACTTTCACATCTTGCCTCATAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000138658-C4orf21:NM_018392:12
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.274 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAATGCAACGTGGCTACTCCA
R:
CCACTTGGAAAGCACAGCTCA
Band lengths:
353-1049
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)