HsaINT0039085 @ hg19
Intron Retention
Gene
ENSG00000081052 | COL4A4
Description
collagen, type IV, alpha 4 [Source:HGNC Symbol;Acc:2206]
Coordinates
chr2:227968688-227973338:-
Coord C1 exon
chr2:227973297-227973338
Coord A exon
chr2:227968769-227973296
Coord C2 exon
chr2:227968688-227968768
Length
4528 bp
Sequences
Splice sites
5' ss Seq
CCGGTAAGA
5' ss Score
10.1
3' ss Seq
ATCTTGCTTTTTTTTTTAAGGGT
3' ss Score
9.53
Exon sequences
Seq C1 exon
GGAAATCCCGGTGTGGGAGTAAAGGGGCAAATGGGAGACCCG
Seq A exon
GTAAGAATTCCCTCTTGCTCTGAGGAGCAGATGGTGACGTGTGTGTGCTGCTCAGGGGTGGAGGCTGTTCTGATTATTTGAACTTGTACTCATTATCTAGTCACTGCCCAATTTTATGGCTGAGAACTTTTCTTTGCCGAATTATTATGGCACCATTACCCTTGACTGTAAAATGAAAGATCTGACACAATTTAACACTACTTTCGGGTTAATTTGTGCAACACATTTCACCCTAGCAAACAGATTGAACATTTTTGACAATATATTATGTCCAGAGTAACAGCTTTGTCAAATCACGGATTTGTTTTGCTTAATTTCACATAAATCCTAAACTCCACCCTTAAATATGCATATAAATACAAATATAAATGACTGGAACCAAGAGCACTGAGCAATACACAATCTCCAACCCACTCCTTTTCTATGCCTGTCCTCCCCGTCTCCTCCCCCTGCCACTCACACCCACTGTCCTTTTGGCCGACATGTAAAACTTAGTAAGAATAAGCTTTAGAAAAGTGATTTAAGGGCTGAGCACGATGGCTGATGCCTGTAATTCCAGCACTTTGGGAGGCTGAGGCGGGTGGATCATGAGGTCAAGAGACTGAGACCATCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAATACAAAAATTAGCTGGGCGTGGTGGTGCGTGCCTGTAGTCCCAGGTACTCGGGAGGCTGAAGCAGGAGAATTGCTTGAACCTGGGAGGTGGAGCTTGCAGTGAGCCAAGATTGTGCCACTGCACTCCAGCCTGGTGACAAAGCAAGACTCTGTCTCAAAAAAAAAAAAAAAAAAAAGAAAAGTGATTTAAGAAGGCAACTCACCTGGAAACAATCTGAACATCCAGCAGTAGGTGAGTGGCTCTTTCAACAACTGAGGGCAAGTCAATATTAAGCATCTGCTCCATGCCAAGCTAGGACTGACACTGGGTGTGGGGATTTAGCAAGACAGACCTGATCCCTGCTCTCATGGAGTTCCAGCGTGATTGAGTAAGTCATGGTACAGTCATTTAACAGAACGGCACAGGAGTCAAAAATATATATAACAACTTCATGATGTGGGGAAGTGCCTGTGATATAATGCTGAACAGAAAGTACAGGTTACAAAAATATAAACTCAACTTTGTAAAAGCAACAGCAACAAGAAAGACATTAAAATATACACAGAGAGGGATTTCTCAACCTCAGGCTGCTGCTATTTCATTGTTGTGGAGGCTGTCCTGTGAATTACAGGATGTTTAGCCACATCCCTGGCCTCTCCCCACTAGATGTCAGTAGCATCCCGTCCCTCCAATTGTGACAACTTAAAATGTATCAAAACATTGCCAAATGTCCCTGTGGGAAGGGGTTGCCTAACTACTTTCCCCTTCCCCCAACCTTGAGATCTCTGGCTTGTAGAAATGACTGAATGAAAATATACCAAAACAATGTTTTTCAAGTTTGGGAAGCCATGGAGCTCTGGAATATGTTCGTCGAAGCCACAGGAGCCCGTGTGCCATTGCAGAATCCAGCAAGCATTGGCATCTTAGTGACTTTCCGCGCCAGTCCAATCAGACACATTTGCAAACTCAGGCTGTGGAATAACTTGGAAGTATTTGGCTATGAGGTGGCCATTCAAATGATCTCAAATGTGCTTACCTTAATTCTTTTAGATTGTCAGGTGAATGAACACATAATTTTACAATTTTGGGCCAGGCCCAGTGGCTCACGCCTGTAATCCCAGTACTTTGGGAGGCCGAGGTGGGTGGATCACCTCAGGTCAGGAGTTCGAGACCAGCCTGGCGAACATGGCGAAACCCCGTCTCTGCTAAAAATACAAAAATTAGCCGGGCATGGTGGCGTGTGCCTGTAGTCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATTGCTTGAACCTGGGAGGTGGCAGTTGCAGTGAGCCAAGATTGTGCCATTTCACTCCAGCCTGGGTGACAGAGTGAGACTACGTCTCAAAAAATATAAATAAATAAAATAAGATAAAATATTGATGCAGAATTCTCAGATGTTCTAGAGCATGTTTGCCCACCTCATTTTAAGAAACACTGCCCTAAATGGTTGCTATTTATGCCTACATGATATAATTATGGACCTTTTACATTTTAATTCTTCATAGTTTTCCTTCTTTGTACTTTTGACTATGCTGAGTATATGGTACTTTTACAATATGAAAAAAATAGCAGTATGACCAATATTTTGAAGAAGCCGGCTGCTTGTCAGCTTTTAAGGGTTTTGTTCAGGTTTATCTCAATTACAAGAATAAGAGTGGCTATCTTTACCAATACATGCTATGCTTTTACTCATGTTTTGTTAATGTGCTTGTTCAATGGTTTATTCACACAGCAGATATCTTTAGGGCAGGTGCTACACCAACACTGTGTTAGGTGTGTAGATAAATCAAGGAAAAAAAAACAAAACAGACAATGTTTCTAATCTGGCTTTTCTTCAATTTCCCAGGTTTAGGTAGAAATTGAACTCTTTTTTTTTTTTCTATTTAAACTTGATATTCTTCTAAAAATTCCACCTATCAAAAGCATTAGTAGTTTTAGTAATGATATATTGGGGAATTTACTTTGTTACCCTCAATACGGGAAGCATTTTATGTATATTATCTATTCAATGGAAGAATAGTTTGAGGTAGGTAATATTACAATCTCCATTTCACAGAGAAGAAAAATGAGGTTTCAAGGAAGTAAGGAAATGAGGACTGAGAGAGGTTTTAAGGAACTTGCCCCAAGTGACAGAGCCAGTAAGGGCCTGGTTTGCAAACATGGGTGACCTATGTATAGCCTGTTCTTAACTATGACAAAAAGAAAGATCATACTAAGTGTAGAATAATAGTAATACCCAGAAAAGCACAAAATATTTATTTTCTAATTAATGGTGAGAATTTATGATTGTGGCAAAATTCATTCAAGAAACATTCTTTTCTTCAGTAGAAAAACATCTATCATGGCATAAATAAAAATTTTGGCTATTATTTTACAGTTTTAAAATATTATTGAAAATAAATAGAAATAATCTAATCTAACCAGAGTGAGATGGCTTAATACATCACAGTACATTCTTGTGATAGATTATTTATTGGCACTAAAAATCAGGATTGTTACGTGAGGCCAGGAGTTTGAGACCAGCCTGGCCAACATGGCGAAATCCCATCTCTACTGAAAATACAAAAATTAGCTGGGCACGATGGTGCATTATCTGTAATCCCAGGTACTCAGGAGGCTGAGGCACAAGAATCACTTGAGCCCGGGAGGCAGAGGTTGCAGTCAGCTGAGATTGCGCCATTGTGCCCCAGCCTGAGTGACAGAGAACACTCTGTCTCAAAAAAAAAAAAAAAAAAAAATCAGGATCCTGAAGAGATTTTAGTATAATAGAAAAAGGCTCACAAAATATTGTAAGAAAAATATAAAATTATTTAAAAATTTAATAAAATATGCTGTATATTTTAAATCATGTTTATATATTTATTATAGTATTCTGATTATATTTTCATAAACATAAAACAAATTGTTTATTCACCTATATACACATATATGTACATATATACACATATGTACACACACCACCAAAAATTATATCAAAGTTTTAATAGGCCGGGTGCGGTGGCTCACGCTTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCACCTGAGGTCCGGAGTTCGAGACCAGCCTGACCAACATGGAGAAACCCCCGTCTCTACTAAAAATACAAAATTAGCCGGGCATGGTGGCGCATGCCTGTAATCCCAGCTACTCTGGAGGCTGAGGCAGGAGAATGGCTTGAACCCGGGAGGCGGAGGTTGCTGTGAGCCGAGATCGCGTCATTGCACTCTGGCCTGGGCAACAAGAGTGAAACTCCATCTCAAAAAAAAAAAAAAAAAAAGTTTTAATAGAGATTACTTCTGGATAGTAGGATTTTTTATTTATTTATTTATTTATTGAGATGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCACAATCTCTGCTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTCAGCCTCCCAAGTAGCTGGGACTACAGGCGCCTGCCACCACGCCCGGCTAATTTTTTTTTTTTTTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGGATGGTCTCGATCTCCTGACCTCGTGATCCACCCACCTCGGCCTCCCAAAGTGCTCGGATTACAGGCGTGAGCCACCGCGCCTGGCCCTGGATAGTAGCATTAAGAATCATTTTCATTTTTTAAATTTATTTTTAACAATAAGTGTGTATTAAATTTTTATAAGAAAATAAATATCCTTTTATATTCTATGATGTACTTGCCACAACTTGTATTTTAAATCCATGACACATAGGATTGGAAGCATTATACCACAATACATGGGTGAAAACCTTCAAAACATAAATTAATATGAAATTTTCATTATCTTGCTTTTTTTTTTAAG
Seq C2 exon
GGTGAGGTTGGTCAGCAAGGTTCTCCTGGACCCACCCTGTTGGTAGAGCCACCTGACTTTTGTCTCTATAAAGGAGAAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000081052-COL4A4:NM_000092:12
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=0.704
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(10.3=42.9),PF0139113=Collagen=PU(10.8=71.4)
A:
NA
C2:
PF0139113=Collagen=FE(28.0=100)
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:
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)