HsaINT0090528 @ hg19
Intron Retention
Gene
ENSG00000058085 | LAMC2
Description
laminin, gamma 2 [Source:HGNC Symbol;Acc:6493]
Coordinates
chr1:183191224-183192459:+
Coord C1 exon
chr1:183191224-183191346
Coord A exon
chr1:183191347-183192269
Coord C2 exon
chr1:183192270-183192459
Length
923 bp
Sequences
Splice sites
5' ss Seq
CTGGTATGT
5' ss Score
8.14
3' ss Seq
TTTAAAACTCTGTTTCACAGCCA
3' ss Score
6.3
Exon sequences
Seq C1 exon
ATGTTGATGGCTGGAAGGCTGTCCAACGAAATGGGTCTCCTGCAAAGCTCCAATGGTCACAGCGCCATCAAGATGTGTTTAGCTCAGCCCAACGACTAGACCCTGTCTATTTTGTGGCTCCTG
Seq A exon
GTATGTGAGGAATAATGTCTCCTATAGAGGCCAGCTTATAGGACTAGGAAGTCAAGATAGAGAAATTGAGTTAGAAATTGTGGAAACCATATAACTTTGGGTTCAGGGTAGCAGCATCTCCGGGTAGTGCAACCCCAGAAGAGAGATGGGGGCTAAGCCTGATTTGAGAGTCACTAAGGAATGGCCCAACAGAGCAGAATGTGGTGTCCCAGAGGTCAGACCCTGGTTGAGCTACCTCCTTTAATCAAATGGGAAGTTTCTACGTTTACCACCAAGGCAAGAAACCAAGGACTGTGGCCAAACCTATGGGTCTATTGAGAAGTAGGTGGAAAGCAAAAACAAAGCATTTCTTAAAACTTCAAATACCTGTAAGTTAAAAAAAAAAAAATCAATCAGTGGTACGTGCCTTGGTGGAAAAGCGCTGGCTAGAATTCCGATCCCAGTTCGTTTCCTTAGCTCATATGTGATTCTTGGGCAAGTTGTTCTCTTAACTTCTCTGAACTTCAGTTTTCTCTACTGTTAAATGGGAATACTAATGTCTGCCTCCCAGAATTATTGCCAGCAAATGTGATGATATTTGTGAAGGCATTCTGTCAACTAAAGCATTATGTAACAAGTTGTGCTATGCTGATAGGCCTGGGATTTTTACAAAACAGTCTGTCATAAGGGCCACATCATGAATCACCTAATAGATGGAATTGTCTTATAACAAGGCCCTCTTATCATTTCAGTAACTAACCCTCCTTCATAGCCCAAAGTGTCATAGCCATGTCCAGTACCAGGTCCTGACTCTCCTAGCAAGGAGTTTTGGGGCAGCATGACACAGGACTTCAACAGAAATTGCCGACACCAGTGCAAACTTGCATGTGTTTGCCTCTCCAGTTTCACAACTGATCTCAATCTTTTAAAACTCTGTTTCACAG
Seq C2 exon
CCAAATTTCTTGGGAATCAACAGGTGAGCTATGGTCAAAGCCTGTCCTTTGACTACCGTGTGGACAGAGGAGGCAGACACCCATCTGCCCATGATGTGATTCTGGAAGGTGCTGGTCTACGGATCACAGCTCCCTTGATGCCACTTGGCAAGACACTGCCTTGTGGGCTCACCAAGACTTACACATTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000058085-LAMC2:NM_005562:6
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.024 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0005213=Laminin_B=PU(51.9=64.8)
A:
NA
C2:
PF0005213=Laminin_B=FE(48.1=100)
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:
ATGTTGATGGCTGGAAGGCTG
R:
AATGTGTAAGTCTTGGTGAGCCC
Band lengths:
310-1233
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)