HsaINT0090256 @ hg19
Intron Retention
Gene
ENSG00000112769 | LAMA4
Description
laminin, alpha 4 [Source:HGNC Symbol;Acc:6484]
Coordinates
chr6:112476767-112480082:-
Coord C1 exon
chr6:112479934-112480082
Coord A exon
chr6:112476909-112479933
Coord C2 exon
chr6:112476767-112476908
Length
3025 bp
Sequences
Splice sites
5' ss Seq
CAGGTAATA
5' ss Score
8.55
3' ss Seq
CAATGTTTGTTTATTAACAGGAA
3' ss Score
7.93
Exon sequences
Seq C1 exon
AATGCGTCAGGGATTTATGCAGAAATAGATGGAGCCAAAAGTGAACTACAAGTAAAACTATCTAACCTAAGTAACCTCAGCCATGATTTAGTCCAAGAAGCTATTGACCATGCACAGGACCTTCAACAAGAAGCTAATGAATTGAGCAG
Seq A exon
GTAATATCCTGGTTTTAGAAATGCAAATATCTACATGGGGTGAATAAAATATTACTATTCAATTCCATATGTCAGAACTACTGGGATACAATTTTACCAGGTTGATTAAGGTTGGGTATGCTTATGTGTTGATATGTTGGTTGGTTGGTTGGTTCCTTGGTTGCTTGGTTGGTTGGTTGGTTGGTTGGTTGTTCCATCTGAGAGTCCATCATTGTTCATTGCAATTGTTTGGGGGAGCTGGTCTTTTTTATTTAAAAAAAATCTGTCATATTAAAGGTCTGTGTTCCGGGAAGAGGGGGGTGTCTGTTCCACAATTTTTAGTAGGATGACCAAAGACAATGTATAAAACATTGTCAAATAAATCAGATCCCTTTAGAAGGTCTAATTCTAACATTACCTATTTATTTCATAGACAGCATTATCTTTCCACACCCAAGTGTCTTAAGTAAAACTGGTCGGGAATTGGCAATATAACTGACTTCTGATAAATACTCCACAGTGCCCAGCAGGAACTATTTGATTTCAACACCTGTTAAGAGAAAATCAATTGGCAATTTTCCTCCCAGCACCTAGAATAGAATCACACACCTCTTGGACACTCAATTAATGTTAACTGAAAAGTACTGAAAGATCAGAATTGAATTCATGACCCTGAAATAATAGGCAAATAATGAGATCATTATAGAGAAAGACTAGGAAAAAAGGACCAGTAAAGGTCATTAATAAAATAAGAACCAATATTAACTTCTGTTCAAAATATAAATCACCTTCTTATTCTTGATTGCCAAAATTTTCAAACACTCTTCCAAATCTCCTACGAAGAGAGAAGAAAAGAAAGAGAGAGGTCATATAAAATCTTGGTGTGTCAGTGGGTGAGACAGTGCCATATCCCACTCGGTATCATGGCCCTAGAAACATGAGCTTTTGATGAAGGCAATAAAATGGAGCTTAGAAAAAACACTATTTTGATAATATACTATATTAGCAGAATGTTGTTTTTGAGATCCATCTTATGGCTCTCTTCATTATTCTTTTGTCATTTTGTACCTACATCCCATTCATTGGGATTCCAAAATATAACTTCTGTGTATAATGCCACTCTGCAACAAACAGTGTTCCAGCATGATTCTAAGACAGTTACTACATGCTTTACGTGAAACATGATCCAAAATATCAATCACCCTCAAGTCCTTTTGTATTTAGAATATTTCTGACTATATATTCATGAAAGCATTTCAACTTAGAGACATCTTCATTCAAAAGGTGAGTATCCTTCCATATCTGTCTGGTGTACACAATGATTTACGTGCTATGCTCGAACAAAGATAAACAAAATTCATTAAGAAGCTTCCATTTCAATAGCACATGTTTAATTTGAATACTGAGTTAGTACTTGTTCTGTGCCTAGTATTAAAAGCAAAGTAATAAAGGCTTTGTTTCATGATCTTTGGTACATCTTACCACTCTCGCCAGCAAAATTTTAAAATATTAATAAATATTTGTAACATTTTGTTTCTTTTGTCCCTTTTTTAAAAAATGTTTTCTTGTCTGCCTTCCCCAGATTTTGCTATCTGAGGCCATTTTCTCAGAAGGGGTTGTGGGGAGGAACAGGTAGTGAGTATTTAGATTAGACTCCCCTCTGTAGAGCAGAGCCCCATGACTTCTATAGGCCCTAGACACTTTTGCCTTGGTGGGTTCCTTTCTCCATAGAAAAAGTAAAACCTTTATTTCATGTCTGCATTGGTATAAAGATTAATACCATTATTATTGTTATCCTCATTTTTTCCTTCTGATTGAAAAAAAAATGAAAACGCTGTGCCTAATGGATGAGTCAGCCCTTTTGTAGAGGGGGTAGAATGATTATAGACTTGGTTAACAGAGAGGGAAGTAGCCAAAGAAATATAGAGAAAGTCCCTCTAAGGGAGCACACAGGGACTGGAACTGGATGCTGGAGATTGAGGAACAATTACCGAGCTCAACAGGTCAGGCGGTTTGAAGACAGGAGCCAGTGTGGGATCTGCAATGTCATATACTGGGTCACGGAGGACCTTCTGGAAGTTACTGACAAATGAGGTGATGATACTAATCATCGATGTTTGGGACTGAGAAAAAAAAATAAGGAATTGGTGGATTTAAGACTGAATAAAATTAAGACAAAGGATTTAGACGAACTGCGGAAGTGGAGGTTAGAGTTTATATTACAGAGGCAGTAGAAGTATTTGTCAATAAAATAAATTATGCGGGTACACATAGAGTTTTAAAATCCCAATTCAGGAAATGGTGTAGGTATAATAATAAACCCTGACGATTAGCAGATGCCAGGCATGGTATACCAAGCATTTCTATATTTTATTCCTGTTATATCTCACATTATTAGCCCCTGTGTGCAAGTGTGCAAGTACCCTGTGTGATGGGTACTCAGTAAATGTTGGATGAACCTTACACAGGCCAGAGAGGGGCAAAGGCAGAGACTATCGTGTGAAAGGGCAGGGGTGAGGGTGGGCTGAGGTGGGGCTGTGTGCTGAGGAAGGGCTGGGGCTGTCTCACTCCTGAGGCCCAGGATGCAGCCAGGCCTCAGGAGTGAAACAAACCTTGACAATACGTGCCCTGGCCAAGCTCTGCATACTCTCCTAGAGCCTTGGCTTCCTCTACAGAAAGGAAATAACAATGCTGATTTGGATAAGCACTAGGTAGTCATCATAATGGTTCATTCCTCTGCCTGACTTCCATCACATAAACAAACTCCTGCAAGAAGAAGTGCAGAGGGCTGTTTTTAAATCGTCATTCCCTTTTCCTGCTGCTACTGCCAGACAGGCAGCTGTCAGAGAACCAAAATGCTGTTCAGCAAAGACAGAAGAATGCAGAGGAGGTGTGACCCTCAAGAAAACCTTGCCACACTAGGTGACTTTGAATAACAGGAAGGAAGCATCTGTGATCCTAGAAGTATTTAAAAAGCAAGCATTAAACATGGCCCCATTCCCCAAGAAGGTAAGAAGGAGAAATAACAATGTTTGTTTATTAACAG
Seq C2 exon
GAAGTTGCACAGTTCAGATATGAACGGGCTGGTACAGAAGGCTTTGGATGCATCAAATGTCTATGAAAATATTGTTAATTATGTTAGTGAAGCCAATGAAACAGCAGAATTTGCTTTGAACACCACTGACCGAATTTATGAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000112769-LAMA4:NM_002290:14
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.339 A=NA C2=0.117
Domain overlap (PFAM):
C1:
PF101234=Mu-like_Pro=PU(53.3=96.1),PF142651=DUF4355=PU(42.6=84.3)
A:
NA
C2:
PF101234=Mu-like_Pro=PD(45.7=87.5),PF142651=DUF4355=FE(46.5=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
- 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)