HsaINT0039281 @ hg19
Intron Retention
Gene
ENSG00000130635 | COL5A1
Description
collagen, type V, alpha 1 [Source:HGNC Symbol;Acc:2209]
Coordinates
chr9:137715262-137716701:+
Coord C1 exon
chr9:137715262-137715315
Coord A exon
chr9:137715316-137716445
Coord C2 exon
chr9:137716446-137716701
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-COL5A1:NM_000093:61
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=0.553
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
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)