HsaINT0039153 @ hg38
Intron Retention
Gene
ENSG00000188153 | COL4A5
Description
collagen type IV alpha 5 chain [Source:HGNC Symbol;Acc:HGNC:2207]
Coordinates
chrX:108620259-108621892:+
Coord C1 exon
chrX:108620259-108620426
Coord A exon
chrX:108620427-108621802
Coord C2 exon
chrX:108621803-108621892
Length
1376 bp
Sequences
Splice sites
5' ss Seq
CAGGTAATT
5' ss Score
8.55
3' ss Seq
CTTATTGATATTCTTCAAAGGTA
3' ss Score
5.68
Exon sequences
Seq C1 exon
GTTTACATGGAATACCAGGAGAGAAGGGGGATCCAGGACCTCCTGGACTTGATGTTCCAGGACCCCCAGGTGAAAGAGGCAGTCCAGGGATCCCCGGAGCACCTGGTCCTATAGGACCTCCAGGATCACCAGGGCTTCCAGGAAAAGCAGGTGCCTCTGGATTTCCAG
Seq A exon
GTAATTTGTTTAAAGTTTTCTCTGATTTGGATTAAGGAAATTAAAACTAATACGACTCTGGTAGATAATTCCCATGTTACACTTTTCTAGATTGACGTGATCCCTTAAGGATGAGCATTAAATATCTATGACTGCAGGAAGCTCACTTTGCTATTTTCACTGCACATTTTTCTCTGTGAGAGTTCCAGTTATATATTACTGTATAACAAACAACCCCAAAACTTAATGATTTTAACCAACCTTTTAATTTTGCTGAAGATTTTGCAGCTCTAGAATTAAGGGATGACTTGACTGGTTCATTTATCTCTAACCCACGTTGCCCCAGCTGGAGTGTTTGGGACTGAAAGGTCTACTTCTAAGATGGCACTTCTCTGACATCTGGGTGTTCATTAGCTCACATGTCATCTCATCGTCCATGGTACCTCTTCGCATGGCTTAGGCTCCTCACATTATGGTAGTATAAGGCTGGTTGCTCCCCTTCCATGGCAGCTGGCTTCCAACAGAGAGAATCCCACAAGAGAAAAGTGAGTGTTTCAGGAACTACAGGTAGAAGCGGCAAGATTTCTTTTCTTTCGCTCTCTCTCTCCCTTTTTTTCTTTCTTTTTCCCTTTCTTTCTCTTTCTTTCTCTTTTCTTTCTTTCTTTTCTTTCTTTCTCTCTTCTCTCTTTCTTTCTTTCCTTTTCTTCTTTCTTTCTTTCCTCTCTTTCTTTCTCTCTCTCCTTCCTTCCTTCTTTTTTTTTTTTTGAGACAGGGTCTCACTCTGTCACCCAGACTGGAGTGCAGTGGGACATGATCACAGCCCACTGCAGCCTCAAACCCCTGGGCTCAAGCCATCTTCCTGCCTCAGCCTCCTCCCAAGTAGCTGGGACTACAAGCACATACCACCACACACAGCTATTTTTTTTTTCTTTTTTTCTTTGTAGTGATGGAGTCTCACTATGTTGCCCAGGCTGCTCTCAAATTCCTGTCCTCGAGCAATCCTCCCACCTCAACCTCCCAAAGTGCTAGGATTATAGGCATGAGCCACTGTGACTGGCCTGTAAGACTTCTTTTGATCTAGGCTTGGGAGTCACACAATGTCATTTAGTCAAGTGTGAGGTACAGAATCAACCCTAGTTCCAGGTGAGGGTTTTATAGTAGATTGTACATACTGGGACATATGGTTCACTGGGGGGCCATCTTTAGAGATTAGCTACCAGACTGAGTCTCCTTATTCATGGGTATCAGCAGTAGTGGGCACTATGGTCAAAAAGTCTAAAACTTAACAGTGCCTTACGTCCAACCCTCAATAGTTTTCTGGTTGACATCTTAAAACTTACTTTTTATGTTCCCTAAGTCAAAGAAAGGCAAACATTACTTATTGATATTCTTCAAAG
Seq C2 exon
GTACCAAAGGTGAAATGGGTATGATGGGACCTCCAGGCCCACCAGGACCTTTGGGAATTCCTGGCAGGAGTGGTGTACCTGGTCTTAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000188153:ENST00000361603:31
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=0.947
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(29.5=31.6),PF0139113=Collagen=PU(67.2=68.4)
A:
NA
C2:
PF0139113=Collagen=PD(31.0=58.1),PF0139113=Collagen=PU(42.9=87.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGGAATACCAGGAGAGAAGGGG
R:
AGACCAGGTACACCACTCCTG
Band lengths:
246-1622
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