HsaINT0039254 @ hg19
Intron Retention
Gene
ENSG00000130635 | COL5A1
Description
collagen, type V, alpha 1 [Source:HGNC Symbol;Acc:2209]
Coordinates
chr9:137690254-137693853:+
Coord C1 exon
chr9:137690254-137690307
Coord A exon
chr9:137690308-137693799
Coord C2 exon
chr9:137693800-137693853
Length
3492 bp
Sequences
Splice sites
5' ss Seq
ACTGTGAGT
5' ss Score
7.94
3' ss Seq
CAGTGACTCTCTCTTCACAGGGT
3' ss Score
8.69
Exon sequences
Seq C1 exon
GGCCCTCCAGGCAAGGATGGACTCCCAGGACACCCTGGACAGAGAGGCGAGACT
Seq A exon
GTGAGTATCGAGGGTGCTGGGGGACGTGGCTGGCTGGCTCTCTGACCACCCTGCACGTGGGCACAGCCCTCGCTGCCCAGCGCCATCTAGGACCCTCCTGGCCTGGGAGAGACAGGTTGGCCTCAGAAAGGCTCCCAAGGGCCGGGCCGGCTTCCGCTGACTCAGAGCCAGGCTGTGAGGCAGGGCCAGGGCAGAGCAGTCATGCAGGCCGGCAGCGCCTTATGGCATCTGTGGGCAGAAGGCAGGTGTTGGCTTTGGGCTGGTTTTGGAAACTTTGGTGAGAGGCCACATTTAAAGACACACACAGATTATCCTGGGCCGACTGAAGCCTCATGCATCCAGCCTTATTTTCCCTCTAGAATAATGCTGAGTGCTACCCCGCTTGAGGGATACGTCTTTTAATTGAGAAAGTGCTGGGAAAGGGTCTACATGTTACTCAGCGTCATTCAGTCATTCGATGCTGCAATACTTCAAGAGGGCGGCTGTGGGCCATGCACCAACCCCACCCACGTTCACCCGGGCCCTTCCAGCTCCAATCCAGGGGGTCTGGAGGATGCCTGCAATGTCCCTTTTTACACTAAAGAAAACAAGCGCCAGTCAGGTGGAAGTGGCCTCTAACTAGTCACTCCGCTGGGCACATGGTCTTTGTAGTCAGAGACTCCCCTTTGACCTTGCCCTTCACTTTAGAAATGCATATCACAGGCTACTTCATCCAGACCAGAAAGGACTCCAGTGTTTTCAGTTGGGAGAAAAAGCCCTCATCAGAAATGGGATCATTTTCCTGGCCCCATCAGCCCTTCGAAATTTGGCCCAGCTCCCTAAAGGTGTGTTTCAGGAAAGGGTGCAGGCACGCCTGTAACCTGGCCCACACCTACAAGCTTGGGGCTCCAGGCTCTGAATATCTGGGGACGTGCAGTGTCGGGTGACTTCCTCGTCACCACGCTGTGTTCCTTCTCCGAGTGCCCACCTACTCTGTCCAGCTTAAAGGATGAATTGCACAGATGCAAACATTTCCCACAGAGGAGAGTGAGGGGCATGCCAGGATCACTGCAAGGGTCCCTGCAGCCAGGTTTCTAGGGATCAAGGTCTCTACAGGACTCTCCCAGCAAAAGCAGGTCCCCTCGTGGAATGGGTCTCTGAGTGCCCTGTTGAATATATTCTCCATGCCTGCTTTGAAAAAATCCCCTTTGTCTCTCTTTGGTTCATCGTGATGAAACCTCTTTTAATTATACCTTCACTGGTGTTCTGCACGGCGCATGCTGCCTGATAAATGGAGATTGCTTTGCTCTTTTGTTTATAGAGAAAAATTAAAACATTTCTTCTGAGCTTTGCATATTTTTCTCTAATGCCTTTTCAAGGAGACAAGATAGAAGGTTTTACATATTATGTGCTTTTCTCCCTCTGACTTATTCTGGACGGAGGCTGGTGAAAGAATTAAGCTGCTTGTCTCTGCTCAGAAAGTTGCACATGTACTTCCGGCTGCCTTCTGCCACCCCGGCCACCTCTCTAGACACATGGCGCTGGAGTGATGCCTGTGTCTCTGAGAGCCACTTGGGACATAGCATCTCCTCCATGGGCTAGTCCAGACAAGCCTTCCAGAAAGAGCTTCTCTGCAGTGTTGATTTCCTTCTTTTTTAAAAATATGAAACACCAACGGTCATTATTTCTCCTAAATGTGAGCCAGAAACTTATTTCTCAGCAAAGGGCTAAGGTCATATTCTGTCCTCAACAGCCAGGGTGGCCGAGGGCCCTGGGGAGGCCTTTTTTGTTTCGTGTTAACTTTGACATTAGCAAAACTTAACCAAGGCTCCGATCTCCCTTCAGGCTCTTGAGCTCTTCTCCCCGGGTCCACTGAGCAGGGCATGCCCTTGACACCCATCCACCGTTCCTTACTTCTGACCCCATAAGTGCAATGAACATTAGAAACGATCATTCTAGCCCACAGCTGAGCTGGGCTTAAAGAGGCGAGCCCTCCTAGAGTTTGCAAAGAAGCTAAGTCTGGGCTGGGCACAGTGGCTCACGCCTGCAATCCCAACACTTTGGGAGGCCGAGATGGGCGGATCACCTGAGGTCGGGAGTTTGAGACCAGCCCGGCCAACATGGTGAAACCCCGTCTCTACTAAAAATACAAAAATTAGCCAGGCATGGTGGCAGGCACCTGTAATCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATCGCTTGAATCCGGGAGGTGGAGGCTGCCGTGAGCCGAGATCGTGCCATTGCACTCCAGCCTGGGCAACAGGAGTGAAACTCTGTCTCAAACAAAAAAAAAAAAAAAAAAAAAAAAGAAGCTAGTCTGCTGTGGGTTCATGTGGCCCCGTGGCTTGGTGTGAGGTTTTGCCTCTGACTGCTGGACAGTGAGTCAGTGAGCCCAGGCCTGAGGCCGCTCACCCTCCAGCCCTAGCTTGGCCTCAGGGCCAGCCACCTTCTCCTCCAGCGTCTAGAGTTTGCCTCGAGGCCTCCGGGTAGAAGGTGTGCATGTCTCCACCAGTGTCATGTGGCACCTGCAGATGGCTTCTCGCTGGCACCTGTCATGCTCTGCAGACGTGCCTGGAAAAGAAGCTTATGTTGCCTTAAGGTCATCTTTCTCCTTTGAGGGAGAGTACAGAAGTCGTGGCGACACCCACAGCCAAGCCAGGATCGTTATCTACGCGTGAGCATGCAGAGCGGGCGTGAGATATTCCCGCTGAATCAAGCTAAAAATAACGCATCCAAGCTGCCGAGTTATGAAAGCAGCTGGCCCTCGCTCTTGCCTGTTTTAAATACATGCTGAGGAGCACGCGGGCAGAGTCACCCGTCGTGCATCAGAGGCGTTCACGCCAAAGCAGGTCAGTCGTCACAGAGCCACTGCTGAGAAACAGCCAGAGGTAGTCGCGGGTCCAGAAAGGGCACCAAGCCAACTCAGAAAAGGAGCGTTTGGTGACATGATAAAGGCGAATCGCGTCGGCCTAAAGATGCAGAGGCAGGAGAGCAGCCAGTGAGATGAGCTTGTGTGGCTTCGTTACCCTCGTGAAATTAGTGCAAACGCACGGTGGCTCACGCCTGTAATCCCCGCACTTTGGGAGGCTGAGGCAGGTGGATCACGAGGTCAGGAGTTCGAGGCCAGCCTGACCAACATGGTGAAATCCTGTCTCTACTAAAAATACAAAAATTTGCCAGGTGTGATGGTGTGTGCCTGTAATCCCAGCTACCCAGGAGGGTGAGGCAGGAGAATCACTTGAACCTGGGAGGCAGAGGTTGCAGTGACCCAAGATCGAGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCTCCATCTGAAAAAAAAAAAAATGAAACAAGAGACATGGGCCTCTTACACAAAGTCTGGAACATCTACTCTGGGGGGAAGGGAGGTGGGGGGCAAGCGTCCTGCTGAGAACAGTGCAGGGCAGGGTGGCGCAGGCCACTGCAGCACCGTCAGTGCAGTGACTCTCTCTTCACAG
Seq C2 exon
GGTTTCCAAGGCAAGACCGGCCCTCCAGGCCCCCCCGGCGTGGTCGGCCCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000130635-COL5A1:NM_000093:37
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:
NO
A:
NA
C2:
NO
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
- Genotype-Tissue Expression Project (GTEx)
- 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)