HsaINT0024055 @ hg19
Intron Retention
Gene
ENSG00000138658 | C4orf21
Description
chromosome 4 open reading frame 21 [Source:HGNC Symbol;Acc:25654]
Coordinates
chr4:113481889-113483641:-
Coord C1 exon
chr4:113483527-113483641
Coord A exon
chr4:113482152-113483526
Coord C2 exon
chr4:113481889-113482151
Length
1375 bp
Sequences
Splice sites
5' ss Seq
AACGTAAGT
5' ss Score
10.74
3' ss Seq
ATTTGCTTCATTTTTATTAGGTC
3' ss Score
8.58
Exon sequences
Seq C1 exon
TGGTTGTCCATGCGTTATTGGTTTGTAATGCTAGCACAGAACTGACTACTTTGAAAAACATTCAGGACTACTTTAATCCAGCTACTCTACCTCTAACACAGTACCTGTTAACAAC
Seq A exon
GTAAGTCATTTTTTACCTTTGAGTCATTGGTATTAAAAAATGGTAATCAGAAGTAAATATGAAAATTCAATAAAAGTACAGTATATAAATGTTGCCAATAAAATTGTAATTATTTTTCAGACTATGACATTATTCTCTGTCAGTGGTTAAAAAGAGAAAAGGGGCTGGGTGCAGTGGCTCATGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGTGGGCAGATCACCAGAGGTCGGGAGTTCGAGACCAGCCTGACCAACATGGAGAAACCCTGTCTCTACTAAAAATACAAAATTAGCTGGGCATACTGGCGCATGCCTGTAATCACAGCTATTCGGGAGGCTGAGGCAGGAGAATTGCTTGAACCTGGGAGGCGGAGGTTGCGGTGAGCCGGGTGCCATTGCACCCCAGCCTGGGCAACAAGTGAAACTCTATCTCAAAAAAAAAAAAAAAAAAAAAGAGAAAAGGAATTATGCATTATTTTTCATCTGTTTATTAAGGTTTGAGCTAATAAATGTTACTGTACATTTTCACTTCATCAAGAGATAATTTAAGGATCATTTCAGTATTGATTTTATTTTTTATTATCTGTATTTTTATATTACAAATTATTTAACATTTAAAGGAATCATTTTACAGCTGGAATCCAGTGTGTATATTGCTACTGATTTTATTCTCGATATAGCCATATCTCATTTTGAATTTCTCAAGCACCATGTCCCTTTTTAAAAAATTGGAAGTGATATTATATTAAATGCATTAAAATTGATAGGAAAATCCAGTTTTCAATTTGGAATATTATTATCTACCTGTGATGTTTTATTTTTCTCACTACAATGAAGTCCTAGGTAAAAAAATAAATATCCTTTGATTTCATTATGTTATTTATCCAATTTGAAATGAATTTTCATGGAAATAGAAATAAGACCAATTCATGTGATGTAGTTTTACCTGAAATGAGGGCTAGATTAATTATCTAAGTTAGGTTTGTATAATAGAGCATGGGTTTTAAAGTCAGTCCGCCACTTATTTGTGGTGTGGTATTGGGGGAAAAAATTCAATATTCTTGTATCTGTACTTGGGATAATTAACTAACTATTTCCTAGTGTTGTTGTGAAGATTTCATCAAGTAATATGTAAAATGCTCAACAAAGTGTCAGCATGTAGTAAGTATTCAACAAACGTCAGTTCTCTTCTACCCTCCTCGATATTGGAGTATGTATCCATTTACAGTATATATCCACTTACTGTTTATTTCCATAAAAAACTGTTCTCTGTAATGCTTACAAAGTGATGGCTAAGTTATGAATTATTCTACTCATCTTTTTCAAATGCCCCTTTTTTTAAAATTGTTTATTTGCTTCATTTTTATTAG
Seq C2 exon
GTCTTCGCCAACTATAGTTAGTAACAAAAGAGTCAGTAAGAGAAAATTTATCCCACCAGCCTTCACAAATGTCAGTACAAAATTTGAACTACTCAGCCTAGGAGCAACATTGAAGTTAGCTAGTGAGTTGATTCAGGTACACAAGTTAAACAAGGATCAAGCTACAGCTCTAATTCAAATAGCTCAAATGATGGCATCACATGAAAGCATTGAAGAAGTGAAGGAACTGCAAACTCATACCTTCCCTATCACAATCATACATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000138658-C4orf21:NM_018392:18
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF130861=AAA_11=PU(23.7=44.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGGTTGTCCATGCGTTATTGGT
R:
GCAGTTCCTTCACTTCTTCAATGC
Band lengths:
345-1720
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)