HsaINT0039317 @ hg19
Intron Retention
Gene
ENSG00000204262 | COL5A2
Description
collagen, type V, alpha 2 [Source:HGNC Symbol;Acc:2210]
Coordinates
chr2:189918885-189921752:-
Coord C1 exon
chr2:189921699-189921752
Coord A exon
chr2:189918939-189921698
Coord C2 exon
chr2:189918885-189918938
Length
2760 bp
Sequences
Splice sites
5' ss Seq
AGAGTAAGT
5' ss Score
9.35
3' ss Seq
TATGTTCTGTTAATTGACAGGGT
3' ss Score
7.18
Exon sequences
Seq C1 exon
GGTGGCATAGGAGAAAAAGGTGCTGAAGGCACAGCTGGAAATGATGGTGCAAGA
Seq A exon
GTAAGTGAAAGTATTCCTTTTCTAGCTGGGCTAGGAACCAACATTACAGTATCATATGAGTTTCCCTGAACCTTCCAAAATAAAGTCAGTCATGTTTCCTTGGTAGTCAGGAGTTGGAGAATAATGGCATGTGAGATCTGCTGTGATTCAACCACGGTTTATTCATTTTGCTTACCCTGAATTAAATGAAACTTAAATAAAAACATATTTATTGTGCCTATGAGATAAGTGCCTTAAGGGGATGGGGGCCCTCTTTATCTTTCTCTATCATCTTTTTATTTCATACACAAGGTTTATTTCTGTTAAAATGCTAATCTAGTGAGCTGGCCAATACTTCATTCCAGCATAGACAAGTAGAGCTTTGTGGAGTCACCAAAGTTGTGATAAATGTTTCTCAGTATATTGGATGTTGGGGTGAGAAATTTACTGCACAGTGAATCGTCATTAATGTTATCATTAATAAACAGTTTGAACAAGCAGAATGTCCAGAAGGATGGTCAACTGCAAAGCATTGTTTAATGTCATGTCAGAAATTGACATTTAACAAGCGTTAGGTCTTTGAAATTAGAATGCATTTACAATTCCAAGGACAATCAGACTCGAAGGACAATATATTTTCAGACATAAATGATTTCCTCATGTAAGAGTGGCTAGTCACAATGGCTTAAACATCCATCATTTTCTGGAATAGTACCTGATATTTGACTAATGATTTCTGTTTCAGTATGACATGGTTTGCTGTTAGTTGTCATGTGTGCCCTGGCAATTACAGTTGTAACATAATAAAAGAGAACTGCTATTTGGTTCTGCACATTGAGTCATTGTTAATACATTGGTTATAATAGCTTTAGATTAAGGAAATATAGTGAAATGTAGTAGAAAATTTTCATCTTAAGGGTAATTAGTCCTTTTTATGCAAATTTAATTAAGGATGCACCACTTCTTTTAACAAATTATGCACAAAAGATACACCTTGCCTTTTAGTTAAATCTAATATTTAATTTAATATTTCAAAAATAGTCAAGTAAATCTGGCATATTTTTAATATTTTACATCATGGATGTCCTGGAATGCATAAGTAGTGCAGTACTATTTATAGGAACGATGCATTGGCAGTTTGTTTTAAGGGAAAATCTAAAATACATATCAATTGTGCCTATGAACTAACTTTGAAATTGCAATGTGATAGGACCAGGATGTAAGCAATGACTGCTTTATTTTTAATGAGGACACTACATTGTTGCAGGAAAGAAGCAGAGCAAAGCACTTACTGCAATCTCATAGTAGGGAAAAAATGAATAACATGTTTTCTCTGTATAAAAAATCTATAAACATAAGTAATGAAGTGATATTTATATTTCATCAAATCCTTTAAAGAAGTATATTACATAAATTATTGGAATGATATCATTCCATTGTAGATCCAGAGACTATAAGAACACAGATTTCTTATGTTCTTGTCAAATCTATAAAATTAAAGTCATTTTTGTTCCTTAAGTTTCTTTAGTTGTACATACAGAAATTAAACGATGAAAGAATATTTGGGCTGCATATGAAGAGGCAAGACACAGTTATAAGATAGAGAACTTGTTTTAAAGAGGACTTCAATATTCCCACAGTTTCAAGTTTGTGATTACCTGTCAAGAAGACTCAGGTTGTGTCCCCATGTGTTAGCTGTACTGTCCTCTAAGTGTTAGCTCTCCTATGCCCATAAATCTCAAAGTAGCTGGGGTTTTAGGCTGTAAACTTTAGCTACTTTTCCTTTTCATCTCAAAAGAATGAAGAAAACTGGCTGGGCGCGATGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGTGGGCGGATCATGAGGGCAGGAGATCAAGACCACCCTGGCTATGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGTGTGGTGGTGACAGACGCTTGCAATCCCAGCTACTTGGGAGGCTGAGGTAGGAGAATGGCGCAAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATGGTGCCACTGCACTCCAGCCTAGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAATGAAGAAAACTAAGTCAGGCATAGTGGCTTGTGCCTGTAGTCTCAGTTACTCTGGAGTCTGAGATGGGAGGATCACGTGATCCAGGGCAAGCGTTCAAAGATGCATGTGCTGTGATCACATCTGTGAATGGCTACTGCACTCCATTCTGGGCAATGTAGAGTGGAGACCCTGTGCCAAAAAAAAAAAAAAAAAAAAAGGAAAAAACACCTAAAATGCCTTAACACAATTTCAATTTTTAAAAGTAAAAAAGTGATATTTTGCTATTATAATTTAAGAATATAATATTATATGCAAAAGAAGGAAAGCCTCTTTTCAATTTGTGGTCAAATGTCCGAATAAATATTAGCAAAGCTAATTATGCTAAGAAATAGAAACATTTTTGTAGCTTAGCATTAATGTAGTGCTAATGCCTGAAAACAGTTTTATGTATGCATGAATTAGGTTGCATGAAAGAGATTAAAACACTGTGTGGAGAAAATATGGTGGAAATGGTATTAAACTAGACAGAAAACTCTTGAAAATATATAGATTATATCATTTATTATAGATAATGATTTGCAAAGGCAGCCAAATTATAACAAAATAGTCGTTTCTTTTTTGTTTGTTGATTTGCTAAGCATGAAGATTTCTGTGCATTTTTTACCTCAATATGCCTATGTTCTGTTAATTGACAG
Seq C2 exon
GGTCTTCCAGGTCCTTTGGGCCCTCCAGGTCCGGCAGGTCCTACTGGAGAAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000204262-COL5A2:NM_000393:35
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(9.5=44.4)
A:
NA
C2:
PF0139113=Collagen=FE(20.2=100)
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)