HsaINT0024061 @ hg19
Intron Retention
Gene
ENSG00000138658 | C4orf21
Description
chromosome 4 open reading frame 21 [Source:HGNC Symbol;Acc:25654]
Coordinates
chr4:113468441-113469536:-
Coord C1 exon
chr4:113469409-113469536
Coord A exon
chr4:113468565-113469408
Coord C2 exon
chr4:113468441-113468564
Length
844 bp
Sequences
Splice sites
5' ss Seq
AAGGTAACC
5' ss Score
9.24
3' ss Seq
TTTTTGAAATTCTGTTTTAGGTT
3' ss Score
11.02
Exon sequences
Seq C1 exon
GTTCGAGTAGTTGGAGTTACCTGTGCAGCCTGCCCATTCCCATGCATGAATGATCTTAAATTTCCTGTAGTTGTGCTGGATGAGTGTAGTCAGATAACTGAACCGGCCTCTCTCCTTCCCATTGCAAG
Seq A exon
GTAACCTAAAAGATTCTTTCCCCAGGGGTAATACCTGTAATCCTAGCACTTTAGGAGGCTGAGGCAGGTGGATTGCTTGAGTCTAGGAGTTTGCGACCAGCTTGGACAACATGGCGAATCCCCATTTCTACAAAAAATACAAAATTAGCTGGGCATGGTAGTGTGTGCCTAAAATCCCAGCAACTTGGGAGGCTGAGGTGGGAGGATTGTTTGAGCCCAGGAGGTCAAGGCTGCAGTGAGCAGGGATTGAACGACTGCACTCCAGCCTGGATGACACAGAGTAAAACCCCGTCTCAAAAAAAAGAAAAAAAGAAAAAGAATAATAATACTGAAGCATGAAAGGATTAAATAACTTGCTGGGTCTCTAAAATATAATGGAGTTCAGATTTGATATAGGTTTGTTTATAAAACTTTGATTTTTCCCCACTATATCCTACTCCTATTTAGGAAAACATTTAGCCCCTAAGAACCCAATTTACTTCACTTCTAAAACAAGGGTTTAAGCTAAATGACTCCTAAGAAAGACTTTAATTTTAAGAGTTTATGGATTCTAAAAACCAGCATTTCCCAAATATGCTTTGTGAAATATTAATTCCATGCAGAGGCAAGGGGCACCTACTAGGTTTTATGTGCAGGGAGGGCAACTAAATTATATAAAGGATTCTTTATTGCATAACTTTTCAAAGCCTTTAATGCGCTTAATAGCACTACTAAGCTTTATTAGTACTCAGGATACTTCATGGCATTTGAATATTTCGAAGTGCAATTTTGGCAAACAGTGCAATAAATGATGTTAATGCACCCATTTTAATTGCTTAGATTAATTTTTGAAATTCTGTTTTAG
Seq C2 exon
GTTTGAGTGTGAAAAGCTGATTCTTGTTGGGGATCCCAAACAGCTACCTCCTACTATTCAGGGTTCTGATGCAGCTCATGAAAATGGATTGGAACAAACTCTTTTTGATCGACTTTGCTTAATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000138658-C4orf21:NM_018392:23
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.141
Domain overlap (PFAM):
C1:
PF130861=AAA_11=FE(17.9=100)
A:
NA
C2:
PF130861=AAA_11=PD(9.4=52.4),PF130871=AAA_12=PU(5.9=26.2)
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:
CGAGTAGTTGGAGTTACCTGTGC
R:
TAAGCAAAGTCGATCAAAAAGAGT
Band lengths:
246-1090
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- 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)