HsaINT0039164 @ hg19
Intron Retention
Gene
ENSG00000188153 | COL4A5
Description
collagen, type IV, alpha 5 [Source:HGNC Symbol;Acc:2207]
Coordinates
chrX:107920730-107923981:+
Coord C1 exon
chrX:107920730-107920863
Coord A exon
chrX:107920864-107923908
Coord C2 exon
chrX:107923909-107923981
Length
3045 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGA
5' ss Score
9.79
3' ss Seq
TAATGATTTTATTTATTCAGGGT
3' ss Score
6.53
Exon sequences
Seq C1 exon
GTCTACCAGGTCCAGAAGGTCCTCCAGGTCTCCCTGGAAATGGAGGTATTAAAGGAGAGAAGGGAAATCCAGGCCAACCTGGGCTACCTGGCTTGCCTGGTTTGAAAGGAGATCAAGGACCACCAGGACTCCAG
Seq A exon
GTAGGAAATGGAAGTAGATATCTGATGAGAGAAGAATGTGGGTGTTTGTATTCAAAATGTGAATTCTAAGCTGCATCATTTTAATTAACACTCACTAGACAAGGTTCTATGTGTGGCTCACTGGCGAATTAAAAAGACAGTAGAAGGCAAGTTTCCTATAGTCTCCTAAAGGGACTTTGTTGTATTATAGTCAGAGTTCCTGAAAAGATACTTCACCTGGAGTCTTTGGTATGCATATTTGGATTTGAGTAGCCTTCATTTCAGTGAAAGCAAATTTATGCAAAGGAGACATGCATATTAGAGCATTGCATATAGATGAATCCACCCATAGAGAAGTAATTATGGTGAATAGAGGCATCTTTTAGGCTTTGAAATTAGATAAAGTTAGGGTCAAATGTCAGCTCCCCTGCACACTTCTGCTTTGTATCTATGAGGAAAACAGACACTGGGTTTCTGTCTTCACCTATAAAAAGAGAATAATAACATATCCACTCATGTGCTTTCTATGTTGGTTTGAGTGACCCAGAGCAGAGAGTCACATTCCTCTTTATGGGTTCTCAAAACTGCCTCCATTCGGTCAAGATGATTGCTGGTGGATTTGGCAGTCAACACAATCTGGACTGTCTTTTAATTCTGAAGACTGCTTTATGGCAGAAAAAAAGTATTTAAAGTAGTGATCCTTAAAGCTTTTCAAAATCTAATCTTTTTCCCCATGCCATCACTATTCTTCCAGTTACCTAGACTTAAAAATTTACTTCTGTTTACTCATTCTCTACTCACTCCCTATAAATATGCATATTTCCAGAAACAATTAAGAGTAAGTTTCACCTGCTATACCCCTTTACCACTAAATATTTTAATGCAGATTTCTTAAGATTAAAAATATTCTCATGTTTTATTATAAGATGACAATAAAAAGCTATGGGATTGTTTATATTTTATAAAATTCTTACCAAATGTCTTGGCTGCAGCCTGTAATCCTAGCAACTTGAGAGGCTGGGGCAGGAGGGTTGCTTGAGGCCAGGAATTTGAGACGAGCCTGGACAACATAGCAAGACCCTGTCTCTAAATTTTTTTTAATTATATAACCACAGTACACTTATTAACTTCAGAAAATTTAACATAGATATACATTAATTTCTATCTTTCATATTCCAGTTGGGTCCAATGACCTAATAATGTTCTTAGCATTTCTTCTTCCAGTACAGGATCCAGGCCAAGTCATGTTTTGCATTTAATTGTCATATCTCTTTAGCCTTCTTTAATCTGAAACAGTTCCTAAGTTTATTTTCTTTTTTTCATGACCTCGACATTTTTAAGAAATTGTACCACCACCCCCATTTTTAAATAGAATATTCCTTTTTTGCCTGATGTTTATTCATAATTAGATTCAGGTTATGCATCCCCAGCTGGAATACTACATGAGTGGTTCTGTGTCCTTCTCAGGCTAACCGATAAGGAGGTCCATGATGTCTATCTGCTTCTCATTTGTGGTTTTAGTTTTAATCATCCAGTCAAGTTGTTGCTCAGTTTCTCCACTGCATCATTAGGTTTTTCCTTGCAACTAATAAAACTGTAGGAAGGCACATTAAGATAGTGCAAATATACCAATACTCATCAAAAATTTCCCTTAGATTTAACATCTATTAATGATTTTGCCTCAACCAGTCTCTAGTGGGATAGTGGCAAAATGATGTTGTTTCAACTCTAGCACTACCTCCACATATACTAGTCAGTCCTACTGTAAGCAAGAGCCCTCCCTTCTCTCTGGTTTACCTATGCATTTCTTATCATTTTTGACTCATTTTTTCTCATGTTTTCCACTAATTTACAATTTCTAAACTATCATTACTTATTTCGATGCTCTCATTGTTCCAGATTTGGAAGCCCCTTCAAGCTGGATTTGATGTTTTTCTGATATGTACTTCCCTCCAACTATTTTTTTAGCACTTTTTAATATTATTTCATAATAAGATGCTCCAGGCTTGTTCCTCTTTCATTCTTACTAACATAAGCTTCGTTGTCCTGCACTTGAAGTAGAGCAATAGCCTCCTATATGATCTTGCTATTCTATATTCTTCCTGTAGTTGGGTGGCTGAGGGGGGATGATTGTTTGAGCCTAGGAGTTTGAGGCCAGCCTGGGCATCATAGTGAGATCCTATCTCTATAGAAAAGAAAGAAAAAACAAAGAATAAAATAATAGTTACCTTTCATTAAGTACACACCACACACCAGTCTTCTAAGCACTTAATATTGTCAGCAAAAGACAATGAGATCTAGAGGAGAAAAAGGAAGAGCTTTATTTTCTGTAAAAAGTAATCTGCGGATTGGGAAGGCACAGCTTTCTGTACAAGCGAAAGTGTGATCTCTGAAGAACAAAGGGAGGGTTTGGCTTAAGTAGGGAAAGTTCTCACCCATGTTCTCAACCAGGTCCATTTATGCAAATGAAGGATTCAGACTTATCAGTTCTGATTGATTGAAATACTTGAGCCCTGATCAGGTGATTTCCAAAACCAAAGCCAGAAGTCTGCCAGATGTTTCTTTCAAATGGCCAATGGGCAGGGGGTGTGTTCAAGCCACAGTTTATCTTCGCAGTGGTTTGACTTGATTGTACAAAGGGAGATCCTGTGACACTTTTACAACATCTTTCCAAGAACACAAGGTATGTGACATTTCCCTTACCCAACCACGGCCAGTTGGTTGTGTTTTAACTTTGCGCACCTCAGTTAGCCATGGGAAGTTCATTTTGTCTGTCAGCCAGGGGTATATTTTAACAATATGAACTGTCTCATTTAATTCTCACCACAACCCTATGAAGTAAATACTGTTATTTTCTCCAAATTTGAGGTGAGAAAACTATGAATCAAGGAGGTTAAATAATCAACTCAATTCACACAAGATAATATAAGGCAAAATTGAGATTACAGTCTTGGAAGTTTGACTCTAGAAATAGTGCTATATGCCACTATGTAATTCTTATGCCCTCAATCACCTTCCTCCCCTCGCTGCAATTTTTTTGTAACATTAATGATTTTATTTATTCAG
Seq C2 exon
GGTAATCCTGGCCGGCCGGGTCTCAATGGAATGAAAGGAGATCCTGGTCTCCCTGGTGTTCCAGGATTCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000188153-COL4A5:NM_000495:42
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=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(57.6=75.6),PF0139113=Collagen=PU(42.3=73.3)
A:
NA
C2:
PF0139113=Collagen=FE(30.8=100),PF0139113=Collagen=PU(32.7=72.0)
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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
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)