HsaINT0039221 @ hg19
Intron Retention
Gene
ENSG00000197565 | COL4A6
Description
collagen, type IV, alpha 6 [Source:HGNC Symbol;Acc:2208]
Coordinates
chrX:107453199-107454970:-
Coord C1 exon
chrX:107454902-107454970
Coord A exon
chrX:107453235-107454901
Coord C2 exon
chrX:107453199-107453234
Length
1667 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGA
5' ss Score
10.57
3' ss Seq
GTCCTGCCTTTGTTTCTCAGGGG
3' ss Score
9.59
Exon sequences
Seq C1 exon
GGGCTTCCTGGTCAGAAAGGATCAAAAGGTGACCCTGTCCTTGCTCCAGGTAGTTTCAAAGGAATGAAG
Seq A exon
GTAAGAACCTGTAAGTCAGATAGCTGAGTAGGCTATAAGCTGGGTTCCCCAGCATTGGGCCCCACCTCCAGTGAAAACATTTCCAGAACTAGCATCTGTGTCTCTATTTAAGGAGCAGACCAAGCTGGATTCAAAAGAATCTGGAGCTTTTTGTGGTGGAAACATTGACATAAATGTTTGCAACTATACTGTCAAAGAGATTTGCTCTGCAGGATCTAGACCAAAAATAGGAGACAGATCAGCAAACAAACAGTTTGCATGGGTATCATTTTCTTTCACAAACCAAGACATTTCCCGGAGGCAGATACCTTTTATCTACTCCAGAATCCTTGTTGTCTGTATTCCTTGGTTTGAAGCCATGTATGTCTCTGCCCATCTCAACATGGCCTTTAGCCAAAGATCCTGGTTCTGCCCTTCTCTGTCACTACACACCAACCCATCACCCTAGCTGGGCCCCTGGATGTCTGCAAAAATTGCCCATCAGCCCTGAGGCTGGCTGGAATCTTTCATCTCTTTCCAGAATTGACAAGAACCTTCTGTGTTCTTGTGACTGTGTTGCCTGATATCCTGCGGGGCCTAAGTAAACCCTGGCTCCAAATGATTGGCCCTATTCCCTTGCAGAGTGGGGCAGGAGTCCATCATTTCCCTGGTAGCAAATGAGAATGTATGTGCCCAACATCTGAGGAGAAGATGCACCAAGTTCACTCAGCTAATTGATGGCACTTTTCTGTCTTCCATTAGTGCATAGAGCCTGGAACATTGGAAATCACTTTGGAAGGCAGTGATGGGGGTGGGTGGCTGGAGAGCCGGACAAGATTTAGGGTATGGGCTTCTAACTATAGATGCCATAGTAGAAGATAGAATGTTTGAGTTGGAAAGGACCTCATGATTCTTGGACTCGTATTGCTCATTTTACAGATAGAAAAACTGAGGTGTACTGAGGCTATGTGACTTGCTCAAAGCCAGTTCACTAAAGAGCTAAAACTCAGGCAGTGCTCTTTCCATGCTACAGAGAGCTGATTTTTTACTGTAAGCCAAGTGGAGTAAGACTAGCAGGTGTCAAAATTTGGTCATTGTCTTAGAAAACATTGATTAAATGGCTTTGCCAAATATCAAAGAGACCCTGGATCCAGTGGAACACAACAATTTTCACAAGATGGTTATATTACTGATTCATGCAGTAACTAAACATGCAGCAAAGTAATTAAAACATAATCAGAGAGTGTATGCTCTGTTGATTTTCCCTTGAAATGACCGATTTGCATCGTATACATATGGGCACAGAATCTTTGGGGATGAAGGCACACAGGAAGGTAGCTTTGCTTTCCTCCAAAAGGAGTAGGAAAATCACTAGCCCACAGAAGTAGTTTCTAATTGATAAGTACCTAGCAAAGGTGAAAATTAATTAATCCAAGTAAAATGTGAAATCCTGTTCAGCCAAGGCTATAATATGTGTCTTCTACAGTCCAGATTTTTCTTACAGAAAAAATAAACAATCTAAACAGTCGAATATGTCCAATTCATACATTATTTAAAACACAAGACTTTGACAGAGGAGGCCCAAGGTTCAGAGATGTGTTTTTGTCCCTATAAATGTTAGGTTAGTTATCTGAAATATTGCAGGCTTAATTTATTAAACTCTTCAGTGTCCTGCCTTTGTTTCTCAG
Seq C2 exon
GGGGATCCTGGGCTGCCTGGACTGGATGGAATCACT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000197565-COL4A6:NM_033641:7
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.899 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(19.7=52.2),PF0139113=Collagen=PU(11.9=30.4)
A:
NA
C2:
PF0139113=Collagen=FE(18.6=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
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)