HsaINT0076610 @ hg38
Intron Retention
Gene
ENSG00000143341 | HMCN1
Description
hemicentin 1 [Source:HGNC Symbol;Acc:HGNC:19194]
Coordinates
chr1:186057234-186061964:+
Coord C1 exon
chr1:186057234-186057401
Coord A exon
chr1:186057402-186061850
Coord C2 exon
chr1:186061851-186061964
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:ENST00000271588:46
Average complexity
IR
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
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