HsaINT0090384 @ hg19
Intron Retention
Gene
ENSG00000091136 | LAMB1
Description
laminin, beta 1 [Source:HGNC Symbol;Acc:6486]
Coordinates
chr7:107575860-107577722:-
Coord C1 exon
chr7:107577538-107577722
Coord A exon
chr7:107576102-107577537
Coord C2 exon
chr7:107575860-107576101
Length
1436 bp
Sequences
Splice sites
5' ss Seq
GGGGTGAGC
5' ss Score
5.97
3' ss Seq
AATTTCATTTCCTACCCTAGGTG
3' ss Score
9.36
Exon sequences
Seq C1 exon
GAAACTGATTAAAGATGTTACAGAAATGATGGCTCAAGTAGAAGTGAAATTATCTGACACAACTTCCCAAAGCAACAGCACAGCCAAAGAACTGGATTCTCTACAGACAGAAGCCGAAAGCCTAGACAACACTGTGAAAGAACTTGCTGAACAACTGGAATTTATCAAAAACTCAGATATTCGGG
Seq A exon
GTGAGCATTTTTTGGTGCAAATAGTCCCAGACAATGGATTTAACGATATGTCTAACGTTTTAATATAGCACTTTTGGGGAAAAAAAAAAGTTTTCTAATAAATTTTAAAACTTTTGCTCATCCAGTTTCTGGCACAAATGAGGATCAAAGTCCCCATTTTACAAATGTGGGACTTGGGCACAGAGAACCTAAGAGACATAGCAAAGGTCCCACAGAGTGAATGGCAGTAGTTGTATCAGAATGGTATCCATTTCCTGATTTTTTTTTTTTCCCTCCAGTTAGTAGTTTAATCCCCTGGCCTTTTCTTGGAAGGGGGTTCTTTTGAATAGTTAAGGTATTAATACTTCTGCAAATCCTTTCACATTCAAGAATGCTGCTTGGTCAGAAAAAAACTTTTGCAAATCATTATTTATATCATAGACTGTAAAGGATCCTCAGCAAAAAGTGAATGTAGAAATATGTTACATCATACTGTCCAACTATCCATACTGTTTTATGCATGATTGCTTTTGGACTAAAGCTAAAAACATGTCATGCTGTTATATATAATACCGTCATCCCTTGGTATCCATGGGGGATTGGTTCCAGGACCCACTGCAGAAACCAAAATCCACAGGTGGTCAAGTCCGTTATATAAAATGGCACTTGCATATAACCTATGCATATCCTCCTATATACTTCTTTCTTTTTCTCTCTCTCTCTTTCTTTCTTTCTTTAAGAGATGGGCTCTTGCTATGCTGCTCAGGCTGGTCTTGAACTCCTGGACTCAAGTGATCCTCCCGTCTCAGACTTCTGAATAGCTGAGATTATAGAGGTGAACCACCACACCCAGCTTTACTTTTTTCTTTTTTTCCCTTCAGTATATTTAAAAGTAATCTGTAGATTACTTACAATACCTAATACAATGTAAATGCTATGTAAATAGTTGTTATACTTTATTGTTTAGGAAATAATGGCAAGAAAAAAGTCTGTACACATTCAGTACAGATACAACCATTTTTTCCAAATGCTTTCCATCCACAGTTGGTTGAATCCACATATGTGGAACCTACAAATATGGAGGGCTACTATATTAGTCATTTGAGTGGATCCGAATAAAGGATTGAGAAAAGTCATCTAGTCATATAATCTTCAGGCTGCCTGAAACCAGCTATTTATAAAGAACTGGATGTTTGCTTGTGTATAGAAACAAGATTGCATGATTTTCTTAATTTTTCATTTTTCACCCAGATGTTTGCCATACTCGAGCTGGAGTAGGTGCTAATGGGACAAAACATATTCATTGCTCATGAAAACTGTACTTCATAAATATTTTTTCTTGAATTTTAAAACTTTACAGTAAATTTAGGACCCGAAGACACCAAATATAGACACTGCTTGGGGAGGAAGCCTAGTATGATGAGGTTAACTGTGGGCAATTTCATTTCCTACCCTAG
Seq C2 exon
GTGCCTTGGATAGCATTACCAAGTATTTCCAGATGTCTCTTGAGGCAGAGGAGAGGGTGAATGCCTCCACCACAGAACCCAACAGCACTGTGGAGCAGTCAGCCCTCATGAGAGACAGAGTAGAAGACGTGATGATGGAGCGAGAATCCCAGTTCAAGGAAAAACAAGAGGAGCAGGCTCGCCTCCTTGATGAACTGGCAGGCAAGCTACAAAGCCTAGACCTTTCAGCCGCTGCCGAAATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000091136-LAMB1:NM_002291:26
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.455 A=NA C2=0.617
Domain overlap (PFAM):
C1:
PF041117=APG6=FE(43.4=100),PF0154413=CorA=FE(47.3=100),PF061607=EzrA=PD(55.8=84.1),PF057146=Borrelia_lipo_1=FE(51.7=100),PF0157614=Myosin_tail_1=PD(51.7=96.8),PF0001516=MCPsignal=PD(61.9=95.2),PF064286=Sec2p=FE(84.9=100),PF0003816=Filament=FE(58.5=100)
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:
ACTTCCCAAAGCAACAGCACA
R:
TAGGCTTTGTAGCTTGCCTGC
Band lengths:
342-1778
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)