HsaINT0039145 @ hg19
Intron Retention
Gene
ENSG00000188153 | COL4A5
Description
collagen, type IV, alpha 5 [Source:HGNC Symbol;Acc:2207]
Coordinates
chrX:107840607-107842100:+
Coord C1 exon
chrX:107840607-107840798
Coord A exon
chrX:107840799-107841931
Coord C2 exon
chrX:107841932-107842100
Length
1133 bp
Sequences
Splice sites
5' ss Seq
CCTGTGAGT
5' ss Score
7.21
3' ss Seq
TTAAACTTTTCCCTTTTTAGGGT
3' ss Score
12.87
Exon sequences
Seq C1 exon
GGCATTCCAGGAGCTCCAGGTGCTCCAGGCTTTCCTGGATCTAAAGGTGAACCTGGTGATATCCTCACTTTTCCAGGAATGAAGGGTGACAAAGGAGAGTTGGGTTCCCCTGGAGCTCCAGGGCTTCCTGGTTTACCTGGCACTCCTGGACAGGATGGATTGCCAGGGCTTCCTGGCCCGAAAGGAGAGCCT
Seq A exon
GTGAGTTGGTTTGATATTTTTGGTTTTGTGATGTTAAATTTTCACTTAGAAATGTTTTCTAAGTTAATTCAAAGGATGGGACTGATGCTGAGATAAACACCCAATCAATGCTTAAAACAATGTGACCATACAGTAATGGCACATTGTTACTGACTACGTAGGGTTTCTGCACTACTCTTTTCTTTCACTTGTTTTGTAAACTTATTTTTCTTAACCCATTAATATTGAATACTATTTTCTATGAATAGGTGGGCAGGAGGTTAAGATGTTTATGAGACAGTATAAGGTTCCCCATCTCTTAACCCCCACATATCTTTCCTTGGGTTTACTTAAACCTCATGACTGGGCATGGTGGCTCACACCTGTAATCCCAGCACTTTGCGAGGCTGAGGTGGGCGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACATGGTGAAACCCTGTCTCTACTAAAAACACAAAAATTAGCCGGGCATGGTGGTGGGCGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCACTTGAACCCGGGAGGCGGAGGTTGCAGTGAGCCGAGATTGCACCACTGCACTCCACCCTGGGCAACAAGAGCAAAACTCCATCACAATAAATTAAATAAATAAATAAATAAATAAACCTCATAACCAGCAGTTTAACTTGTTTCTATATATATAGTAAGCTTAGAGAATAGTACAAGTAGATAGCCATGTTCAATGTGCCACAGAACTGAAAGATTTAACATAAATGAACAATCTTATTTTGTACATAACACACAGCCCAGGATATTTAGGTAGGAAGTGATATTTTATAATGTTATCTAGACTATAACCTTTCTGACTTACACTAAAATGTAAGCTGCATAAAGTCAGAGATTTTTGTGTATTTTTGTTTTCTGTTGTATCACCAGCACTTGACACATAGTAGGAGCCCAAAAATATTTGTTGGAGGAATGAGTAAGTGGAATGATCACACATACCATCTCATAATACCACTCACTTATATAGCTTTTAAGAAGAACTATTTATGGCTATATCCTTTCCCCAGTTGTATTCAGTACCAACCTACAGATAGTTGTTGTATCTATATGTTTCTGTATTAAACTTTTCCCTTTTTAG
Seq C2 exon
GGTGGAATTACTTTTAAGGGTGAAAGAGGTCCCCCTGGGAACCCAGGTTTACCAGGCCTCCCAGGGAATATAGGGCCTATGGGTCCCCCTGGTTTCGGCCCTCCAGGCCCAGTAGGTGAAAAAGGCATACAAGGTGTGGCAGGAAATCCAGGCCAGCCAGGAATACCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000188153-COL4A5:NM_000495:24
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.960 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(33.3=31.2),PF0139113=Collagen=PU(83.7=64.1)
A:
NA
C2:
PF0139113=Collagen=PD(12.2=10.5),PF0139113=Collagen=PU(83.9=91.2),PF0139113=Collagen=PU(1.7=1.8)
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:
GCATTCCAGGAGCTCCAGGT
R:
CTGGATTTCCTGCCACACCTT
Band lengths:
342-1475
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)