HsaINT0076667 @ hg38
Intron Retention
Gene
ENSG00000143341 | HMCN1
Description
hemicentin 1 [Source:HGNC Symbol;Acc:HGNC:19194]
Coordinates
chr1:186165111-186166303:+
Coord C1 exon
chr1:186165111-186165173
Coord A exon
chr1:186165174-186166183
Coord C2 exon
chr1:186166184-186166303
Length
1010 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGT
5' ss Score
10.65
3' ss Seq
CTTTTTGTTTCTTCTTTAAGATG
3' ss Score
9.38
Exon sequences
Seq C1 exon
GAGATCGCAGTAATCAGTGCCCCTCCGGGTTTACCTTAGACTCAGTTGGACCTTTTTGTGCTG
Seq A exon
GTAAGTACAGAGATAAATAAAGGGTTTTCTTTTAATGAAAATGTCAATATTGGATAGCATTTAATGGGTATCTATTGCCCTTTCACTAGGTATTTAATCTTCACAACAGTTCTGTAAACATCCCATTTGACAGCTAAGGAAATTGAGATGTAGAAAAGTCAAACTATGGAAAACCACTCAGCATCAAGTGGCAGAGCTGCATTTGAATTTAAGTTAATTCCAAAGCCCATGTTCTCTGAATTTGGCCACAGCCAACTGTGTCAGAGATAGTGACTAAGTATAGATGTGGAGTGAGCAGACAGACAATGCTATACTTTATCTGGTGGCTTGATTGCCGTGGCTGTGAGAGAGCCACAACATTAAGTCACCTAACCCTAGAATTAATCAGAGGACAGGCAGGATTGTGGACTTATGACTAATGATTAAACCAATTTTATCCCACCAAAGTACCAGCACAAGAGAGGTACAGATAACTGCTAAGTAAATGGCTTGAGGAGCTTACATTTACATACACAGTGCTTTTCTTTCATTGGTAGGCAATGTAATATAGTCTTGTGATAAAGAGGTGGTCTTTCCACTGCCCAGGCACAAATCACAGCCCTGCCAGTAATGACTTGTATGACCTTAAGCAATTTATGTAACTTCTTTTTTCCTCAGTTTTGTCCTGCAAAATAAGGATAGTAATAAAAATACTTATCTCCTAGGAATTCTGTGATGAAAGAGTTAAAGCAGGTAAAAGGCATTTAGAGCACAGTAGATGATAAATATATTTTAGCTATTATCATTGTTGTTTTAGGATATAATCTAACCATCTATTCACTATCAAGGATAACTCAGATGCCTCAAATTATTTTTATTCAGTGAATTCATTTTGTGGCACTTAAAGCATTTTCTATTATATTTGATTCAACTTCTTGGCCTCTATAAGCAGTTATTTTTACTGGCTTTAATAACTCCCAGAAAGTAAGGATTTTACATACTGATTTGGGCCTTTTTGTTTCTTCTTTAAG
Seq C2 exon
ATGAGGATGAATGTGCAGCAGGGAATCCCTGCTCCCATAGCTGCCACAATGCCATGGGGACTTACTACTGCTCCTGCCCTAAAGGCCTCACCATAGCTGCAGATGGAAGAACTTGTCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000143341:ENST00000271588:98
Average complexity
IR
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:
PF146701=FXa_inhibition=PU(4.9=9.1)
A:
NA
C2:
PF146701=FXa_inhibition=PD(92.7=92.7),PF0764510=EGF_CA=PU(0.1=0.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping 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:
AGATCGCAGTAATCAGTGCCC
R:
CTTGACAAGTTCTTCCATCTGCA
Band lengths:
182-1192
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