HsaINT0076637 @ hg38
Intron Retention
Gene
ENSG00000143341 | HMCN1
Description
hemicentin 1 [Source:HGNC Symbol;Acc:HGNC:19194]
Coordinates
chr1:186106884-186108597:+
Coord C1 exon
chr1:186106884-186106965
Coord A exon
chr1:186106966-186108460
Coord C2 exon
chr1:186108461-186108597
Length
1495 bp
Sequences
Splice sites
5' ss Seq
ATGGTAAAT
5' ss Score
6.41
3' ss Seq
GTATTTGTTCTCACACCCAGTAC
3' ss Score
5.99
Exon sequences
Seq C1 exon
GTGGAGGATACAGGAAGATATACATGTCTGGCATCCAGTCCTGCAGGAGATGATGATAAGGAATATCTAGTGAGAGTGCATG
Seq A exon
GTAAATTTGACAAAATATCCTACAGTCTATCATACACACACCTAATTAGAAAACCCTGGGACAACACCACAGCACATCACAGGATATGTTTATAAGTTAGGGAATATATATTTTGCAAATCTGAATCTTTTTTTTTTTGAGACGGAGTCTCGCTTTGTCGCCCAGGCTGGAGTGCAGTGGCACTATCTCGGCTCACTGCAAGCTCCGCCTCCTGGGTTCACGCCATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGACTACAGGTGCCTGCCACCACGCCCGGCTAATTTTTTGTATTTTTGGTTGAGACAGGGTGCAAATCTGATTCTTATATTTGACTAATCAAACGCTGTTGGGGGGCAGTTCATGGATTGTTTTTGAGTTATTTGATTAGTTTCTGCATTAATAATTTGTATTCATTGGTTTAAAATAATAGAATATAAACTATGATGAAGAAAATTTAAAAATCCAGAATCTCATCACACAAAGACTTTTTTGCATATAAATGTTTTGTCACAAAAATATGATGATAGAAAATGCATGTTTATATAGTGTACCTATAGAATTTAACTTGCTTTTATCTCAATGGTTTGGTGAACATTTTCATGTCAAGAAATACATTTTAAAAACATTTTTAGTGACTGTATAGTATCCCATTTTACTCCATATTTTTGGAGGTTTAGGCTATTTCTATATTTTTACCAATATAAACAGCCCTGCTATGGATAACTTTGCATGCACATGTTAGCCCATTCCCTTTATTTTGAGAAATTTCTGTAAGTGCACTTGCTTGGTTACACACACACACACACATACAAACACACTCACTCTTCTAAGGATTTTGAAACTAATTGTCAAATTACTTCCTAGAAGAGTTGGGCCAGTTAGACTCGTCCAATATGCTTTTGACATTGAAATAGGAATTATTCTTTATGGGGAGGAATAATTAAAAAACTAACAGAAGATCTTTGGTTCATTCTCATAGCCTAAATGACTAGGCAGCGCAAACTGTCTGGGATTTAAGTGCCCCCATCATCCCACATACAAATTAATTGACACGTAAATTCTGTAAAAAAAAAAAAAAAAAAAAAAAAGTCACATGAAAAATACAGTCTGTATATTATGATGGGCACTCCCTGATTTAGTAATTTTTAAATCTTATGTTCAGAGAAAATTACTACCAAGTGTATAACCCGGACAACGGCTCCCTTCTTTGTGCCTCCATTTCTTTACTATCAAATGGTGAAAATAATGCAATTATATTACTTCCATCATGCATGTAGTTGTTGGAAGGATTTCTTTACTTAGTGTACATGAAATTGCTAAATAAGGTTAAAAAAAAAACACTTCCCACTGTTTGTAATTATCTAGGCTATAAATTAAATGAGTAATGTTTTAATTTTATGCCTCTTATTATTTCATATAGCAGAACCAACATTTTTTGGATACCTATGATAATACAGATTGCTTTTGTTGTATTTGTTCTCACACCCAG
Seq C2 exon
TACCTCCTAATATTGCTGGAACTGATGAGCCCCGGGATATCACTGTGTTACGGAACAGACAAGTGACATTGGAATGCAAGTCAGATGCAGTGCCCCCACCTGTAATTACTTGGCTCAGAAATGGAGAACGGTTACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000143341:ENST00000271588:70
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.393 A=NA C2=0.196
Domain overlap (PFAM):
C1:
PF0767911=I-set=PD(29.1=89.3)
A:
NA
C2:
PF0767911=I-set=PU(46.0=87.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTGGAGGATACAGGAAGATATACATG
R:
ACCGTTCTCCATTTCTGAGCC
Band lengths:
214-1709
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