HsaINT0024068 @ hg19
Intron Retention
Gene
ENSG00000138658 | C4orf21
Description
chromosome 4 open reading frame 21 [Source:HGNC Symbol;Acc:25654]
Coordinates
chr4:113538596-113541346:-
Coord C1 exon
chr4:113541158-113541346
Coord A exon
chr4:113540847-113541157
Coord C2 exon
chr4:113538596-113540846
Length
311 bp
Sequences
Splice sites
5' ss Seq
ACTGTAAGT
5' ss Score
8.59
3' ss Seq
AGTTATTTTAATATTTTCAGGGT
3' ss Score
6.39
Exon sequences
Seq C1 exon
GTGAAACCTGGAGATGACTTAGAAAGTGATCGATACTTAATCACAGTTGAAGAGGTTAAAGTTGCTGGAGCCATAGGTATTGTTAAGCAGAATGTCAATAAAGAAGCACCAGAGTTAAATTCAAGGACATTTATATCCTCTGGCCGATCTCTTGGATGTCAGCCCTCTGGCTTAAAAAGGAAGTTTACT
Seq A exon
GTAAGTTTTGCTATGGAAAATAATATATCAAAATATATTTATAAAATTGTCTCGAAAAGTAGTGAATTTTGAAGTTATTGTACTCTGTCATTCAAAGGGCACTTCATAGTATACTTAGGTAGAAAGGAAGTAAACCCTACTTTGAAAAATCTTATTACAAATGAATGTACTTTGACAAACTTTAAATCTGAATTATTACTTTACCTTAGGCAAACCAGAAACAATCCTTCTCCTTTTTTTTTCTTAGCCAGTTCATTTCACATTTTCTTAATGGGTAATGGTACACCTAACAGTTATTTTAATATTTTCAG
Seq C2 exon
GGTTTTCAAGGACCACGTCAGGTTCCAAAGAAAATGGTTATTATGGAAAGTGGTGAATCAGCTGCATCACATGAGGCTAAGAAAACTGGCCCTACTATTTTTTCTCCATTCTGCAGCATGCCTCCTTTGTTTCCTACTGTTGGCAAGAAAGATGTAAATAATATACTGGCAGACCCTGAGAACATTGTGACTTACAAGAACAGGGAGAGAAATGCCATGGATTTTTCTTCGGTTTTTTCTCCATCCTTCCAGATTAACCCAGAAGTGCTGTGTGAAGAAAATTATTTTTGCTCACCTGTCAATTCTGGAAATAAGCTTTCAGACTCTTTACTGACCAATGAGCCTGTGAAAAGAGATAGTTTGGCATCTCACTATTCAGGAGTTTCACAAAACATCAGAAGCAAAGCACAGATATTAGCTCTTCTGAAGTCCGAATCATCTAGTTCATGTGAGGAACTAAATTCTGAGATGACAGAGCATTTTCCTCAAAAACAACCACAAGGAAGTTTAAAAATTGCTACTAAACCAAAGTACCTAATTCAACAGGAAGAGTGTGCTGAGATGAAGAGCACAGAAAATTTATACTACCAGCATCAATCAGAAAATACCATGAGAAATAAAAGCCGGTGGGCCATGTATTTATCCTCACAGAGTTCACCTATACATTCTTCTACTGTAGATGGGAATGATACAGAAAGGAAACCCAAGGCCCAGGAAGATGATGTAAATTCTAATTTGAAAGACCTTTCATTACAAAAAATTATACAGTTCGTTGAAACGTATGCTGAAGAGAGGAAAAAGTATAATGTAGACCAGTCAGTCGGTAATAATGATCCATCCTGGAATCAGGAAGTAAAATTAGAAATTCCTTCATTCAATGAAAGCAGTAGCTTACAGGTTACTTGTAGCAGTGCAGAAAATGATGGTATATTATCAGAATCTGACATTCAAGAAGATAATAAAATACCTTTTAATCAAAATGACAAGGGGTGCATTAAAGGATCAGTTCTCATTAAAGAAAATGCTCAGGAGGTAAATACATGTGGAACACTGGAAAAGGAGTATGAACAATCAGAGTCATCTCTGCCAGAACTGAAACATCTCCAAATTGAATCTAGTAATAATTCTAGGATCTCTGATGACATTACAGACATGATTTCTGAAAGTAAAATGGATAATGAAAGTCTTAATAGTATTCATGAATCTCTGAGTAATGTAACACAACCATTTTTGGAGGTAACTTTTAATCTGAACAATTTTGAGACCAGTGACACTGAGGAGGAATCACAGGAAAGCAACAAAATTTCCCAGGATTCAGAGAGTTGGGTAAAGGACATTTTGGTTAATGATGGCAATTCATGTTTTCAAAAGAGGTCTGAGAATACAAACTGTGAAGAGATTGAGGGTGAACATTTGCCATTCTTAACATCTGTTAGTGACAAACCTACAGTGACATTTCCTGTTAAAGAGACTCTGCCATCACAGTTTTGTGATAAAACTTATGTGGGTTTTGACATGGGAATATGTAAAACTGAAAACACAGGAAAAGAAATAGAGGAGTATAGTGACACATTAAGCAATTTTGAATCTTTCAAGTGGACTGATGCTGTATACGGAGATAATAAAGAAGATGCTAATAAACCTATTCAAGAAGTCAGAATTAACTATGATTTTGCTTTACCCCCGAATAAATCTAAAGGTATAAACATGAATTTACATATTCCTCATATTCAAAACCAGATTGCTGAAAACAGTAATCTATTTTCAGAAGATGCTCAACCTCAGCCTTTTATTTTGGGAAGTGACTTAGACAAAAATGATGAACATGTTTTACCCTCAACTTCTAGTAGTGACAACAGTGTCCAACTATTAAATACCAATCAGAATCACTATGAATGTATTGCACTTGATAAATCAAATACCCACATTTCCAATTCTTTGTTTTACCCACTGGGAAAAAAGCATCTTATTTCCAAAGACACAGAAGCACATATATCTGAACCTGAAGATTTGGGAAAGATTAGAAGTCCACCCCCTGACCATGTTGAGGTTGAAACTGCCAGAGAAGGCAAACAATACTGGAATCCTAGAAATTCTTCAGAACTTTCTGGATTAGTAAATACCATTTCTATTTTAAAGTCGCTATGTGAACACAGTACTGCTTTAGACAGCTTGGAAATATTGAAAAAGAAAAATACTGTCTTTCAGCAAGGAACTCAACAGACGTATGAGCCAGATAGCCCTCCTGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000138658-C4orf21:NM_018392:5
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.032 A=NA C2=0.445
Domain overlap (PFAM):
C1:
PF103824=DUF2439=PD(30.3=36.5)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCCGATCTCTTGGATGTCAGC
R:
TCCAGAATTGACAGGTGAGCA
Band lengths:
356-667
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)