HsaINT0076610 @ hg19
Intron Retention
Gene
ENSG00000143341 | HMCN1
Description
hemicentin 1 [Source:HGNC Symbol;Acc:19194]
Coordinates
chr1:186026366-186031096:+
Coord C1 exon
chr1:186026366-186026533
Coord A exon
chr1:186026534-186030982
Coord C2 exon
chr1:186030983-186031096
Length
4449 bp
Sequences
Splice sites
5' ss Seq
CAGGTATTA
5' ss Score
7.26
3' ss Seq
AAGATGGTTTGCTTCTGCAGGAG
3' ss Score
6.08
Exon sequences
Seq C1 exon
CTCCTCCAAGCATCATAGGAAACCACAGGTCACCTGAAAATATTAGTGTGGTAGAAAAGAACTCAGTATCTTTGACTTGTGAAGCTTCTGGAATTCCCCTGCCTTCCATAACCTGGTTCAAAGATGGGTGGCCTGTCAGCCTTAGCAATTCTGTGAGGATTCTTTCAG
Seq A exon
GTATTAGAAATTCTGGTAGCCTTATAATCTTGTTAGCTTCATACGGCTACAATTTCTCCTTAATTTCAAATTGCTCAGTGTTTTTATTGTTTTATTTTTTAACCTACTGCTTACTGTAATATTCACTAATCATATTAAGAAAAAATATTTAAAAGGATGTAAGAAACTATATGAAAATGAGAAATCTCCAAATATCTCTAGACCCCTTTAAAAAACAAATCTTGGCACTCGCTGATTACGACAGTCATGGAGATGTCAAAGCATTCATGCTACAGTGAGCATCCACCAATTTGAAAATAATTATAGGAAGTGCTGAAATTGAATTCAAATTCTACAGTGAATCCTAGTATATAAAATACTTCTATAACCAAATATTAATATTTCAATGTATTCATGACTAATCTCAATGATGTTTACATTTCTAAAATGGGTAGTTTCCTGTGAGCTAAGACTTTATTTTCAAGAGATATTGATCATATTCCTCATATAATTTTGTGGGAAAATCTAAATAGCTTGTCATTTGTGGATCAATATAAGCGTAGAGAGAGGCAAGCTGCAGAAATCTGCACTTGGCCCATTTTATTAATGACTTGGTTACAGACTAAGATAATCTTGCCAAGTTTTTGGTTAATAAAAAGCTTAGATACTTAGAAAAATACCTAATGTGTGATTGAAGGCATCAAAATTCAAACACACCTCATGCTGGAGCTTTTGGGTTAAAGCTAACAAGATGAAGGTTAAGTAAGGCTCATGATGGCCCTCTATATAATTATCTGATTATGCTAATTTATGATCTCTTTGCACTTACGGTCAAACCAGTTATGAACTTATGGTGAAGTATAGCTTCAGAACTCTTAATATGAAAAGATGTCTGAATTGTGTTAGTTTCTCAGTATGCATTAATACAATGCGATTATCAAGACAACAAATGTAATATTTTGCCACATCAATAAACTATATTTTCTCCAATAAGAAAAGCAAGAGATCGTGTGCACTATAAACTTAGCAGAACTTATTAGAAAGACAAGAAGAAAGGCTTAATGACAGTATTTGCAAAGGAAAATAACTATGATGGGAAATTATCACATAATGATTAATATGTCTGTATTTAACCTGGAAAAATAAATCTTGTGGTGTATTTGGTATCTAATCCAAAGTAAATTTAAATATTTGAAGAGCCATGGTGTAGAAAGGATTATGTTGTTTTTTTCTAGTTCCAGAGGTTAAAAGTAATGTCAGTATATGGAAGATTCTAGGGATAGATTTGTGTCTGAATATAAACAACTTAAAAGATTATTTAGCTTGCTTAAAATCAAGATGAGCTACTTTAAGTGGCAGTAAGCTCCCTTCACCTAAATGTGCTCAAAGTTTACATTACCACTACTGAAGGCATATTCAGAAAAGATTTTTTCCTAGTGCTGGAATTAGGTCTAAAAAACCTAAGTTCCCCCTGTTTCTTCCCGATCTTGGTTTATAACTGATAGGAGCTTGAGGAAGAATGTACATTACCATTAACCACATTTATTGTCTATAATACTCACTATATTTATGACCTCAGACTAGTTACTTAACTTTGCTAACTTCAGTTTGATAACTTGTAAAGCGATAATAATAGTATTTGCCTCAGGGTTTTTGTAAGGATGAAATGAGATACCTAAAACAGTTAACACAGCACTTGCTTCTATGGTAAGCATCCAATACCTATTTCTTGTTATTGTCATAGACAACCTGGTAAAAGGTTTGTGGTCTCCCTGTCCTGGGAAACTTTCCTATGTCCTTACTATGATGTTTTCACTTTGACAGGACTCTCAGTCTCTGTTGATCTTAAGAAATACATACTAATGACAAAGATTGTATTAAAATGTGGTTACCAAAGCCTAAACACATTATCTTCTTGGCTTGAAATTATATTCATCTTTCTGGCTTTTTAAAAAATGTTCACTTGCTAAGGAAGTAGGGACTCTTATTAAATATAGTAAGTGCAGCAGAGCTCCTGGAAGTGAAAAAGGCAAGCTAAAGTGATGTGCTCTAGCTTGTTACAAATTTACAGAAGTGGTGTTTTGGTTTTATTTATCTTTGTTGTGCTTGACTAGCAGCTGGAGATCCCTGAGTGAACACATGATAAGTATTTCACCTTGTGGTGCTGCCAAAGGAGTTATTCAGTTTAACAGTCTGAACATGTTGTGTTGTGCAATAGGTAAATGAGAATCGAATGGCATATGTCTTGCTTGGTCTTCAGTCTCCTGTACATGCCTATTTCATTAATATTAGTCCTCCTGAGAATTTAAGCATAGCTTTTCTAAAAGCAGTACTTTGGTGAAGACCCTATCATTGTTATGAAGTTATCTGCCAGAAACAGATAACTGTTATAAAAATTTAATAGGTACAAGAAACGTCTCCATATAAGTATAATTTACTGTCAGAACCCATTTTTGGTTTTCACTGGATTAAGCGAGAAGTCCATGAAAAAAGAGAAAAGGAGAATCGTGAAACTTATGAGGTTGACGTTTGTAGAGCCAGCAGTGATTCATAAAAGTTGTATTGCTTTAATACCTCTCAACTGGAATCATATTATGATCTCACTAATCTGAAGTGGCAGTGAGTGCTTGAATCCTTCCCTAATTGACATAAGTTTTTAAAGCATTTTTACTTTTTAAGTAAACAAAATTTCTGTTTACTTAAATTCAATTGGGAAAAAAAGGCTAAATTCAGGTAATTAGCTTTGTTTGTCTAAATAAGATACTACTAAGTTCACCTTTCAGTGGGTTTAGGGTGGGAAGGTTGCTTATAGAAAAAGTTCAATGTCAGCTTGTGTTTACATAAACAGAAAACAGATAGAATACCCCTGGGAAACCAGACCCAGGTGAACATTTACATGAAAATTTCATGTTAACCATTATACTGTTTTTAATTCAAATTCAGGGTGCTAAGCAAAAATATACCAGCTAGAAAATTATTACACAATCCAATAAATGACCTACTTTTTTGTTGGACCTTACTCCTCAAATGGTGCCCAGGACTTTGTTCTCTCAGTGTCTCTTAGTTCTCTGCAGGTTTTGTTTCATCTCATTTGTTGGCTCCTCTGCTTTTATCTTTAAATAGAGTTCTCCTCCAAATTACACCCCCAGTATATTAGAGTTTCACTTTCAGTCTACATACATTTCTTGGATGAATATTTCTTCAAACAAAATGTTACATAGATGTTCAAAATACAAAAAGAAGCAAAAGCAGTGTATCACTAGTGCATGAAGTGACCCCATAACATTTTATATAATGTAGGATTCCATGAAGCTTAATTGAAAGCTGGTAGTCTTCATTCTCCTATCTTCCTTATATTAGGTTGGTGCAAAAGTAATTGTGGTTTTTGCCATTGAAAGTAATGGTAATATATTGATGTCACCCAAATCTGGGTGTCTGGGCTGGTTGTCTTTCTGATATTCCCATATTACATGTTCAATGGAAAACTAGGACTCTTTTCCTAACCATCTGATCACAGGTGTCTTTCTAAGCACGAATCAGATCATAAGCCCTGTTTGTTTATACACTCCATAGTCTTTAGTGAGTGCAATAAAATCTAAATTCCTTAGCATAGCATTCATGGGCCCATACAATCTGGCCATACTCCATCTAGCCTCATCTCTTACCATTTTCTCCACCTGCTCTGCTTTTGATACCACTTCTCACACCTACTTTCTACCTCTATCTATCTCTTCATTCATACTCCACTCACAATAGCATCTGTATTAGTCTGTTCTCACACTACTGTAAAGAAATACTCGAGATTGGGTAATTTATAAAGGAGAGAGGTTTAATTGACTTACATTCTGCATGTCTGGGGAGGCCTCAGGAAACTTAAAATTATGGCAGAAGGGGAAGCAGGCACCTTCTTCACAAGGCGGCAGAAGAGAGAGTATGTGAAGGAAGACCTGTCAAACGCTTATGAAACCATCAGATCTTATGGCAACTCACTCACTATGATGAGAACAGCATGTGGGAAACCATTCCCATGATCAGGTCACCTCCACCAGGTCCCTCCCTTGACCTCCCACCAGGTCCCTCACCAGGGGATTATGGGGATTACAATTCGAGATGAGGTTTGGGTGGGGACACAGAGCCAAACTATATCAGCATCTCTCAACTCGTGTTAAAATATACTTATCTTTTAAGATCATATTCAAACATCACCTTCTCTGTGAAACAACATTTCTTGCTTGCTGTCACCTAACATTATATTTATTTTTTTATCTATTGAACTAGAAGATTTTTCTGAACTATTTTGTTTTATAGAAGTTTAAAATGTGATTTTTAAAAAAGCTTAACATAAATTCATTTTAAGGGCCTCTAAAGCATACTGATTAAATTTTTACCGAAATTGAGCATCACTTGGATGGCTTATAAAGTTTCATTTTTCTTTTTAAGTTATCTTAAAAAGATGGTTTGCTTCTGCAG
Seq C2 exon
GAGGCAGGATGCTACGGCTGATGCAGACCACAATGGAAGATGCTGGCCAATATACTTGCGTTGTAAGGAATGCAGCTGGTGAAGAAAGAAAAATCTTTGGGCTTTCAGTATTAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000143341-HMCN1:NM_031935:46
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.035 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0767911=I-set=PU(57.0=86.0)
A:
NA
C2:
PF0767911=I-set=PD(41.9=92.3)
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:
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)