HsaINT0039276 @ hg19
Intron Retention
Gene
ENSG00000130635 | COL5A1
Description
collagen, type V, alpha 1 [Source:HGNC Symbol;Acc:2209]
Coordinates
chr9:137710846-137712069:+
Coord C1 exon
chr9:137710846-137710899
Coord A exon
chr9:137710900-137711961
Coord C2 exon
chr9:137711962-137712069
Length
1062 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGA
5' ss Score
10.57
3' ss Seq
CTGTCTTCATTTTCCCACAGGGT
3' ss Score
11.78
Exon sequences
Seq C1 exon
GGTCCCCCAGGACTTCCCGGCCTCAAAGGAGATTCTGGTCCCAAAGGTGAAAAG
Seq A exon
GTAAGAGGGGCCTCCCTGCCCCAGCAACTGTGACTCGGGGCCTTCAAATTTGTGGCCGTGGGTCTCAAACTCAACAAGCTCTTGATCCGTCACCTAAATGTGTCAAGCACCTGCTGCAGGCTGGTGGTGGGGAACCTGAGGGGTGACAAAGGAAAATAGACACGCTGTGTTTGAGGCTTGGCCCCTGCCTCTGGGGGGTCCTGAGCAGCTCGGGAGATCCCGGAGGCCCCTGCGGTATTGACGGAGAACCTTCCAGCTAGGCACAGAGGCCCCGGCTGATGGGTGTCCAGGATCCCAGGTTGCTGCTCTCCCTGGGCTGAGCGGCCCCAGATCCTTTCCGCAGGAGGTGTGAGGACATTTCTGCAGTGGGAGCAAAGCCCTTTTATTTTTCTAACTGCTGGGAATTGTTTTCCACTTGCATTGATTTATTTACAAACATAAAAGGTACTCAGGAGTGAGATGGTTGTATATGAAGCAGAAGGCAGTGAGGGCCCTCTCATTTCCACTCTGACGTCCGCCACCACTGCCCCCAGCCCCAAGGCAAATGAGAGCTGGGGCTGCCTTGCGAGGCTTGCCCTGGGTTCCTAGAAGACAAACATAGACAGCGAGTGTCATGGATTCTTCTTTTTTTAGAAAAACAACCCATGATTGTAATATCTATAATACTCTGCATCTTTCTTTCCGTGTCAGTCCACAAACTTTGTTTTAGTTCCGTATAGGAGCAGGCGTTCGGATTTGCCATAGGAAATTGGAGAGCGTATACGAAGAGAAAGACAGAGATAAACATTACCACTCAGGAAAACCCCTTTATCACTTTGGTCTGTCTCAGTGTCTGTGGCTCCCTGTCTGTTTTTAGACGTGACTGTGGCCAGCGAAGGGCCACCTCGGACCTGCCGTTTCGTCACCTGGCCCCTCTGTTGAGCCTGTTCCCCTTCCAGGGGAGGCTGACCATGATGTAAAGCTTCCTGTGCCATGGCTGTGCTGCGTGCTAACTGGCCCACCGTGGCCGAGCATGAGGCGTGGCTCCCTCAAATGCCCCTTCCTGTCTTCATTTTCCCACAG
Seq C2 exon
GGTCATCCAGGCCTGATCGGGCTCATCGGTCCTCCGGGTGAACAGGGTGAGAAGGGCGACCGTGGTCTCCCTGGCCCCCAGGGCTCCTCCGGTCCTAAGGGAGAACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000130635-COL5A1:NM_000093:57
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=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PU(25.4=94.4)
A:
NA
C2:
PF0139113=Collagen=FE(52.2=100),PF0139113=Collagen=PU(7.9=13.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping 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
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)