HsaINT0039121 @ hg38
Intron Retention
Gene
ENSG00000081052 | COL4A4
Description
collagen type IV alpha 4 chain [Source:HGNC Symbol;Acc:HGNC:2206]
Coordinates
chr2:227010313-227012297:-
Coord C1 exon
chr2:227012181-227012297
Coord A exon
chr2:227010502-227012180
Coord C2 exon
chr2:227010313-227010501
Length
1679 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGAG
5' ss Score
7.1
3' ss Seq
TTTTTCCTTTGTTCCTCCAGGGC
3' ss Score
12.66
Exon sequences
Seq C1 exon
GGTGCAAAGGAGAGCCTGGGCTGGATGGCAGGAGGGGTGTGGATGGCGTCCCTGGGTCTCCTGGGCCTCCCGGACGTAAAGGTGACACAGGAGAAGACGGCTACCCTGGAGGACCAG
Seq A exon
GTAGAGTTTCAGTCACTCCTCTTTTCTCTGACACTGTAAACCTTAGAGTTGTATACAAAATCTCTGATCTCTCAAGTGGCTTTCCAAACTGGATCCTATTCAGATCATTTGCCTTAGATGCTGACTCACCAGGTATCAGAGACAGAAACAATGAGAACAGAGTGGGATGCATCTCTTATGTTCTAACTGATGTTAAACCATCATAAAACCTAGACAAGGCCCTGCATCCTATTCAGTATTTTCCCAAACTGCTATACATCATCATCAAAGTCTTGGCCATTTCTGCAGTTCACTTTTCAAGGTCATGAAGGGACGGTCAGCCTGGTGGCTGTGGGATCACCCTTAAGAGGCTGTGATGAAGACCTCAGGGACGGTGTGTGTGTTCTCACCCTCTCCAAGTGGCCAAATCGCCTGGTTTCCTGAGTTCACTTCATCTTATCATATAGCCATTAGTACACTGATGTAGAAAACAGGGCTCTTTCTTAAAAGAAAAAAAATGGGAAGTGGTGTTGGGAAAGGGGACATAGGACTCTTCAGAATAGAAGTGTGAAACAATGCACCATGTAGCTCGTTAGGCGCATGGATCCAAAGAGCCTGAGACACAATCCCATCTCCAGAGAGTCCCTGGCCAGGGATGCAAACTCCTGTACCAGGTTAGTAGTGAGTAGAAACGAATGAGGAGGGCTGGGTGAGGTCTGTAGCAAAATGGAGCTTTGGCTAAAAGCTGCAGCGCAGCTCCAGCCAATTATAGTCTACAGAAATGTGGGCCTACACTCTACACTCTCTTCGTTCAAAATATCAACTTGTAAAATCCTTACAGGTCAAAACACACGAGCAGGCCTGATTCAGTCCACAGGCTACCACTTTGTCGTCTCTGGTTGACAGTGTAGATGGGGAGAGCCTGCCAGTCTTGCAGAACCAAGGGTAGAACACAAAAAATACCTTTTGGTTTCAATGTCTAACTTCACCTTTTGCTCTTGGCAATTAGAAACAGCTCCTGGCCTTCTGCAATAGTTCAGCCCCTTAGAGGTGCCGAAGGATACAGACCCTGCTCACGTTCTCTAGAACTGTTGATTTCCCATCTGCCAACAAGAATGCTAGAACAAGGCCTTCCTTCCATTTCCCTCTCTTCTCGAAGAGGAGAGCCAAACTTGTAGATGTGGATCCCAAGCCTTTGGCTTTCTCAGAATGGAACTGATAATATGCTGGAACCAGGGAAGAGGTCTGGGAGGTGTAAGAAAGACCGACTTTGGGGAGCACTTGCTCAGCAGTTCAGTCTGGGGAGTCCACACTTGGGGTGTGTCATTACACTGTCCTTGTTCTTTTCTTCCCAGCGTATTTCATAACTTAACTTTTTGTTATGCTTATTGTTTCTTATTTCTCTCTCTTCCTCAAGTGTAATGCAAGCTCTATGAGGGCAGGGATTTTCCTCTGTTTTTTGTCTTTATGCTAATGTAGCCCAGGCATCTAGGAGTTGCTTGGAACAAATACTTGATGAATGAGTTGTTCTATGTACTGCAGCTGTGTAGCTGTGTACGTTCCAGAAGGCGAGGAGGGGCTGAGTCATGCTCCCCTCTGCTCCCTGAGTGCTTAGCACAGTGCCAGAACAGAGGTGCTTAACATATTTGTTAAACCAAACCCCCTAACCTGCCTTCAATTTTTTTCCTTTGTTCCTCCAG
Seq C2 exon
GGCCTCCTGGTCCCATTGGGGATCCTGGGCCCAAAGGGTTTGGCCCTGGATACCTCGGTGGCTTCCTCCTGGTTCTCCACAGTCAGACGGACCAGGAGCCCACCTGCCCCCTGGGCATGCCCAGGCTCTGGACTGGGTATAGTCTGTTATACCTGGAAGGGCAAGAGAAAGCTCACAATCAAGACCTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000081052:ENST00000396625:45
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=0.281
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(36.7=45.0),PF0139113=Collagen=FE(65.0=100)
A:
NA
C2:
PF0139113=Collagen=PD(31.7=29.7),PF0141314=C4=PU(39.8=67.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTGCAAAGGAGAGCCTGGG
R:
AGGTCTTGATTGTGAGCTTTCTCT
Band lengths:
303-1982
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