HsaINT0039281 @ hg38
Intron Retention
Gene
ENSG00000130635 | COL5A1
Description
collagen type V alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:2209]
Coordinates
chr9:134823416-134824855:+
Coord C1 exon
chr9:134823416-134823469
Coord A exon
chr9:134823470-134824599
Coord C2 exon
chr9:134824600-134824855
Length
1130 bp
Sequences
Splice sites
5' ss Seq
CCGGTAAGT
5' ss Score
10.91
3' ss Seq
GCTCCTGTTCTGTCCCCCAGGGC
3' ss Score
11.07
Exon sequences
Seq C1 exon
GGTCCAACTGGCCCGAAGGGTGAGGCAGGCCACCCAGGACCCCCAGGCCCCCCG
Seq A exon
GTAAGTAGCCCTTGAAGCCCAGAAAGCGGGACGGGGGCTCTGGCTAGCTCCGAGGGAATTGAGAAAGCAACTGTGTGTGTGTGACCCCTCCTGAGACTCATGAAGCCCATGTGGCATGCCCGGGCCTTGTCCCTCGCACGCAGCCGGGGAAATGAGCCACACAGGTCTATCACAGGAAGCTTACAGGCCAATTGGCCCTGAGAAGAACAGCTGGCCAGGAGAGAGAGGATACACGTGTGTGCTGTGTGTGCATGCATGGTATATGAATGTGTGAACGTGTAGTATATGCGTGTATGTGACTGGGCACGTGTGTGTGCATGTCTGTATGTGTACGTGCATCCTGTATATGTGCATGCATGTGTAATGTGTGTGTACATGGTTTGTATGTGCATGTGTGTGTGCATGATGTGTGTATGGGTATGCATGCATATATGTGGGGCACATATGTGTGTGCATGTGTAGTGTGTGTATATTGTATACGTGCATGCATGGCCGTGTGTGTGTGCATATGTATATGTGTACATGCATGTCTGGGATATATGTGCATGTGTGTGTGTGTGTTGGGATGGGGGAGCACTAGACAAGGCCCTGGAGGTGAAAGGTGAAGCCCAGTTTGAACCAGGGCATGGCGAGTGCACTATTGGACACCCCCCTTTGGTTGTGGAGTCTCTCCAACTCCCATCGTCATCTTAGCTGTGGCCTTCTGGAAGTGAATGGCTCTTTGCATCAGGAGGCATTCATGTGGCCCCACTGTGTTCAGCCCCAGCTAGGGCTGCAGAGGCCAGACTGGGGAGACCTGGTCCCTTTCCTCAAGGCTTGGCCTTTTGTGTGGCTGAGGGCAGGATGGCAGATGCAAGCCCAAGGCTGCAAACTGTTAAGTTTCAGCTCTAGAGAGAAAGGAGAGGTGCTCCATGCTGGCAAGCACCTGGCAGTGGGGATGGGTGTGGAATGTTCCAGAGACTGGAGGAAGGGATGGAAACAGTTCTAAGGCGGACAGATGTCCATGTAGCCCAGGTTGCCAGGCCCCAGGGAACCCCTGCAGATGTGGCCCCAGCTGTCCCTGCTCTGCTCATATCCTGGGACCCTTCCCATCCTCCATCACCCACCGCTGCTCCTGTTCTGTCCCCCAG
Seq C2 exon
GGCCCCCCGGGAGAGGTCATCCAGCCCCTGCCAATCCAGGCATCCAGGACGCGGCGGAACATCGACGCCAGCCAGCTGCTGGACGACGGGAATGGCGAGAACTACGTGGACTACGCGGACGGCATGGAAGAGATCTTCGGCTCTCTCAACTCTCTGAAGCTGGAGATTGAGCAGATGAAACGGCCCCTGGGCACGCAGCAGAACCCCGCCCGCACCTGCAAGGACCTGCAGCTCTGCCACCCCGACTTCCCAGATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000130635:ENST00000371817:61
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=0.747
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(27.0=100)
A:
NA
C2:
PF0139113=Collagen=PD(12.7=9.3),PF0141013=COLFI=PU(12.7=31.4)
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:
GGTCCAACTGGCCCGAAG
R:
CATCTGGGAAGTCGGGGTGG
Band lengths:
310-1440
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