HsaINT0076664 @ hg19
Intron Retention
Gene
ENSG00000143341 | HMCN1
Description
hemicentin 1 [Source:HGNC Symbol;Acc:19194]
Coordinates
chr1:186120738-186122003:+
Coord C1 exon
chr1:186120738-186120875
Coord A exon
chr1:186120876-186121881
Coord C2 exon
chr1:186121882-186122003
Length
1006 bp
Sequences
Splice sites
5' ss Seq
CTGGTTAGT
5' ss Score
6.32
3' ss Seq
GAATGTCTTGTAATTCCCAGGAG
3' ss Score
5.61
Exon sequences
Seq C1 exon
GTTCAGCAATGAGAAAGATAGTTTCTATTCTAAATCCCATTTATTGGACAACAGCAAAGGAAATAGGAGAAGCAGTCAATGGCTTTACCCTCACCAATGCAGTCTTCAAAAGAGAAACTCAAGTGGAATTTGCAACTG
Seq A exon
GTTAGTGTCAGCTGAATTTAATATTCTATTACTATAAAAAGTGCCATGAAGATAGGTGATTAAGAAAAATACGTGTTCCCACATAGAATAATTTGAAACTTTTTACGCAATCTTATAAGTGATATAAAAGCAATTTCATGTTTTCCTGTAAACTTGTACTAACATAAGATCATAAGAGGTCATGTGTTCTCAAGCAGTCATTTTATACCCTAAAAGTTTTTCTCCTCTCCTCTTTTCTTCTTTTTAAAAATATTTTCTCTTTAAATCCATAGAGAGGATATTAAAGACCAAACAAAGAAGGAAAATGAGTTACTGTTATTAATTAAAGACCTTCTTTGTCTTTAAACCAAGATCCAATTAGGATACTTTATAGCAGTTCTTTATGAAAAAGATAGAAACAAAGCAAACCTAAAGGCTTTTCACTCATCCCTAGTCTTAAGGAGTATGGGTTAGCTATTCATGACCCTTTCCATGTACATACAGATGTTTAGAGAGCTCCATTTCAAGCCTCTTCACAGTTGGTCAGCCTCAATAGCAGTGACCTTTAAGGAAGAGGGGCTTGAGGACGGCTTATCTTTAATCAACATTTAATCAGTGGAGAAGACAATTGGTTCTTTTCATGGGCATCCACTTACTCAGATGTCCTTTGTTACTTTTTGAAGCATCAGAAAGAACAAAGCACTGTGGCCAGACTAGTGGTTTTTGCCAGTCACAGACAATTCATTTTTATAAGAGTGCTTTGTTATTGCCTGTGAATTTAAAGTATGAAATTCGTGTAACCGTTTGCCACATTTTTGCTACATAAAAAGAAATGTTAAAAGAAACTGAATTCAATAAACCTAACTCTTTAATTGGGAGGTTAAGTGCTATTTCAGTTCTCATCATCTATACTTATTCAAGTTTGAACTCAAAAAGCATAGCTGAACTGGTATGTAAGGTAAATCTGCTCTGTGCTTACAGAAACCATATTTTTTTGCTGTCAAAATGAATGTCTTGTAATTCCCAG
Seq C2 exon
GAGAAATCTTGCAGATGAGTCATATTGCCCGGGGCTTGGATTCCGATGGTTCTTTGCTGCTAGATATCGTTGTGAGTGGCTATGTCCTACAGCTTCAGTCACCTGCTGAAGTCACTGTAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000143341-HMCN1:NM_031935:95
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:
PF074747=G2F=FE(24.5=100)
A:
NA
C2:
PF074747=G2F=FE(21.3=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:
CATTTATTGGACAACAGCAAAGGA
R:
TTTACAGTGACTTCAGCAGGTGAC
Band lengths:
222-1228
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)