HsaINT0090527 @ hg19
Intron Retention
Gene
ENSG00000058085 | LAMC2
Description
laminin, gamma 2 [Source:HGNC Symbol;Acc:6493]
Coordinates
chr1:183189960-183191346:+
Coord C1 exon
chr1:183189960-183190096
Coord A exon
chr1:183190097-183191223
Coord C2 exon
chr1:183191224-183191346
Length
1127 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAAG
5' ss Score
9.06
3' ss Seq
TGATTATGTTTGTGTTCCAGATG
3' ss Score
10.91
Exon sequences
Seq C1 exon
GTGTCGATCAGGTTACTATAATCTGGATGGGGGGAACCCTGAGGGCTGTACCCAGTGTTTCTGCTATGGGCATTCAGCCAGCTGCCGCAGCTCTGCAGAATACAGTGTCCATAAGATCACCTCTACCTTTCATCAAG
Seq A exon
GTAAAGCCTTCTATTTTCTAGGTTTTAGTTTTTTAATGTTGTACAGGGCTTTGTGTTTAGAGACAACCACCTCCGCATTCACAGGATGGATTCTCTTTAGAAATTCTCTTATAGTATTGAATGTACATTATTTTGTCAGGGCACTCAGGCATATCCTGATGTCTTGAAAAAGTCATAGGCTGAAAATAGTTCATTCATACTAGTGAATATAACTTAAAAGAATAACTAAAAAAGAGACTAGATTTTTATTTCCCTGAATTTTCCATCCCCATCTATTTCAAAACCACGAAGGAATCATTCATTTGGTTTGGAGAGTGTATGAGTCTTCCTGGAATTCACGTTCACTAATAATGCTGTTTTCACATATAATAAATGAGCTGATTTATGTGAAATTAGTTCCCAAGCTACAGAACACTATAAAAATATTGGAAACTGATATTATTTCAACATTAAGTCTGAGTTTCCCTTTGAAAAGACTGGACCCGGGCCAAGCGTGGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCCGAGACAGGTGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACATGGTGAAACCCCGTCCCTACTAAAAATACAAAAAAATTAGCCGGGCGTAGTGGTGGGCACCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGTGAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTGGGTGACAGAGCGAGACTCCGTCTTAAAAAAAAAACAAATGAAAAAAAAATGAAAAGACTGGACCCTCTCACTTCATTAAGGTGAGAGCTTTTTATATAAATACAAAAAAATGCAAATTACAGGCAGAAGAAAACCTGCTATCTTATCACGAGTCAGACTCAAAGATGAGAAATCATAGCAGCTGCGGGATGGGAGCAGGTGAAGTTGAGAGCCACATAGAGAGATACATGCAGAATTTTAAGGACCATTTGCAAATGTGGAAATATTGAGAAAACCCCACTTTCTACTCACCACTAGGACTTGTCGGCAAGCAAATCTTTCTTTGTTTAACTTAATAGATGATGAGGGCTTGTCCAATGCAGACTGATTATGTTTGTGTTCCAG
Seq C2 exon
ATGTTGATGGCTGGAAGGCTGTCCAACGAAATGGGTCTCCTGCAAAGCTCCAATGGTCACAGCGCCATCAAGATGTGTTTAGCTCAGCCCAACGACTAGACCCTGTCTATTTTGTGGCTCCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000058085-LAMC2:NM_005562:5
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=0.024
Domain overlap (PFAM):
C1:
PF0005319=Laminin_EGF=PD(34.8=18.2),PF0005213=Laminin_B=PU(3.8=5.7)
A:
NA
C2:
PF0005213=Laminin_B=PU(51.9=64.8)
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:
ATCAGGTTACTATAATCTGGATGGGG
R:
CAGGAGCCACAAAATAGACAGGG
Band lengths:
254-1381
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)