HsaINT0039304 @ hg19
Intron Retention
Gene
ENSG00000204262 | COL5A2
Description
collagen, type V, alpha 2 [Source:HGNC Symbol;Acc:2210]
Coordinates
chr2:189929730-189931223:-
Coord C1 exon
chr2:189931116-189931223
Coord A exon
chr2:189929784-189931115
Coord C2 exon
chr2:189929730-189929783
Length
1332 bp
Sequences
Splice sites
5' ss Seq
AGGGTAAAT
5' ss Score
5.83
3' ss Seq
CACATTTTGGTCATTTGTAGGGT
3' ss Score
8.36
Exon sequences
Seq C1 exon
GGGCCACATGGTATTCAGGGTCCGATAGGCCCACCCGGTGAAGAAGGCAAAAGAGGTCCCAGAGGTGACCCAGGAACAGTTGGTCCTCCAGGGCCAGTGGGAGAAAGG
Seq A exon
GTAAATTTAAATAATACAACACATTCTTACAGTTGTGAGGGAATTATGTGTGTAAGTCTGAGAACAGTAAGGAAAACTAGAACAGTTAAGAGAAATGCTTGCAGGTTCCCTGCACAGTTCAGTACAGTTATGTGCAAATAGAAAGAGCCAACTGACTAATCATTATTCATACATTCAACTAATATTGGTTAAATCACTAGTCTATGCCAATTTGAGCCATCTGTGCTTGGAATTATATCAGTGAACAAGAAGGCTATGGTCCTAGTCCTCATGTGGAGACTAGTAAATAGTTGTTTATTTTAGTGGAGAGGTAAACAATAAACAAGTCAATGGGTAAATAAAAATATATGTACACACTTTAAAAAATGCCATACACACACTAAGTAAAGACATGACACATTGGAGAGTAACTACACATATATGTCAGTGTTGTAATGTTAGATTAGGTGGTTAGGAAAGAGGATCCTCTGAGAAGATAGCATTTTAGCTGAGACCTGAAGATGATGATAAGCCAGTAGAAAACTTGGAAGGAAGAACATTCTTAGCAGAGGAAAAAGCAAATGCAAAGCTGGGAGGGCAGAAAGGACCTGGTGATTTTAAAGACCAGAAGAGGTAGCTGTGACTGGAGCACAGTGAGACAGGTCTGAAAAGAAGAACAGTAATCTCACATTTATCTAGAGCTTTGGAGAATGCAAAGCGTTTCACAAAAATGTCACTAATGCATGTCATTGTTGACATTTTAATTGCTATAGATGGTACCTATGCCTCTCATCTCTAGATATCAGTTTTCTCTGTTTAATTTTACTATGAATCGTTAGAATATTTCCTTGCTTCCTTCCTTCCTTTCTTCCTTTTTTTTTTCTGACATAGTCTTGCTGTGTTGTCCAGGCTGGAGTGCAGTGGCACCATCTTGGCTCACTGCAACCTCTGCGTCCAAGGTTCAAGAAATTCTTGTGCCTCAGCCTTTTGAGTAGCTGGGATACAGGCACTTGCCACTATACCCAGCTAATTTTTGTATTTTTAGTAGAGACAGGTTTTCACCACGTTGGCCAGGCTGGTCTTGAACTCCTGACCTCAGGTGATCTGCCTGCCTTGGCCTCCCAAAGTGCAGAATATTTCTTGATTTGAGGAATTATTTGGCTCAGTACTTATATATTCTTCAAAATTTTAAAGTTTTTCCATCGAGTCAGATTTTTCTCATGCATATCTATAGCCATGTTGGCTTGATGATGGCTCCTAAAACTTTATAGTGCTAAAAATAAAAATCACCTATTCATTACATATTGCAAAAATATCAACAACAATTAAGAATCACATTTTGGTCATTTGTAG
Seq C2 exon
GGTGCTCCTGGCAATCGTGGTTTTCCAGGCTCTGATGGTTTACCTGGGCCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000204262-COL5A2:NM_000393:23
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=FE(41.2=100),PF0139113=Collagen=PU(5.3=13.9)
A:
NA
C2:
PF0139113=Collagen=FE(20.0=100),PF0139113=Collagen=FE(17.9=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)