HsaINT0024048 @ hg19
Intron Retention
Gene
ENSG00000138658 | C4orf21
Description
chromosome 4 open reading frame 21 [Source:HGNC Symbol;Acc:25654]
Coordinates
chr4:113508436-113511030:-
Coord C1 exon
chr4:113510880-113511030
Coord A exon
chr4:113509086-113510879
Coord C2 exon
chr4:113508436-113509085
Length
1794 bp
Sequences
Splice sites
5' ss Seq
AGGGTAGTC
5' ss Score
1.16
3' ss Seq
AGCATTCTGTTTTCTTTCAGGGA
3' ss Score
10.43
Exon sequences
Seq C1 exon
GTGACATCACCAGAAGAAAACATCTCTACATTGAGCCCTGTTTCTACCTTTTCTTTGAACTCAAGAGATGAAGACTTCATGGTAGAATTCTCTGAGACGTCCCTGAAAGCAAGAACTTTACCTGATGATCTTCATTTTCTCAACTTGGAGG
Seq A exon
GTAGTCGTTACCACATTGCTCTAATATCTGTCTATTCATTTAAGATGAAGTTTTTTATTTGAGAGATTATTACACTAAATATATCTTAGAACCAGATTCAGTGTCATATCCCTTGAAGCCTTTCCATAACCTTTCTTCCTTTGAACTTTTTCTATCATAGATAGCTATTCCAGGTACAATATTCCCTTCTAGCTATCTAGTTCCTTCTTGTTTCTCCTCCCAACTTTGTCAACACAGACCCCTGAAAGTATCTTCTACCATTGTCAGTTCTTCTCACAGCTGTAACTCCAGCATCTGACCCCTTTACAGCCCTTTCCTGTTCCAGAGGAATGACTCATTGCAAGTGTCTCATCAACACCATTGGTTGACCTTAGCATAACCTTTTAGTGTCTCTTTTTGCTTTGGGATCCTGAACTCTTCAACTGCTGCTACCACCCTTGCATTCCTAGGACTCTAGGTTTTCATATATTTTGGCCCTTCACTATGAGTCAGCTTCTGCTTCTTGATGAATATAATACTATTCTCTAGGATCCCTTTCACTAAAATTTCTTTTTTTCTCTTTTCTTATAATCTCATCAATATATCTTCCCCTGATTCTGAATTTATGTTGGGTGAGGGGTGAGTTGTAGATAGTTTTTTGATTTTGGATGGATGATAACAAAAAATTCTGTAATGTGAATTGGTAGTTGGGTTAGAAAAGGTTTTATGGGTGTGGTTGGTAGAAGGCAACAAGGTAGAGAAGAATCAAATACACCGGAGTGGGTATTCAAGAAAAAGTGATATGGTAGTGAACAGTAGATGATTTTCACAGTTATACCATGAATCTTTTACTTTAATGGACTTTTAACTTTTCTGTCAGTGTTACTTGATCGACTTGTTAGAATTACAGCATAGCACTTTATAAAAGAATATTCATTGGCTCACCTACTGCTCTGCTACTTTCCAGATGATCTCCAGAGTATATTTCCAACAAGATAGAAACTCTGTCAGGAAGGCACATTATTATAAAATAGGAATCCATAGTATTGTCAGATAAAAACTATAAGCTTGCATAATTCTGATGCAGTATTATTCATTTGTTTATATATTCAACAAATAGTTACTGCTTCTTAGATTTTTAGGAATATATCACTAAAGCTGCTGACACACAGAAGGAATCATTAAACTCTTTCAGACAGAATTTGCCATGAGTTTACCAGAATTATACTCTTATCAAACACCATTAGATCAAAATAAAGCTAAAATCTTTTTTTACTCTGAAGGGTAACATGATAATTCATGAGTGTAAAAATATATAAAGGAAGTTACAATCACATAGTCATATAAATGAACCATGAGCTTCCGTCTCTGGGAAAGAATGTAAAGTAGATATAAAAAACTAGTCTAGGTTCTTATCCTGACTCTGCCACTTAGTAGTTATGCTACTGCTAAGCCTTTGTAATCTCATTTGTAAAATGAGAATGATGCATTTTTGTTGTTGTTGTTAGCTTTAAAGTGCTTTGAAAATGTTAAGTGCTATATAAACATAATTTAGTAATTAGGAAAAAAAAAGGAGGAGAAGAAAAAGAGGGACTTCATCAACCCTAAGAATGTTTCAGTATATATGAATTAAGCTTTGAAATCTTTATTTTTTGAGGTTAAAACCATTAATTTTTTTTTAAGGAAATAAAATAATGTGATTTTTTTTTTCAGAGCAAGTTGCTACATTTTGCTTTTGTATACCCACTGTTTTCTAGAGCCTAGGTGATAACTAGTAGAACATTTTTATTTAATCAGCATTCTGTTTTCTTTCAG
Seq C2 exon
GGATGAAAAAATCCCGTTCTCTGGAGAATGAGAACCTTCAAAGGCTTTCATTATTAAGTAGAACCCAGGTTCCACTTATTACTTTGCCACGTACTGATGGGCCACCTGACTTAGACTCTCATTCGTATATGATCAACTCTAACACATACGAGTCTTCTGGCTCCCCCATGCTCAATTTGTGTGAAAAGTCAGCAGTTCTTTCGTTTAGCATTGAGCCTGAGGACCAAAATGAAACCTTTTTCTCTGAAGAATCTAGGGAAGTGAATCCAGGGGATGTTTCACTTAATAATATATCTACTCAGAGCAAGTGGCTGAAATATCAAAACACATCCCAATGCAACGTGGCTACTCCAAACAGAGTTGATAAGAGAATAACTGATGGCTTCTTTGCTGAGGCTGTTTCTGGGATGCATTTTAGAGACACAAGTGAAAGACAGAGTGATGCTGTCAATGAAAGCTCTTTAGACTCTGTGCATTTGCAAATGATAAAAGGCATGCTCTATCAACAGCGGCAGGATTTTAGCAGTCAAGATTCGGTTTCCAGAAAGAAAGTACTTTCTCTGAATTTAAAGCAGACTTCTAAGACAGAGGAAATTAAAAATGTATTAGGAGGGTCTACCTGCTACAACTACAGTGTAAAGGATTTACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000138658-C4orf21:NM_018392:11
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.142 A=NA C2=0.274
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
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:
TCTGAGACGTCCCTGAAAGCA
R:
GTGAAACATCCCCTGGATTCACT
Band lengths:
343-2137
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)