HsaINT0076574 @ hg19
Intron Retention
Gene
ENSG00000143341 | HMCN1
Description
hemicentin 1 [Source:HGNC Symbol;Acc:19194]
Coordinates
chr1:185932900-185935047:+
Coord C1 exon
chr1:185932900-185933027
Coord A exon
chr1:185933028-185934933
Coord C2 exon
chr1:185934934-185935047
Length
1906 bp
Sequences
Splice sites
5' ss Seq
TTGGCAAGT
5' ss Score
2.72
3' ss Seq
TGCGTTTTTGTTTTTTTCAGAAG
3' ss Score
10.37
Exon sequences
Seq C1 exon
GTATAGGATGACCTCAGATGGTACCTTATTTATCAAAAATGCAGCTCCCAAAGATGCAGGGATCTATGGTTGCCTAGCAAGTAATTCAGCTGGAACAGATAAACAGAATTCTACTCTCAGATACATTG
Seq A exon
GCAAGTATAATCACTTTAAAAGGCAATTAAAATAGGATGAATATCACATCAAGCAATGCAAAAGTACTTTTTTGAAATATTAATATTAGTAATGCATACATGGTATTATACTTTATTATTCATTTCACACACTGATTGAAGCAAATATTGTAACCAATTTAAGTTAAAAGTTCATAGAGTGAAAAGCTTCATTAGTCAACAGAAATCAAGGAAGCTTCCAGGTTATGGAATAATTTCATATTGTCCACAAAGTTCTATCTTTCCACTGTTCATCTGTTCTCTGCAATATTTTACTTTTAAATTAATAAATTCTATTTCCTTTCTAGCTTAACTTCCATTTTATAATTTCTACTTATATTAAAAACTGTGTATAATATAATTTTTACTTTTTATCTTCAATTTCCCTCTCCAAACTTAAACATTTATTGGAAGCGTACTTCATGAAAATTATTCTACAGAATATTTCTATTTAATTTTGTCTTTCTTAGTCAAATAAAGGATAAAGGAATAATATACTCAGATCCAGGTTATAAATCGTGAATAATCAATGGCTAGCAGTCCACCCTTTCATTCATTCTTATTCAGTCTCATTCACAGTAAGATAATGAAACTGTCAGTAGAGAAGCAAGGATTCAAAAGAGATAATAAAGATAGAGAATTGTACTTGAAGGTATAGGTGAGGGAGAGAACCAAAATGTCACAAGTATTGAATTGAGAGCCTGGAAAGAAGTGGTCTCATAATTTACATAATGGGGGTGGATATATACGGAAATATAACAAGGCAGACAGACAAGTACTACAGTGGGAGGTTGGCAGAGGGGAAGACTAATTCAGACGGAGGAATTAGCAAAGATTTCTCAAAGGAGACAGGATTTAGGCTCAGTCTGGAGGAATGAGTGGGATTTGAAAGGTTGTGGCAAAGGGCATTTTAGAAAGAGGAAATAGCTTTAGGAAAGGCAAAGAAGACAGGAGAGTAAAAGTCTGTTGTATTTTGGGCTATCAGTGAAGCTCTGTACCTTGTGATAAGTGAGGAACTGTAACAGGGTAAGGTTAAAAAAAAAGCTATGCACCCATTTATAATTTTTGAAAGAGAGTCTATGGAATTTTGAAGGCAGTAGGAATCACTGAAGGTATTCTAGCAGAGAAATTACATGATCTGTGAGAAGTTAACTTAGCTTTGTTTAAAAATACCTCAGCTGAAGCTAGGAAGTCCTAAAATATCTCGTTAAGAGAAAATGTTTAAGTAAACTGAACCATTGGGCAAGCAAGTGAAGCAAACGGAGTGAAGAACAGAAATTTAGAGAATGTCTATATTTAGCATCACAGGGAAAAGAAGGGTCAAAACCAGGAGACTCTACTTTTTGTAAATGCAAATTTTAGGCTTGGACTGCAAATATCTTCCTGTAGTTAGACATGAATATCCTTAAAATGACGTAGAAAATGTTAACAAATTCATCTACGGTTGTATCATCCTCAAGTCTTAATTTAGCTGTCAGTCTTACCATTATCCCTCTTTTGACTATATTTTTCTTAGAATTATTCCTCTCTCTGTTCTTTTAGTATTGTTTCTCTAAGATGTATTCTGATTTCTAAGATGTTTCTTTCCTTGTATAACTCTTTTTCATAAAGAACTTTCGATTAGTTTCCTAAATTTTTTGGAGTTTATGATAATTATTTTTTGTTTTAGTCATTATTTTTTTCCTGATATCATTTCTTTGACCTTGATAAATGATCTTTTTATCACATACACCTATGTGCATGTGCATTACAAGAGTTTCTTTCGGTTTATAAATATTGAAATGGCCACAAGCACATAAATTTTTAAATTGGTTCATTTAGTAAACATAAACAAAATCCATCTGGTCTTGTGCTAAATGTTGACTATTTGCGTTTTTGTTTTTTTCAG
Seq C2 exon
AAGCCCCTAAGTTGATGGTAGTTCAGAGTGAGCTCTTGGTTGCCCTTGGGGATATAACCGTTATGGAATGCAAAACCTCTGGTATTCCTCCACCTCAAGTTAAATGGTTCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000143341-HMCN1:NM_031935:13
Average complexity
IR-S
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:
PF0767911=I-set=PD(46.5=90.9)
A:
NA
C2:
PF0767911=I-set=PU(40.9=92.3)
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:
AGGATGACCTCAGATGGTACCT
R:
CTTTGAACCATTTAACTTGAGGTGGA
Band lengths:
238-2144
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)