HsaINT0076566 @ hg19
Intron Retention
Gene
ENSG00000143341 | HMCN1
Description
hemicentin 1 [Source:HGNC Symbol;Acc:19194]
Coordinates
chr1:186140469-186141263:+
Coord C1 exon
chr1:186140469-186140582
Coord A exon
chr1:186140583-186141137
Coord C2 exon
chr1:186141138-186141263
Length
555 bp
Sequences
Splice sites
5' ss Seq
TGGGTAAGA
5' ss Score
8.91
3' ss Seq
ACCTTTGTTCTTTTATCAAGATG
3' ss Score
6.8
Exon sequences
Seq C1 exon
ATATTAATGAATGTCAAGAATCCAGCCCCTGTCACCAGCGCTGTTTCAATGCCATAGGAAGTTTCCATTGTGGATGTGAACCTGGGTATCAGCTCAAAGGCAGAAAATGCATGG
Seq A exon
GTAAGAAAAGGGCTTTGAATTTAAAGGAATGACACCTCTATAACTTCTTAATGATGTCTGATCTAAATGCATACACTGTGTCTTGGTACTGGTTCCTATATAGGACATCAAGCATGCAGCATGTATGCAATCCATGCAAAACCAAAATGACAAAAAATGCTGTTTTATGAGTTTCTTTTTCTAATTACATACCCATTCTTCATAACATTTCCTCTAATATTTTTGCAAAAGTATATCTATACATATAAATATATGTATGTACATATATATGTATACAAATGAAGTTAGTATATATAAATTTTATTTTTCTAAGAGGAGAAAATGATTGGTATGGCTACCTGCTCTGTAAAACAATATTTTGTGTTTGTTTTTGATTTTTATTATATTTTAAAGTGTGTTACATACATTGTTGAATTTAAGCACTTTAACCTTACACAATGATTATGCAATGAATGTATATATAAATAATATCCCTAAAATCCAAAAGTATGATTTCTCTGGAAAAGTTGAATAAATAATTTTCTTAATCTACATTACCTTTGTTCTTTTATCAAG
Seq C2 exon
ATGTGAACGAGTGTAGACAAAATGTATGCAGACCAGATCAGCACTGTAAGAACACCCGTGGTGGCTATAAGTGCATTGATCTTTGTCCAAATGGAATGACCAAGGCAGAAAATGGAACCTGTATTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000143341-HMCN1:NM_031935:101
Average complexity
IR-C
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:
PF0764510=EGF_CA=WD(100=94.9),PF0764510=EGF_CA=PU(0.1=0.0)
A:
NA
C2:
PF0764510=EGF_CA=WD(100=95.3),PF0764510=EGF_CA=PU(0.1=0.0)
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:
ATTAATGAATGTCAAGAATCCAGCCC
R:
CAATACAGGTTCCATTTTCTGCCT
Band lengths:
238-793
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)