HsaINT0076609 @ hg19
Intron Retention
Gene
ENSG00000143341 | HMCN1
Description
hemicentin 1 [Source:HGNC Symbol;Acc:19194]
Coordinates
chr1:186024525-186026533:+
Coord C1 exon
chr1:186024525-186024806
Coord A exon
chr1:186024807-186026365
Coord C2 exon
chr1:186026366-186026533
Length
1559 bp
Sequences
Splice sites
5' ss Seq
ATGGTAAGT
5' ss Score
11.01
3' ss Seq
TGTTTTATTTTGTCTTACAGCTC
3' ss Score
11.66
Exon sequences
Seq C1 exon
TTAGACCAACCATAACCAACAGTGGCAGCCACCCTACTGAAATTATTGTGACCCGAGGGAAGAGTATCTCCTTGGAGTGTGAGGTGCAGGGTATTCCACCACCAACAGTGACCTGGATGAAAGATGGCCACCCCTTGATCAAGGCAAAGGGAGTAGAAATACTGGATGAAGGTCACATCCTTCAGCTGAAGAACATTCATGTATCTGACACAGGCCGTTATGTGTGTGTTGCTGTGAATGTAGCAGGAATGACTGACAAAAAATATGACTTAAGTGTCCATG
Seq A exon
GTAAGTAGAAAGAGGCTCAATATGTCCATTCACTGGCTAACGTAATCTAGCATCCTGGATGGGAGATATAGGCCTCAAGTACTGAAAGTCATTTATTTATAACCCATCATTTTAAACATATATACCTTTTCCCCAGGTCAGTCTCATCATTTATCCTTCTATGCCTGACCTCACATTATTTACCTTGCTGAAATAAGCGCATATTAGATATTCTTTAAGGAAAGCACACAGTAAAGTAGAAAATTGTTGTCTTCAAATGCTTTTGGTCCAATGCTATCCCAAGTAAAATCTGTTTTTTATGTTTTCCAAATTTGCTGACTTAACTGGGCTTGTATAAACGTAAGCTCCTTAGAATTTACTGACTCACCATCAGTTGAGCATGAGTTATACTGAAGTCAGCTTTAATATTCTAATTCTAATTAATAAGTCATAAATGTCAATAAGAATAGACCAAACATACACATACACAGGGACAATGACTTAGATGTGTACAATTTGAACTATAATTTTTATAGCTATAGGAACAATGGTAAATTTAATGGACACAAATCTTGTAATTTCAACTCAGTTAAGACATGCATGAAGCTCAGTGTTAATATCTTGCAGTTTGCAGCCAACGTGTGTGCCAAAGCTATAGGAATCACAACACAAAAGGGAAGATGAATTAATCTTAAGTTCTTTTTGTTGGATTACTCTTAATTTTTAGAATTAGATGATTGATTTTTTAGGAAATCTTTTCCTATAAGTAGGTTATGAATCCATATTACAAATTTGCAAGAAAAGATGAGTGATTCATATTCACAGTAGCAAAGACATAGAATCAGCCTAGGTGCTGATTAATAAATGGTGGATTGGATAAAGAAAATGTGGTACATATGCACCATGGAATACTACACAGCCAAAACTCATGTCCTTTGCAGCAACATGAATGCAGTTGGAGACCATAATCATAAGTGAATTAATGCAGGAATGGAAAATCAGATGCCTCATGTTCTCACTTATAAGTGGGAACTAAACATTGGGTACTCAAAGACATAAAGATGGCAACAGTAGACACTGGGGACTACTGAAGGGGAAGGAGAAAAGGAGGCAGGAGTTCAAAAACTAACTCTTGGGTTCTATGCTTACCACCTACGTGACAGGATCAATCATACCCCAAGCCTCAGCATCACAGAATATACCCATGTAACAAACCTGCACATGAATCCCCTTAATCTAAAATGAAAGTTGAAATTGCAATTAAAAAAAAGGGGGCGAGTGACTCATACAACATCACTCACCACTATTGGAATAACAATATGAAAATAATTTACTGCTAAGATTGAGGAAGAAGTGACATTTTTACTTCCAGGAATGTCACACACACACACACACACACACACACACACACACAGCTGGTTGTTGTGATTGCTTATTTTGCTTACTATTAATCAGAAAATGGAAGTCTTATTAACATACACTGTTTAGGATTTGATGTTTGATATACAACATCAGGTATATCAAATGTATATCAGGCAACTAATATTTCCATTCCCTGTTTGTTTTATTTTGTCTTACAG
Seq C2 exon
CTCCTCCAAGCATCATAGGAAACCACAGGTCACCTGAAAATATTAGTGTGGTAGAAAAGAACTCAGTATCTTTGACTTGTGAAGCTTCTGGAATTCCCCTGCCTTCCATAACCTGGTTCAAAGATGGGTGGCCTGTCAGCCTTAGCAATTCTGTGAGGATTCTTTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000143341-HMCN1:NM_031935:45
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.011 A=NA C2=0.035
Domain overlap (PFAM):
C1:
PF0767911=I-set=WD(100=90.5)
A:
NA
C2:
PF0767911=I-set=PU(57.0=86.0)
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:
ATTGTGACCCGAGGGAAGAGT
R:
AGGTTATGGAAGGCAGGGGAA
Band lengths:
352-1911
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)