HsaINT0039217 @ hg19
Intron Retention
Gene
ENSG00000197565 | COL4A6
Description
collagen, type IV, alpha 6 [Source:HGNC Symbol;Acc:2208]
Coordinates
chrX:107402692-107403884:-
Coord C1 exon
chrX:107403693-107403884
Coord A exon
chrX:107402979-107403692
Coord C2 exon
chrX:107402692-107402978
Length
714 bp
Sequences
Splice sites
5' ss Seq
TGGGTAGGT
5' ss Score
6.86
3' ss Seq
CCCACTTTCTCTCCTTCCAGGCT
3' ss Score
11.9
Exon sequences
Seq C1 exon
GAGCTCCAGGGCAGCAAGGCCCCTTCGGGATGCCTGGAATGCCTGGCCAGAGCATGAGAGTGGGCTACACGTTGGTAAAGCACAGCCAGTCGGAACAGGTGCCCCCGTGTCCCATCGGGATGAGCCAGCTGTGGGTGGGGTACAGCTTACTGTTTGTGGAGGGGCAAGAGAAAGCCCACAACCAGGACCTGG
Seq A exon
GTAGGTACCAGCTCTGACAGCCAGCCCTGGTCACCTGTCCCCACAAACACCAACAGCCAACCCCTCTCTTCTCCCAGCCCTTTCTAGGTCCACTGTTGTGTAGTGAGTTACAAGCATCAGCTCTGGAGTCAGGTGGATCTGGATTCAAATCCTGGCTCTATCACTTACTAGCTGTGTACACTGCATTAGTTATTCAACCTCTCTAGGCTTTGGCTTCCTCCTTAATGGAACAAAGCTAATTCTAGTATCTATCACACACGCTGGTGGAAAGATTGCATGAATCAATCACCCAATGTAAATTGCTTAGAGCAACATTTGGCATTTAAGCATCCATTAAATGTTAGCAATTAGTAGTAGTAATAATAATAATATGACCTGCAGGGCAATGATGATTACCTGAGAATTAATTGTTGTCTGCAGGTGTGCTAAATCTTAAAAGCAGACTCAGTCTATTAAACGCTGTTTCTTTCAAAGCAGATTAATTAGGGCAGAATTATACAGCTTATAAAAAGATTCTTGTTATTATCAAATTTCCCTGGTGCATTTAAAATAGAATTTGCTCAACACACTTCAGCACATGTACAATGTTACAGGATTGGAAGGAGAGGGCTGCCTCAGTCTGGTGCAAGTGGTTGGATGTAAACCCAAACCACCATCTCGTCAAAGCCCCTCAGCCAGACCTCCCCTGCCCTTGCCCACTTTCTCTCCTTCCAG
Seq C2 exon
GCTTTGCTGGCTCCTGTCTGCCCCGCTTCAGCACCATGCCCTTCATCTACTGCAACATCAACGAGGTGTGCCACTATGCCAGGCGCAATGATAAATCTTACTGGCTCTCCACTACCGCCCCTATCCCCATGATGCCCGTCAGCCAGACCCAGATTCCCCAGTACATCAGCCGCTGCTCTGTGTGTGAGGCACCCTCGCAAGCCATTGCTGTGCACAGCCAGGACATCACCATCCCGCAGTGCCCCCTGGGCTGGCGCAGCCTCTGGATTGGGTACTCTTTCCTCATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000197565-COL4A6:NM_033641:43
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.338 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(35.5=33.8),PF0141314=C4=PU(39.8=66.2)
A:
NA
C2:
PF0141314=C4=PD(59.3=66.7),PF0141314=C4=PU(25.9=31.2)
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TAAAGCACAGCCAGTCGGAAC
R:
GATGGTGATGTCCTGGCTGTG
Band lengths:
350-1064
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)