HsaINT0039088 @ hg38
Intron Retention
Gene
ENSG00000081052 | COL4A4
Description
collagen type IV alpha 4 chain [Source:HGNC Symbol;Acc:HGNC:2206]
Coordinates
chr2:227101865-227102848:-
Coord C1 exon
chr2:227102789-227102848
Coord A exon
chr2:227101910-227102788
Coord C2 exon
chr2:227101865-227101909
Length
879 bp
Sequences
Splice sites
5' ss Seq
CGGGTAAGC
5' ss Score
9.14
3' ss Seq
GATTTTTGTGAATTTATTAGGGG
3' ss Score
4.47
Exon sequences
Seq C1 exon
GGAGAATCTGGTATTGGGGCAAAAGGAGAAAAAGGTATTCCTGGATTTCCAGGGCCTCGG
Seq A exon
GTAAGCATCATTTGCTGTTAACATCAGTGAATTTGGAGATATTTCTCTTTCATGTTTTTATAAAACCAGGTCAGTAGTCCCACAAGCTCAAAAGTGAAGAATAGCTCATGTAAGAACAAAACATTTTGGACGAGAATTATGGAATATCTAAATATCCCAGAGCATCCTTCCATTGACATCATTTAGATAAAACAGGCAAGCAAAAGATAGAAGAATTTGGGAAAAGTGACAGGATTGTGCCATCTCTTGTCTGGCACCTCAGTGCCAGTAGGAAAGTAGCTTGGAATAGTTAATTTAAGTCTATTTGAGGAAACAACATGGTGATATAGGGGCAGGAGCTAGAAAAAAAGTACAATATTAAGCTCCAAACATCACCACATGTCACTAATAGAAAGCCCACTCATAGAGTCACCATGGAGGCCAGACCGCAGCTGGCATGGGCATTGAGTTTATTTGGTTCTAGATTTAGTACTGAATGGGGAAATATTGGTTTCCATGGTCATTTTTATTGCTAATGATGCACAGAGCAACTATTAATTTCCAGGCAAATTATATTGCAGAGATTTTAAAGATATTTGGCCCAGTGCAAGCACTAAGTTAAGTAAATTAAATTTGGAAAAGCAACGACAACAAAAATACATTCTTAATTAAAACACTGGCAATGACATGGATTTTTTGAATAAGACTGAGGATCACTTCAAGTAGCAAATGTTATAAAGAAATGGAATCTATTTTATATTTATTTCCTTTTATTCAGCTAGCTTTGCAAACAGGACCAAATATCCATGGAACAATTTGATAAGGTGAAAAATGATGCACTGAGCTGGTTAATGCATTCTGATTTAATTCTGTTTATCCTGATTTTTGTGAATTTATTAG
Seq C2 exon
GGGGATCCTGGTTCCTATGGATCTCCAGGTTTTCCAGGATTAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000081052:ENST00000396625:15
Average complexity
IR
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=FE(20.4=100),PF0139113=Collagen=PU(21.5=70.0)
A:
NA
C2:
PF0139113=Collagen=FE(15.1=100),PF0139113=Collagen=FE(21.5=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
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