HsaINT0076656 @ hg38
Intron Retention
Gene
ENSG00000143341 | HMCN1
Description
hemicentin 1 [Source:HGNC Symbol;Acc:HGNC:19194]
Coordinates
chr1:186137498-186137972:+
Coord C1 exon
chr1:186137498-186137668
Coord A exon
chr1:186137669-186137801
Coord C2 exon
chr1:186137802-186137972
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:ENST00000271588:88
Average complexity
IR
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
Other Skipping 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