HsaINT0076569 @ hg19
Intron Retention
Gene
ENSG00000143341 | HMCN1
Description
hemicentin 1 [Source:HGNC Symbol;Acc:19194]
Coordinates
chr1:186147548-186151419:+
Coord C1 exon
chr1:186147548-186147898
Coord A exon
chr1:186147899-186151299
Coord C2 exon
chr1:186151300-186151419
Length
3401 bp
Sequences
Splice sites
5' ss Seq
TAGGTAAAT
5' ss Score
6.62
3' ss Seq
TCTGTCTTCTTCCTGAACAGATA
3' ss Score
10.8
Exon sequences
Seq C1 exon
ACATTAATGAATGTGAACAAGTGCCTAAACCTTGTGCACATCAGTGCTCCAACACCCCCGGCAGCTTCAAGTGTATCTGTCCACCAGGACAACATTTATTAGGGGACGGGAAATCTTGCGCTGGATTGGAGAGGCTGCCAAATTATGGCACTCAATACAGTAGCTATAACCTTGCACGGTTCTCCCCTGTGAGAAACAACTATCAACCTCAACAGCATTACAGACAGTACTCACATCTCTACAGCTCCTACTCAGAGTATAGAAACAGCAGAACATCTCTCTCCAGGACTAGAAGGACTATTAGGAAAACTTGCCCTGAAGGCTCTGAGGCAAGCCATGACACATGTGTAG
Seq A exon
GTAAATGTCAGCCATATTACATTTCCTTTCTGTGGGCTCTCTTACTGATCAAAGTATGTGTACAGCACCTGTGATTGTTTGAGTGCAGTGAACTACATCTGATCTCAAGTTCGGAATGACTCAAAATTTCAAGACATTTATTTTGGCACCTAAAACTATTACAGACTTGAGTCAAGTGAATTATGGATTTACATGTGGGCATTCTAATAATTTATTGTGTTATAGTCAGTTTCTTTTTGGTCACCCTGAAGGTGTTACTAAACTTAATACTAAATAGAAATAAATTTCAGTGGCATCCAGAATGTAGTTTATTTAAAAGAGGATGTAAATATTGCCACATAACGTAATGCCATCAGATTATGGCCACATCGGATTGATGGAAAAGCAGTGGTTTAAAAGTGAAAGTTTCAGCTTCTCGGTCGACTGCTTGTTCTGTATAACAACCAACATCCCATTGACTGTTGCTCCACAGTCCTCGTGGAATTGCTGTTTGATTATTGTGTATGTTTGTACGTCACTGAAAAGATAATATGAGTTGGGACAAAATTAAGTTGTTTCTATCACTCTGAAATATGTGCTTGCAGTATCTTTATCTAAATTCACAAGTCTATAATTCCATTTGTTTGCAAAAGTGAAGTATAATTTCCCACTTAAGAATTGAGACCTTGTTTTCAGTCGAGTTGCAAACATTACCATCTGTCACTCATTTAACTCAATTTTCTGTGAACATCTACAATTAGCATGTCATTGACCTACTCAAGGGGAATTAGCAAGCAGGAATTAGTTTTACTATTTGTTAGCTGGAAAAAATAAGCAAAGAAAGAACATAGGAGAGAAGTAAAGAGGGAGGGAAGAAACAAATTCCGTTTAAATTCAAAGCCCACTATGCCAGCCTCATTTTCTTACATTTCTGGAAAGCGTTCTACACTTTGCTTACTCTCTTAACTATGCTTTTTGCTAAACATTTTTTAAACATTTCTTCTCCTTCTATCTTCAATTTTTTTTGTTTCTTTTTCTACCCTTGCCCAAGCCCTGTTACTTCATTATTATCTTCTCAGATGGACTTCTTGGTCAACCTTAGGTGGATTCATCTTCCCATATCATCTCCACTCAGTTGGGCCCTCAGTCCCTCTGGACACTCAAACTTTACCCTTTGCTTTTTAGGTTCATATTTTTTCCAGCACTTTTCTGTCTTTTTTACCCTGATGTATCTGCAGCTTAATATAAGGGATGTGGAAACTTCTCCCTCGTGATTAGCTTACCAGAATTGTTGACAGTGCTCATTTCTTCTACCACCAAACATTAATGCATTAACAATTCTCTACATTTTGTCCCACGTGGTCAAATACTGTTTAATTGCTAAATATGTGGACTCCAGTATTCTTGCTAGTATATTAAACAACACTGTCAATCTGCTACAAACTGTTCTGAGTTTTGGGAAATTTTATGCCCACAATTTTGATCTGACTCTTCATTAAAGTTGTTCACTATTCTCTTATTGACAGAATTAACATCTGATATTTTGTCTTTCAAAGTTTCTTCCAAATAGTCATCCCCACTAGAGGGTTTTCACAGCCTAGGTAATAGGTTACCATCCCATTCTCAACCTTCATTTTAGACAAGCACTTTCTTTTGTTCTACCTTTACTTTCCTGCCCAAAAATCTGTGTTATGAAAAATAAATTTAGCCACACCCTCCACACTATACACCATTAGCTGGTTTCTTCCAAATTATCAGAAGGTCCAAGTTATTTTAAGAAAGCTTCCTGATTAATAACCCACTTCTCTACTTCTTCATCACTATCTATGGCTGCAGTTTCATCATAGTAGAGTCTTATAAATGTTTTCTGTCTTCCGTTTATGTTAAACCAATGTTATGTTATCACAATCGTCTTCCTCAGACAGTCATCTGCTATTTGAGGCAGCCACTCTTTCACAGTAAGGGTCAATCTTGGAGAATCTAAAGTAAAAATTTATAGCTAGTCCATTACTGGATATTTAAGTTTCTTTGGAGGCAATTCATAGGCTTAAACATTTCTTAAAATATGGTATTTTATAGTATTGGGACTAATGAAGAAATATACAGTAAGACTGCCTACAGCTTTGGTATTACACAACAAGACCAACTTGCAATAAGCACCAAATGCTTTTAATGAACTATCTGGGACAGACAAGTTATAAAAGATTCAAATTAACACTATGAAATCTTGTTAGGCTTGGGCTAAAGTTTAGTTTTTGAAGAAATTGATTCTAAAGCATAACAGGAAAAATGACCATTGCATTGCTTCTGAATGCAGAAATCACACTTGGGGGTAGTGTAAAATTCATGCTTGGGAAAGCTCTGTGCTAACAACTTGGAGTTCAACATCATTTACATTTCTGTTATTTTAGGTTAAAGCTGATTTTAAAGGAAAGAAGTAAAAACTCACACAAGTCATAGAATCAACACTTTGGTTAACTAGTCTTCCACTGGTTGGTGTATGCTCAGAGACTATGAGCAAATTTTAATTTTAGTTAAAGCAAAACACCACTGGGACAAGAAATCTTCAGCCTCCCAAATCACATACTTTATCCTTAAAGCAAATATCAATTAATTTTGAATTATCATCTATTCTCACCCTCCTTTTTTTGCCATTTTCATGGCTTTGTTTAATAATAGCAGATAGCCCTTTATAGACTACTTTCCCACATATTACTGTATATGAACCTTTCAACAAAACTGTGAAGTAGGGCAGATGGTCTCAAGTGTCCCTTTTAACAGAAGAATAAATGAGATCTTGAGAAGTTAAATGGCCTGCCAAAGGTAACACAACTATATATGTATGTACTTGTCATTAGTACGTTTGAATTGTATAAAAAAAGAGTATTTTTGTCACAAAAATAAAAAACATTTCCATGTGATATCTGTGTATGGGAAAGCTATGCATGAGTGGGGCTGCAGGGAGAGAGAAAGAGAGCCAAAGTTTAAATACAATAAAAACAAATAGTCCTTTTTGCAAGTAATCTCAATAGGAATATTGTATTTCAGGTAATTTCTACTATTCCTTAAAGAGTTTCATATTTTGGTGGTTTAGGATCCTGTCTACATTTGTTTCCTCTGTCATGTCACTCTTACTTAAGTAATATAAAAATTGACCCGTTTGGGACTTCAGCATATATGTGCTTACACAAAGAAATGTCCATAATTTGTAATATAGTACTGTGTATATAGTACTATATTCAGTATTTTTATAACATAAAAGTATCTTCATAGAAAATAGCTCTGAGCATTTTTTAACACATGAGTATAAAATCACCAAGAAGTTTTTCTAATGTATATCAACAACTTGATGAGAGTTGGCTCTGTCACAGTGTCTGCTTTTTTCTTGTGTAGTGATAACTCTCTGTCTTCTTCCTGAACAG
Seq C2 exon
ATATTGATGAATGTGAAAATACAGATGCCTGCCAGCATGAGTGTAAGAATACCTTTGGAAGTTATCAGTGCATCTGCCCACCTGGCTATCAACTCACACACAATGGAAAGACATGCCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000143341-HMCN1:NM_031935:104
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.034 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0764510=EGF_CA=WD(100=33.9)
A:
NA
C2:
PF126622=cEGF=PU(83.3=48.8)
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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
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)