HsaINT0039215 @ hg19
Intron Retention
Gene
ENSG00000197565 | COL4A6
Description
collagen, type IV, alpha 6 [Source:HGNC Symbol;Acc:2208]
Coordinates
chrX:107404849-107406268:-
Coord C1 exon
chrX:107406122-107406268
Coord A exon
chrX:107404966-107406121
Coord C2 exon
chrX:107404849-107404965
Length
1156 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGG
5' ss Score
9.16
3' ss Seq
TTGGGCTTTCTCTCCTGCAGGCT
3' ss Score
10.96
Exon sequences
Seq C1 exon
GCTCTTCTGGCCTCCAAGGTGATCCTGGACAAACACCAACTGCAGAAGCTGTCCAGGTTCCTCCTGGACCCTTGGGTCTACCAGGGATCGATGGCATCCCTGGCCTCACTGGGGACCCTGGGGCTCAAGGCCCTGTAGGCCTACAAG
Seq A exon
GTGAGGAGGGTGCCAGAAAAAGGAGATTTGTTGGGGAGTTGAGACAGTTTGGCTGAGAGGCTGGCTTGGATGTCCACCTCCAAGGGTGTGTCTTCATCAAGCGTTGCCTCTCTTCCTTCACAAAGCTCCCAAGCTTCCTGTTGGGGAGAAGAAGGGCCAGCAGGACCAGCAGGGTGGTTGTACTTGGTACTTGGCTTTAGAGGATGTGAGGGCAGAGCAAGGTTGCTACTCCAGACCACTCGCCCCTCTCTAATGTGCTGCAGAGAGATGGAGGGAGTGTGGTGGTGAATAAAGGGCCACACAAGACAATGAAAAAAGTCCAAGGCTGGGGGACAGAAAACCTGGCCTCTAATTGGAGTAAGTTAGAAGTCTCTCTGGGTCTCAGTGTCCTCATTTTCTTCCTCTTCTTCTTCCTCTTCTTCTTCTTCTTCTTCTTTTCTTCTTCGTCTTCCTCTTCCTCCTCCTCTTCTTCTTCCTCTTCTTCTTCTTCTTTTCTTCTTCCTCCTCCTCCTTCTTCTTCTTTTTATTTTTTTTTATTTTTGAGATGGAGTCTTGCTCTGTCACCGAGGCTGAGAGTGCATTGGTGCCATCTCACCTCACTGCAACCTCCACCTCTCGAATTCAAGTGATTCTCCCGCCTCAGCCTCCGGAGTAGCGGGGACTACAGGTGCATACCACCACACCCAGCTAATTTTTGTATTTTAAATAGAGACAAGGTTTCCCCATGTTGGCCAGGCTGGTCTCGAACTCCTGACTTAAGGTGATCTGCCTGCTTTGGCCTCCCAAAGTGCTGGGATTACAGGCATGAGCCACTGCGCCCAGCCTCGGTGTCCTCATTTCTGATATGGGATGCTCGCCGTTGCCCTGCATAATTTCCATTGTTGCTAGGAGGATGAGAAGAAGGGAGGAGGAAGTGGGCATGAAGGGGCTCAGAAAGGCTAAGTTGAGGGCACTGCCCCAGGGCAGAGATGCCCCCATGAACTAAGAACTAGCCCAGGCGGCTGCAGCCTTGATGTGCAGTGTGCACACCAAGTCGACAGCCAAGTGCATCGTCTCCTAGTGAGTCTTGGGCATGACACATAAGTCCCCTTTCCTGGGGAAGGTGCCTGGGGACCCTCTACATTGAGTACCCTCCTTTGGGCTTTCTCTCCTGCAG
Seq C2 exon
GCTCCAAAGGTTTACCTGGCATCCCCGGTAAAGATGGCCCCAGTGGGCTCCCAGGCCCACCTGGGGCTCTTGGTGATCCTGGTCTGCCTGGACTGCAAGGCCCTCCAGGATTTGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000197565-COL4A6:NM_033641:41
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(22.2=28.0),PF0139113=Collagen=PU(53.3=64.0),PF0139113=Collagen=PU(0.1=0.0)
A:
NA
C2:
PF0139113=Collagen=PD(45.0=67.5),PF0139113=Collagen=PU(62.9=97.5)
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:
TCTTCTGGCCTCCAAGGTGAT
R:
CTTCAAATCCTGGAGGGCCTT
Band lengths:
262-1418
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)