HsaINT0090277 @ hg19
Intron Retention
Gene
ENSG00000112769 | LAMA4
Description
laminin, alpha 4 [Source:HGNC Symbol;Acc:6484]
Coordinates
chr6:112438942-112440514:-
Coord C1 exon
chr6:112440359-112440514
Coord A exon
chr6:112439102-112440358
Coord C2 exon
chr6:112438942-112439101
Length
1257 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGC
5' ss Score
9.88
3' ss Seq
GAAATATCTTCTTCCCTCAGATT
3' ss Score
9.26
Exon sequences
Seq C1 exon
GTGATATTTATTCGAGAAAGGAGCAGTGGCCGACTGGTAATTGATGGTCTCCGAGTCCTAGAAGAAAGTCTTCCTCCTACTGAAGCTACCTGGAAAATCAAGGGTCCCATTTATTTGGGAGGTGTGGCTCCTGGAAAGGCTGTGAAAAATGTTCAG
Seq A exon
GTAAGCCAGGCATGACCAGGTAGAGCCATTGACCATTAGAGCCAGAAGATCATCTAATTGAGGCCCTCGTCTCACAGATTAGGAAACTAGAAACTAGCACCAGTAAAACTGTAGTTTTCTGGAAATGGGATATCAAAGTAAGTACTGTCTTATGGGCTGCCTGTCTGCCCTGTGGCATTACAAAGTCAGAAGTAATCTTTCAATTCTAAGGTAGATGTCAAATGAAAAAGTTTCAGAGGCATAAATTATCATGAAAATTTATGTCTCAAGGAGATCTTATTTGTTCAGGAAGTACCCATACTTTTAATGTAAAGACATAACAAAAAAGAAAGCAAATCATTGCATTATACATTATTGAGTGAAAAAAAAAGTTTCAGGTCATTATGCAAACTACAATCCCATTTTTCTTACACACACACACACACACACACACATACACACACACACACACAATTTGTAAATGTATAAGGAAATGTGGTTGCCCTGGGGAGAAGTGAGAATATAGTAGAAAAATATTATTTGTGTAATTTAAAAATTAAAAATATTGCACTTATAAAAAATTTAGCAATAAAAGGAATGCATCAAAGGACTAAATTTTTCTTAACATAAATATAGGTTGGATTTTAGCAATGTTAAAAATAATTTCTAAGACCTATTAATATATGTAGATGAAGCAAAAAAGATGGTTTACATTATAATTAGATTTTAGATAAGCAGCCCCAATTCCATGGCAATCTCTTTTTTAAAATGTCCAAATGCAGGACAAAATCAGTTATCTTAAGTGGCCCAAGTTTCATGTCCTGTGATATGATAAATTCTCAACCACAAAAACAGCTCATGAAACCAGAAATGAAAGCTTTCTGCTGTTTATTTGGCTATGGTAGATTTAAGTAAAGAACTTTGCTAGCCCTCATCAGCCTTAGGTGATCTTGGCACAGCTGTCATTCTTGAGGGAAAACTAGGATACTTCTAAATATGCAGTTTGAAAACCACAGCTGCAACTTATTGTGTCAAAGTGTAACATAAAAATGTCCATAGCTTAATTACTACAGGTTGACATTATCAAATACAAAATTCCAGCTTCAAACAACCAGTTAGAAAGCAACTATCCAGGAAAGTACTGATCATTCAGATATCTGAAATAAATGAAACAAGGAATTACGTGGGTTCCTTCAGGACTCAAACCCCCTCATTTTGCTTCCCCTTGGTGCATTTGTGTTGAGAAAATTGATTTTAAGAAATATCTTCTTCCCTCAG
Seq C2 exon
ATTAACTCCATCTACAGTTTTAGTGGCTGTCTCAGCAATCTCCAGCTCAATGGGGCCTCCATCACCTCTGCTTCTCAGACATTCAGTGTGACCCCTTGCTTTGAAGGCCCCATGGAAACAGGAACTTACTTTTCAACAGAAGGAGGATACGTGGTTCTAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000112769-LAMA4:NM_002290:34
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0221019=Laminin_G_2=FE(39.8=100)
A:
NA
C2:
PF0221019=Laminin_G_2=PD(14.1=33.3)
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:
TTTATTCGAGAAAGGAGCAGTGGC
R:
CTAGAACCACGTATCCTCCTTCTG
Band lengths:
310-1567
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)