HsaINT0039108 @ hg19
Intron Retention
Gene
ENSG00000081052 | COL4A4
Description
collagen, type IV, alpha 4 [Source:HGNC Symbol;Acc:2206]
Coordinates
chr2:227914784-227915874:-
Coord C1 exon
chr2:227915693-227915874
Coord A exon
chr2:227914848-227915692
Coord C2 exon
chr2:227914784-227914847
Length
845 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGG
5' ss Score
11.08
3' ss Seq
TTGTTTCATTAAACTGTCAGGGT
3' ss Score
3.83
Exon sequences
Seq C1 exon
GTGATAAAGGAACTCCCGGGATGCAAGGGAGAAGAGGAGAGCCGGGAAGATACGGACCACCTGGATTTCACAGAGGGGAACCTGGTGAGAAAGGTCAGCCAGGGCCTCCTGGACCCCCAGGCCCTCCAGGCTCAACTGGTCTAAGAGGGTTCATTGGTTTTCCAGGACTTCCAGGTGACCAG
Seq A exon
GTAAGGGGCTACTGCTTTGTGGGGGAAGAGACAATAAAACCTTTCTGTTCTTAGGATGTCCGTAAGGAGCTATAATTTGCCAGCGTATATACCATTGCCCTTTCACTGGCTTTTAGAATGTAAGGTGTAGCTCAAGGAGAAAATAGAGCCTTCTAGAAGGCCACGATGAAACTGACATTTCTGACCAGTGCTCCTGCCTGGTTCCCCTAACATAGAGTCATATAATCGCTATCTCCCAGCCTGGTTTAAACCACCCATGAAGACTTGCCTCATGACCACTGGTTTACTGGAATGAAAGTCGTCCTGAAAAATCACCCAAATCCTGTCTTTAAAGTCTTCCAGTTTCAGATATCACAGATTTTGCTTTCAATATATTTCGTCTTCACAACCATGAGTAAAATACCCTTTCAGAATCCAGGAGGTACAATACATGTAGTTGCCAACATTATACTTCTGGAAAACACGTAACTCACTATCCATCTTTTGGAATGAAATGGATTTGTAAAGTCTTTCATATGCTGTGATTTATAATACTATTTTATTTAGTATCAACTTGTTTATTTGTAATTTAAAATTCAAATTAGTAACACAATTACTGTTTCACAACCAAGTGTAGAGAATGGGATGCTACCAGTTGCGACTGAGAACTCTAATTCTGGAGAAGCTATATCAACTTTGAAAAACTAGATACATGTAGTGGGAGGCTTGCATGCATTTAAACTTTCGTTACCACTGCAGATTACAAAAACCAAATTAGTTACAGAAAATTACAACTGGATCGTGTTGTGCATGTGCCATTTGTATTTGAAATCTGATTAAGGCCTTTTGTTTCATTAAACTGTCAG
Seq C2 exon
GGTGAGCCAGGTTCTCCAGGTCCCCCTGGATTTTCAGGAATTGATGGAGCAAGAGGACCTAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000081052-COL4A4:NM_000092:33
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(63.9=63.9),PF0139113=Collagen=PU(53.0=57.4)
A:
NA
C2:
PF0139113=Collagen=FE(31.8=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTGATAAAGGAACTCCCGGGA
R:
CTTTAGGTCCTCTTGCTCCATCA
Band lengths:
246-1091
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)