HsaINT0076642 @ hg19
Intron Retention
Gene
ENSG00000143341 | HMCN1
Description
hemicentin 1 [Source:HGNC Symbol;Acc:19194]
Coordinates
chr1:186084390-186086247:+
Coord C1 exon
chr1:186084390-186084546
Coord A exon
chr1:186084547-186086125
Coord C2 exon
chr1:186086126-186086247
Length
1579 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGG
5' ss Score
11.08
3' ss Seq
CTTTGAAATGTGTCTTCTAGGCT
3' ss Score
7.98
Exon sequences
Seq C1 exon
TTCCTCCATCTATTGCTCCGGGTCCTACCAACATGACTGTAATAGTAAATGTTCAAACTACTCTGGCTTGTGAGGCTACTGGGATACCAAAACCATCAATCAATTGGAGAAAAAATGGGCATCTTCTTAATGTGGATCAAAATCAGAACTCATACAG
Seq A exon
GTAAGGATAATTTAAAACTCCTACCAACTATTTACAAACAGTTTGTAATGAATCAACATTTTAATTCTATCAGTGGGGTCAGCAAATATATAGACTATAACAAATTAGCTAGCATATAGAGGGTTTTTTTCCTTAATATGGACTTAGTTTTTCAGCCTAAAATATTTTTCTGAATTATAGGTCATCTTTTCCATACATAAACCCTGTGGATGAATGTCAGTGATTATATATAGGATTAGATTTATATCCTGCCTTATTTGTTTAGTACCTTTTGGACTTTTATAAAGGCAAAGGATAAAAACATCATTTTATATAAAAGAAAAACTATTCTGTAAAAATAAATACGATCTTTAGTTGTAGAATAAAAGTCAAATTTTATACCTTAAAATACAATTTAGATATTGGCAGAATGTGTAGGGAGGAAAAACAGCATTTTCTCCATTTTTTTTTTTTGCTTTTTTCCAAGCTTTAATACCATAGCTCATAATATGGCAATATCTATTTTTCAAAGGCTAAACTTTAAATCACTAAGAATTTCTGATGTTATAGGTGAGCATCATTTTTTGTATCTCACCTGAGCTATCAGATTATTACTCTGTCAAACATTTGCCATAGCGCTAAAAATAAATGCTCTCTTATGTCCACTTTAACAAAAATCAATTCCAATACATCAGGAAATATAAAACTAGGAGTGCTGCAGTTGAAATTCTATCATGTCTCTTTTTCACCCTTTTAATCTTTTGGCATTGGGAGGTTCAGTGACTTGAAAGTATACACTGTATGGAAAATGTGCCATGCTTTTGAATTAAAAGGTGTGTCAAATATGTTTTATTAATGTTTTTTATTAAATCATTTCTATCATGCACAGTGTGAAATCAAATAGATATTCTAATTTAGATTTACTTTAAATCATGTATGTGTATTTACTAAACCTCCTAAAATGTGAAGTGTTCTAGATTTTAGTTTTGAATATATATACACACATACACACACTTGTTCAAAACTAAATATATATATATATACTTTTTTTGAAATAGATATTGCCATATTATCTACAAGGTAGCCACACATTTAAGGAGACATGCAAAGTACATAAAGGGGTGAGACACACAGACTTGTCATTAGCCATCTGTCAATGGAAATAAACAAATATCAACCTGCTAGGTTATTGTGAAATTTAAAGATAATTTATGCAAAGCATTTAAGATGGTGCCTGGAGTGTATCTGATGCCCAGTAAACAGTGGCTGTTATCAGTGTTCTCATTGTACTGTATTTCTCCTAGGAGAGCCAGGTTGATCATAATATAAGCATTTAGAGAATGTAAGATTCCCTCTTCAGACAATCCTTCCCACAATTACTTCCTGTAAATATTATATCAAGTTTGAGGCTCTAGAAAGCCACTGCCATACAAACATAAACTCTAATGCATAAAGTTGGCCTCAGGGACATGATGTTAATTTTAACATGAGGGAAGAGTACTGTTTTCATCAATTTACAACATGGTACCATGTTAAACTAGCTGGGAAAATTTATGAAAACCTACATATAGTATCTCATGCTTTGAAATGTGTCTTCTAG
Seq C2 exon
GCTCCTTTCTTCAGGTTCACTAGTAATTATTTCCCCTTCTGTGGATGACACTGCAACCTATGAATGTACTGTGACAAACGGTGCTGGAGATGATAAAAGAACTGTGGATCTCACTGTCCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000143341-HMCN1:NM_031935:75
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.094 A=NA C2=0.357
Domain overlap (PFAM):
C1:
PF0767911=I-set=PU(55.6=94.3)
A:
NA
C2:
PF0767911=I-set=PD(43.3=92.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCCTCCATCTATTGCTCCGGG
R:
GTGAGATCCACAGTTCTTTTATCAT
Band lengths:
270-1849
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)