HsaINT0039216 @ hg19
Intron Retention
Gene
ENSG00000197565 | COL4A6
Description
collagen, type IV, alpha 6 [Source:HGNC Symbol;Acc:2208]
Coordinates
chrX:107403693-107404965:-
Coord C1 exon
chrX:107404849-107404965
Coord A exon
chrX:107403885-107404848
Coord C2 exon
chrX:107403693-107403884
Length
964 bp
Sequences
Splice sites
5' ss Seq
AAGGTCTGA
5' ss Score
4.3
3' ss Seq
TTATGATCTGTCTCTCTCAGGAG
3' ss Score
9.06
Exon sequences
Seq C1 exon
GCTCCAAAGGTTTACCTGGCATCCCCGGTAAAGATGGCCCCAGTGGGCTCCCAGGCCCACCTGGGGCTCTTGGTGATCCTGGTCTGCCTGGACTGCAAGGCCCTCCAGGATTTGAAG
Seq A exon
GTCTGATGATGCCACATTAGGAGGCGGGCGGGGCGGGGATGGTGGTCTGGGAGGGTTTGAGGCTGGGGGTGAGTAAAACTTCAAGTCTGAAACTTAATAAACCCAGTGGTAGAGCTTGACACTCCTAAGATGCTCAAAAACTGGGCTCTAAGTCCATTCACTCCCCACTACCCTCTGAGCCTGTGAAGGGATACCCTACGTTCTGGAAGGCAAAGGACTGTTCCAAATCCAAATCCTTTTCTGGGCTCTCTTCCAGTGCTTAAAAGGTCTGACTTTATACTACAGATGGCCCCCTGCCCTTTACCTCCCCTTTTCTACCCAGGGATTCTGACACACATGAGAGGGGGATGTTCAAGGGATAACAACACTTGAGTTAAGGCGTGGCTGTCCATATACCTCTTCTATTTGTGTCCCACTTTATATTGGGGATGACAAATTAGTTGTCCTGAGTAGAGAACAGTTCAGAGGCTCGGTGGGAAACTGTGGCAGTTGATTTGTCATGTCTGTCATGGGCAGGAGAGGAGGGCAAGATTTTACCCTGCTAATCCTAACCCTGCTTTCGATGACTCTGATTCAGCAGCTACATAGTTATCTCCTATGAGGGCCTGCAAGGCTGGACCTGAGAAGTATCCCTCTCCACACCCTAATCCCCACTCAGAGAGACCCCAAGGCCAGGTGGCTATGGGAAGGAAGCCTAACAATGTACTTTGAAAAATGGGGCGTCTGTAGCTGGATACATCTGAGATAGAGTTGTAGCTCTACCACTTACTAGCTGTAGGACATCTGAGCCTCAATTTCTTCATCTAAAAATTGGGGTGGTAATACCATTTTCCAGGGTCATCGTGAGGATTGAGTGAGATAATACATGTGTATAACATGCCTTGGACAATGTGTGGTACAATGTGAGTAGCTGATGTTGTCATTAGCTGCACCACACTCACCTTTTATGATCTGTCTCTCTCAG
Seq C2 exon
GAGCTCCAGGGCAGCAAGGCCCCTTCGGGATGCCTGGAATGCCTGGCCAGAGCATGAGAGTGGGCTACACGTTGGTAAAGCACAGCCAGTCGGAACAGGTGCCCCCGTGTCCCATCGGGATGAGCCAGCTGTGGGTGGGGTACAGCTTACTGTTTGTGGAGGGGCAAGAGAAAGCCCACAACCAGGACCTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000197565-COL4A6:NM_033641:42
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=0.338
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(45.0=67.5),PF0139113=Collagen=PU(62.9=97.5)
A:
NA
C2:
PF0139113=Collagen=PD(35.5=33.8),PF0141314=C4=PU(39.8=66.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGGTTTACCTGGCATCCCCG
R:
CCAGGTCCTGGTTGTGGGC
Band lengths:
302-1266
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)