HsaINT0039199 @ hg19
Intron Retention
Gene
ENSG00000197565 | COL4A6
Description
collagen, type IV, alpha 6 [Source:HGNC Symbol;Acc:2208]
Coordinates
chrX:107420071-107422075:-
Coord C1 exon
chrX:107421914-107422075
Coord A exon
chrX:107420242-107421913
Coord C2 exon
chrX:107420071-107420241
Length
1672 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGT
5' ss Score
10.28
3' ss Seq
TCTCTCCTGTGCTTATTCAGGAC
3' ss Score
10.7
Exon sequences
Seq C1 exon
GTGTGCACGGGAAGCCTGGCTTACTAGGCCCCAAAGGTGAGCGGGGCAGCCCTGGGACACCAGGACAGGTGGGACAGCCAGGCACCCCAGGATCTAGTGGTCCATATGGCATCAAGGGCAAATCTGGGCTCCCAGGAGCACCAGGCTTCCCAGGCATCTCAG
Seq A exon
GTAGGTCCTTCAGAGGAAGAGTCCCACCTTGACAGACTTCAGCTAGGCCCTGGGCCCAGATGCCCTGGGGGGGCAATAGCAGTAGTGGGACATGGTCAGAATTTAGAATGAGACTTGACTTTCCTAAGCTCTCAAGTTTCAAATCTCAAGTCACCCTTGCAGTACCAAGCAGAACAGATTGCTGCAGGTTAGCTTCCAAACTGTTGCCACAAATCTTTCCCCTCCCCCCGCCTCCTCCATGGCCTCATGCCCAGTTTTCAGGTTTCAACTCTCCCGACCTCCCCAGTTAGAGAAGCCACCCTCATCGTTGAGGGAGTCTAGTCCATCTCCATGCCTTCACTGGTGCTGTGGGCAGCCTGCTTTTGGTTGGGGAGAAGCTTGAGCAGAGTGTGACCACACCGGCAGCCTGCCTCTCAGGCGAGCATGCCTCCAAGGACCCATGGCCAAGTGTCTTTTACTCAGCAGTGGGGCCTGACACTTGCTGCTTCCAGACTCGTGTTTGCAGCTTTGCCTTTTTCTCGCACCACCCTCCTCAACCTGCTTCGGTGACTGCACCATTCCCAACCGCCCCTTACTCCTGGCCTAGTGACTGAAGCTGAGTTATTTGCAGAGCCATTAATGTCCTTTTTATTCCCTTTGTCTCTCTGTGTTTCTGAGATCTTCACATAGGCTGCCTCAGTGAGAAAACACAGCACACAAGCTCACAGACTAACACCCCCAATGGCTCTGCCACTCAGGAATGTATCTGATTATACACTATAACATGGCCTTGCTTACAAGGCCAGGGATCCCTGAGCTCCTGCTGTGGGGTTGGCTCCCATTGAATTTTTCCCTTGTTGTGGAGTTCCCTTCACAGCCTCCCATTTGAATCCTGGGGCTTGCAGCTACTTGATGCTTTTCAATCCATAGAAAGCCAAGTCAGCCATTCATTTGGGTCCTTGGGGACCCAAATACCTCTGTCGTCATGATTTAATCCTTTCGTTTTTTAATTTCCTTGCTTTGTACCTGAACATTCCACTTTGGCAGCAGCTCAGGAGGTTAATCCCATTGACCAACTTTAAAGCGTGGTGAAAGACGTCTCAGAATACCTAGGAGACCAAATGGGCCTTGTGGGTTTCTACAGTACTTGGCACTAGGGGGTCTTTCAACCTTAATGCCAAGGAACTGGCTGACTTAACTGATTGCTTGAGGGATTAAAAGGGCAGCCCTGTATCCAAGGCTCCCTGGGAGGCTGAAACAACAGCTCAGCTTTAACCTCTACTTCACCGATTGGCTCAGGAAACAGCCATTGTGGCGTGATTCAGACTGGAAGTACCAGGAAACTGGAGCCTACTTGCCACCCTGGCTTCCTAGAGCTCCATTCAGGGGCTAAAGTGTAAACCACATTCACAAAGAGACAAAAAGTTATAATCAGAAGGGGTTTGCTCTCCCTGCCAGCTAATGTGCCATGCTGGAAGTAATAACCATTGGCGTGGCACTCTGGGTAGTAGATGCTAACGCTTCAGCCAACTAAGAACTCTGCCTGTTAGCAGTTTGCATGTGCTATTGTTAAAGGGCCATTTACAAAACCTAACAAGCCAAACCAATCAGAAGCTATGATATAGGCAGTGGCCCAGATCTGGCCAGAGCCTCACTTGACAGCTGTCCTGTGTTCTCTCCTGTGCTTATTCAG
Seq C2 exon
GACATCCTGGAAAGAAAGGAACAAGAGGCAAGAAAGGTCCTCCTGGATCAATTGTAAAGAAAGGGCTGCCAGGGCTAAAAGGCCTTCCTGGAAATCCAGGCCTAGTAGGACTGAAAGGAAGCCCAGGCTCTCCAGGGGTCGCTGGGTTGCCAGCCCTCTCTGGACCCAAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000197565-COL4A6:NM_033641:27
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=PD(46.8=52.7),PF0139113=Collagen=PU(57.0=81.8)
A:
NA
C2:
PF0139113=Collagen=PD(41.8=56.9),PF0139113=Collagen=PU(60.3=65.5),PF0139113=Collagen=PU(4.4=5.2)
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:
GTGTGCACGGGAAGCCTG
R:
CTTGGGTCCAGAGAGGGCTG
Band lengths:
332-2004
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)