HsaINT0090387 @ hg19
Intron Retention
Gene
ENSG00000091136 | LAMB1
Description
laminin, beta 1 [Source:HGNC Symbol;Acc:6486]
Coordinates
chr7:107569857-107571945:-
Coord C1 exon
chr7:107571801-107571945
Coord A exon
chr7:107570065-107571800
Coord C2 exon
chr7:107569857-107570064
Length
1736 bp
Sequences
Splice sites
5' ss Seq
CCCGTAAGA
5' ss Score
5.66
3' ss Seq
GACATCTTTGCTTTTCACAGAGG
3' ss Score
7.43
Exon sequences
Seq C1 exon
GTCTCTGAAGCAAAACTGAGGGCAGATGAGGCAAAACAAAGTGCTGAAGACATTCTGTTGAAGACAAATGCTACCAAAGAAAAAATGGACAAGAGCAATGAGGAGCTGAGAAATCTAATCAAGCAAATCAGAAACTTTTTGACCC
Seq A exon
GTAAGAAATTTTTTCATTTTACTTTTAGACATTTGTTTCTGTGTGATTCTCTGTTTACATTTTAGATAAAATCCATTTCTGTCAGGGTACTAAGTGACATTTCCAAATAAGAAAAACGTCCGTATATTAAATGTTTCCACTTCTTAAACTTATATATGTGTATCAAATAACTTTCTCCAATGTTACGCAGATACAGACACACCTGATGGGATACTCAGGTAGCCAATCAAAAGTCAAATATTTACATTGAAAATTGAACGTGGAATTTGTTAGAAATTACGTATAGTAATTTCTAACCTTAAAGAAGTGGAGTTTGTTATTTTGGCATTGCCCCCAAAGCTTTGTAATTCTATTATTTACAGGATATTATACCTATAGTTAGTTAAGAGTGTTGCTAGTCACAGTTCAAGTGTTACCAGTAAAGATGGTTTTGGCTGCAAATTACAGAAAACTCTCAAGTGAAAGGGACTTAATCAAAAAGGATGTTTATTATCTCACATCTTAATAAGATATCCAGTAGCAGGATAGCTTCCTGGGTCTGCGACCCACATACTTTTCATCTTTCTACTCTACCATCTTAAGCATATCAGCTTTGTCCTCTAGCTCCTCATGGTTACAAGGTAGCTGCCAAAGTTCCAGACATCATATAAAGATTAATAATGGAAGAAGAGACCACCTATTCCTTGCATCTTTTTAAAAAGGAGGAAGTCTTCCCTAGAAGCCTTTAAGCAGTCATCCTTATAAACCTCACTGGCCAGCAATAAGTCACATGCCAATGCATAAATGTCACTGGAAAATGGAAATGCGATTACAGTAATTCACAAACTAATATTTAATGCTGGGTTGATAATTTTACCTGACTTAGAGGCAGGTACCTGAAAAAAAATCAGTATTCTGTTAGCAAGAAAAAAGGCATGGCTAATAAGGAGTCAACAGTATTTGCTAAGGATATCTTAGGTAATATTTTATGGAAGCCATCATTCAAGTACATATTTTATTTGAATAAATCCTCTGGGGTCCATTTTTATGTTCAATAGTTTAAAACATAAGCAAAGCTTGAAAGTAAATGAGGATCTGACGTATTTGAAGCTTAACTTCATAAACTTTTTTTTTCACCATCTTCCACATTTTACATTTGAAACTCCTTGGCTTTGTTGACAACCCATTATTCCGGTTCTCCTGCTTCTATAATTTTCTCCCTTTCTATAATTTCCTGAATCTAGATCATTTGTAGGAAATATCAAATCTCCATATCTGCATTCACAAGTTTCTGAGCTATTCGTCCAACCTCAATTAAAAGATTTCATTGCCTTTAAGTCTCAGCTTTAAGCTCTGGCCCTCTATGGTTTTCCACAATGTTCAGATTCACTCTGCTATACTTTCCCGTAACATACTCTGCCGTTCCTGTCTCCCCATCTGGAATTGTCCTTTCTTCTTTCAAATTCTATTATCCCTTAAAATCTGATCAGCTCCTCATCTTCCACGAAGGTTTCCCTCACTACCCAGCCTAAAACAAATTCTAGTAGTACTCAATTGTCTGCAGTTACTTTTTTGTGTGTGTAGGTCTCATCTCCCCTCAAAATCCCAGATAGATTATAAACTCTTAAACAGGAAGTTAGTGTCTCTTGGTGTGTAACCCCACCATGCTAGTCCATAGTAGATGACCAGTAAGTGGTTGAATGAATGAACCATCTATTCTTTTCACCTCTTTTTGGGGACATCTTTGCTTTTCACAG
Seq C2 exon
AGGATAGTGCTGATTTGGACAGCATTGAAGCAGTTGCTAATGAAGTATTGAAAATGGAGATGCCTAGCACCCCACAGCAGTTACAGAACTTGACAGAAGATATACGTGAACGAGTTGAAAGCCTTTCTCAAGTAGAGGTTATTCTTCAGCATAGTGCTGCTGACATTGCCAGAGCTGAGATGTTGTTAGAAGAAGCTAAAAGAGCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000091136-LAMB1:NM_002291:29
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.551 A=NA C2=0.357
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
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:
TCTCTGAAGCAAAACTGAGGGC
R:
TAGCTTCTTCTAACAACATCTCAGCT
Band lengths:
342-2078
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)