HsaINT0090529 @ hg19
Intron Retention
Gene
ENSG00000058085 | LAMC2
Description
laminin, gamma 2 [Source:HGNC Symbol;Acc:6493]
Coordinates
chr1:183192270-183194855:+
Coord C1 exon
chr1:183192270-183192459
Coord A exon
chr1:183192460-183194742
Coord C2 exon
chr1:183194743-183194855
Length
2283 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAAA
5' ss Score
8.59
3' ss Seq
TTTGATTTTAAATTATGCAGGTT
3' ss Score
5.87
Exon sequences
Seq C1 exon
CCAAATTTCTTGGGAATCAACAGGTGAGCTATGGTCAAAGCCTGTCCTTTGACTACCGTGTGGACAGAGGAGGCAGACACCCATCTGCCCATGATGTGATTCTGGAAGGTGCTGGTCTACGGATCACAGCTCCCTTGATGCCACTTGGCAAGACACTGCCTTGTGGGCTCACCAAGACTTACACATTCAG
Seq A exon
GTAAAAAGAGAGACCATAAGTAGGTCAATTAGAGCAAACTATGATTGAAGTTCAAGTTTGTTCTTTATTCATTCAATCATCATTCATTTGTTCAACAAGCCTTTCTGAGCACCTTTTACGTACCATGAAGGTTGCTATGTGCTGAGAAAGGACATGATTCCTTCCCTCAAGCAGCTGACAGGCTAATGGGAGAGAAAAATGAATAGATAATTACAGTGCAGTTTGTCAAGGGACAGAAATAGGCAAGGTGGACACAGAAGTTCTGAGCACATAAAGGAGGCATGACTGACCCACACTGGAATGATGAAGGAAAGCTTCCCAGGACCACATGACAAATGTGAAAGGCAGCCCTCTAAGGAAAGAGAAGGGAGGAAAGGTTAACAAGGCAGAGGAAATGCAATGCTTGAAGAAGGTTTGTGCATTTAGAAAATTCCAGGTGGTTGAGCACGAGTGAAGCATGAAGTCGGCGATAGGAGTGCAGTGAGAAGTGAGGTAGGAGAAAGAGGTGGGAGTGACTTTATGGATGGCTTTGTGTGTGTCTACAGGGATTGCACAGTATCCTGCAGAATAGGGATTCTGCATGGTGTTTGCAGAGAGGTTGGGGAAGGGAGCTGTGCCTACTAAGTGCTCAGTAGTGCACTGGAGGCTGGGAAATAAAGATGGAACATGGTCTTTGCCTTCCAAGAGCTCATGGTCTAGTACAATGTATAACATGTCAAAAAGCAAGCATAATACAGTAGGATAATTGCTTTAGGGGTGGTGCATGTTCATGGGGTCTTGGAAAGTGCCCGATTCTGCCTGGAGGAGTCAGGGAAACCTTCAGGAGGAGGCAATGTGTGGTCTAAGAATGGAAAGGTCCACAGGGCTTTTCCAGGGAGAAAAGTCAGAGAAGGGCAACCTTCACATGTGAATATATGTGGGGATGCAGAAAGGCATAATATAGGGGAGAACTGGCAAGCAATATTTATAGCTGGAATACAGCATGCATAAGGAAGATGGGTAGATACATTTGCAAAGGTTGGAAAAGGACCCATCATGTTGGGCCTTGTGTGTCATGTCAAGGAGCTTAGATCTTGTCCATGCTGGAAAGACGATGCAGAGCCATTGAGAGATTGTTAAGTCAAGAAGTGTGATCGTCAGGTGTGAAGGCTAGGTGCAACTACAGGCACCATATAGATGATAGTTTGGGTCGGGTCCTTAACTGGACCATCAGAACACATTCAGAGTGGCTCAACTGAGAGTGGTTAGGTGCCTAACCCAAGGCAGGGGTAATGGCAATAGGGAAAAGAAGACCCACAGAACACAAACAAAGAATTGATCAAATATCCGAGTATACGTGTTCTAATGATACACACACACACACACACACACACACACACACACAGCTCTCCTGCCTGGAATACTCGTTCCCACCTTCCAGGCTTTGTGAACTTACTCTTTGAGATTCAGCTTACATGTTCTTCCTTTGTATTAGCCTTCTCAGAATCCCAGCTAAAGTTACAGTCACTTTGTTTTTCCATGGTACTCTGTGCATGCATCTGTTATAGCATTCATGGCATTGTATTATAACTGTGTCTACCCACCTGACTCCCCTGGCTGGATGTGATCATCTCTCCCTGTTGTCTTTGTGTCCTCCAGCCTGACATAGCTTCTAGCCCAAACCAAGTGCACAGTCAACTTTTATTTAACAAATCAGTGAATGAAACGAAGGTGGGTAGGGTTGTTCCTGGATGAGTAAAAAACAAAACAAAATTTAGAAGAACAGCACAGGGGCTGGTGATATGTTACAGTGAGCCAAAATGATGCCAAATTAAAAAGTATTAAGTGTGGACAATGTAAAAGTGGAAACTGATTTTTGAAAAAAGTAAGTAAAATGTGCTCAGATAACAAATAAATGATTTTTTTTAAAAAAAATGAATAGTAGCTCTTGAGAATCAGAACTTCTGGAACGTGGAGATGTTCCTAATACTAGCTTATGGGTGGCCAAGAATAGAAAGTGGTGTCTGAGAACTTGCGATCATCATGGTTTCAGGTGATGTCACCCCTGGATCTGGACTTCCCACACTGGGATGCCCTCCATCACTTCCTCTGGGGTTTGTCCTCCCCATGGAGTGAGGAAGGTCCAAGTACATGCCTATGAAAAGGTGGCTCTCAGTCCTATGCCCCCTTCTAAGCAGGACTGGGAAGGGGCTTAGCTGTTCCCGTATCCTCAGGCATAATTTATAACAGGTAGGTATGTGGTAAGAATCGGATTTTTAAAGCTTTTGATTTTAAATTATGCAG
Seq C2 exon
GTTAAATGAGCATCCAAGCAATAATTGGAGCCCCCAGCTGAGTTACTTTGAGTATCGAAGGTTACTGCGGAATCTCACAGCCCTCCGCATCCGAGCTACATATGGAGAATACA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000058085-LAMC2:NM_005562:7
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:
PF0005213=Laminin_B=FE(48.1=100)
A:
NA
C2:
PF0005213=Laminin_B=PD(47.3=55.4),PF0005319=Laminin_EGF=WD(100=33.9)
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:
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)