HsaINT0038962 @ hg38
Intron Retention
Gene
ENSG00000187498 | COL4A1
Description
collagen type IV alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:2202]
Coordinates
chr13:110211869-110212479:-
Coord C1 exon
chr13:110212417-110212479
Coord A exon
chr13:110211923-110212416
Coord C2 exon
chr13:110211869-110211922
Length
494 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAAT
5' ss Score
8.88
3' ss Seq
ATGCTCTGCTGTCTCCCCAGGGG
3' ss Score
10.2
Exon sequences
Seq C1 exon
GGAATTCCTGGCCAAGACGGCCCGCCAGGCCCCCCAGGTATTCCAGGATGCAATGGCACAAAG
Seq A exon
GTAAATCCAGAACCGAGACCCTCCTTTTTGTGTGTGTTTACGTAATTTTTGCATATTAAGGAGTCAGGTAGTGTGATTCTGTTAATAGAGTTTTATTTGCCACAATTGGAAAGTTGCTTGTCTTAAAGTTTGCTTTATTTAGTAAGGAAATACAGTTTTCCCATATTTAGTGTACCAGAAAGATATAATTGTTCCTTTCTTTTTTGTAGACTTTTATCCTAAAATTGCATTTAAGCACGAAAGTTATTACCTATAATCATTTACTACATCACGTAAGAAAATGCCATTATGGGCCTTTGTCCCTATTAATGATACTATCAAGTCTATTTCTTCTTTCATAAAGTGGTACCCAGTAGCACAGCTTGTGACAAACTGTTTTTAGGAAATGATTTTAACCAACAAATGAAGGGTAGGGCAGAGTGATGCATGCGATGTCAGGGCTGATGTGTCTGCCACACACAGTGCGTATGAATGATGCTCTGCTGTCTCCCCAG
Seq C2 exon
GGGGAGAGAGGGCCGCTCGGGCCTCCTGGCTTGCCTGGTTTCGCTGGAAATCCC
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000187498:ENST00000375820:6
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=PD(16.5=76.2),PF0139113=Collagen=FE(33.3=100)
A:
NA
C2:
PF0139113=Collagen=PD(10.3=44.4),PF0139113=Collagen=FE(25.8=100)
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:
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
- Autistic and control brains
- Pre-implantation embryo development