HsaINT0076656 @ hg19
Intron Retention
Gene
ENSG00000143341 | HMCN1
Description
hemicentin 1 [Source:HGNC Symbol;Acc:19194]
Coordinates
chr1:186106630-186107104:+
Coord C1 exon
chr1:186106630-186106800
Coord A exon
chr1:186106801-186106933
Coord C2 exon
chr1:186106934-186107104
Length
133 bp
Sequences
Splice sites
5' ss Seq
CAGGTACAC
5' ss Score
7.29
3' ss Seq
AATGGTTCACCTTTGTATAGTGG
3' ss Score
3.31
Exon sequences
Seq C1 exon
TTCATGGTGGATTTTCCCAGTGGTCTGCATGGAGAGCCTGCAGTGTCACCTGTGGAAAAGGCATCCAAAAGAGGAGTCGTCTGTGCAACCAGCCCCTTCCAGCCAATGGTGGGAAGCCCTGCCAAGGTTCAGATTTGGAAATGCGAAACTGTCAAAATAAGCCTTGTCCAG
Seq A exon
GTACACCTCCTTATTTAACTGATAGGCATGTGTTTAATAGACCTTCATTTCTGTCTTCTACCTATGGATTGCCCCAGTGTAAGTATTCCCAATTGAAATATACCTGATGGTGTAATGGTTCACCTTTGTATAG
Seq C2 exon
TGGATGGTAGCTGGTCGGAATGGAGTCTTTGGGAAGAATGCACAAGGAGCTGTGGACGCGGCAACCAAACCAGGACCAGGACTTGCAATAATCCATCAGTTCAGCATGGTGGGCGGCCATGTGAAGGGAATGCTGTGGAAATAATTATGTGCAACATTAGGCCTTGCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000143341-HMCN1:NM_031935:88
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.017 A=NA C2=0.034
Domain overlap (PFAM):
C1:
PF0009014=TSP_1=WD(100=87.9)
A:
NA
C2:
PF0009014=TSP_1=WD(100=87.9)
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:
TTTTCCCAGTGGTCTGCATGG
R:
GTCCTGGTCCTGGTTTGGTTG
Band lengths:
242-375
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)