HsaINT0076571 @ hg19
Intron Retention
Gene
ENSG00000143341 | HMCN1
Description
hemicentin 1 [Source:HGNC Symbol;Acc:19194]
Coordinates
chr1:186157015-186160085:+
Coord C1 exon
chr1:186157015-186157141
Coord A exon
chr1:186157142-186158643
Coord C2 exon
chr1:186158644-186160085
Length
1502 bp
Sequences
Splice sites
5' ss Seq
AGGGTATGT
5' ss Score
8.34
3' ss Seq
GATATGTTTGTTGTCCTTAGGTT
3' ss Score
10.44
Exon sequences
Seq C1 exon
ATATCGATGAATGTCTGGAGCAGAATGTGCACTGTGGACCCAATCGCATGTGCTTCAACATGAGAGGAAGCTACCAGTGCATCGATACACCCTGTCCACCCAACTACCAACGGGATCCTGTTTCAGG
Seq A exon
GTATGTCTTGCCTTCTCATCCCAGACATGCTTTTGAAAATCCTTCCTCCCACTCCTTGACCAACATAAACTTTAGTCTCTTGTCATGTGTAACTCACAGGAAGTCACTAACTCCAGGAAGATGTGGGGTTACAGTAAGTATTCTCTTCAATGAATGGGCAAGAAATGAGCTCATCCTGCAGCAGCCACTGCCACCCAAGCTCACTCTTGGCTGCCAGTGTTGCCTGGAGCAGTCTTCCCAGAATATAACATGTAACATGGTGGGTTCTGCCTCAGCAGCAAGTGTTTGATGGAGTGATAGAGCCTGCCTTTCTTTAAAGTTTTTCATTTCTGTTGTGTTGCCTCAGGGTGGTAAGGGCTCTGCACACTTAGAGCCCACCATGAAGCATCTTTTCTGTTGCTTCACTGACTCACCGCTCCTTGAGAACGGAGATGAGTGAGGAATGAGTCAGTTGTCTGCCCGTTCATACATCATCTTGCTTATATTTCCTTCTGTCTGAAACAGGCTTTTCTGCATTCTGAATAAACTACCATTCTGTTTTCTCTCTCCCCTTCCAGAAATGTTGTACTCTATCCAGGTACCAAGTTAACAGGGTGATTGAAAACAAGTGATAATATTCCTCTTGGATAGGCCCTGCTAATAGGAAGGTGTTTCTGAAACCAAATACTGGCTGGAGCTCACTTTGTTTTCCTCTTGGTAATGCTTACCAAGTTACTGCAGCATAGTCAAGTGTGGACTGCCCAGAATCCACCAAAAACCTATCTGCAATTGGTCTGATGGGACATGGAATAGGAAGGAGAAAATTGAAAATACAGACTTAACAAAACCTCTAAAAATACTATTACTGAAGAATCCTATCTTCATAAAATGGTTCTCTGTGCATTTTTTCCCTTCTTTATTACCATCGGTTTCTGGCAAACAATTTAAAAGTCATCATGACTCAAAAAGCAGTCAGTGTGCACTCTGGTAAAAGAAAATAAAGCTTTTTAATCTACAATAATGTGAACGACAATTACAAAAGAAGTACCCCTTTCTCACCAGAAATCCTAATTGACCTTTTATTATTTTTAGAAAAAATGTCAATATATTTTGTTTCACCTTTTAAACAGTGTTAGGATACTATATAATTAAAAAGTAGCTTGTATTCCTCTTTAAGAAGTACTTGTTTCCAATATATATGCAGAAGCTCTTGTTTCCAAAACTGACTTTTCATTTTAAAGAAAATACTCTTGTGGCATTCATACTTACTTCAATGGCTCAGACACTTCTGCTTTTAATGGAGCTGCAAGATACGTATTTGACTTCACACCAGCATCTTCTCCTAGTCATCTGGTGTCTGGTTTGAGTTAGTGACACAGAAGACGACTGAGTCTTACCGCTTTTACAGCCAGGCTGCCTACTGCATGCAGTGCCTAAAAGTTGTCATGGATCATGATCACCTATATCATGCCTCCTCCTACTTCCAGATAACTATGTGTATTTGATATGTTTGTTGTCCTTAG
Seq C2 exon
GTTCTGCCTCAAGAACTGTCCACCCAATGATTTGGAATGTGCCTTGAGCCCATATGCCTTGGAATACAAACTCGTCTCCCTCCCATTTGGAATAGCCACCAATCAAGATTTAATCCGGCTGGTTGCATACACACAGGATGGAGTGATGCATCCCAGGACAACTTTCCTCATGGTAGATGAGGAACAGACTGTTCCTTTTGCCTTGAGGGATGAAAACCTGAAAGGAGTGGTGTATACAACACGACCACTACGAGAAGCAGAGACCTACCGCATGAGGGTCCGAGCCTCATCCTACAGTGCCAATGGGACCATTGAATATCAGACCACATTCATAGTTTATATAGCTGTGTCCGCCTATCCATACTAAGGAACTCTCCAAAGCCTATTCCACATATTTAAACCGCATTAATCATGGCAATCAAGCCCCCTTCCAGATTACTGTCTCTTGAACAGTTGCAATCTTGGCAGCTTGAAAATGGTGCTACACTCTGTTTTGTGTGCCTTCCTTGGTACTTCTGAGGTATTTTCATGATCCCACCATGGTCATATCTTGAAGTATGGTCTAGAAAAGTCCCTTATTATTTTATTTATTACACTGGAGCAGTTACTTCCCAAAGATTATTCTGAACATCTAACAGGACATATCAGTGATGGTTTACAGTAGTGTAGTACCTAAGATCATTTTCCTGAAAGCCAAACCAAACAACGAAAAACAAGAACAACTAATTCAGAATCAAATAGAGTTTTTGAGCATTTGACTATTTTTAGAATCATAAAATTAGTTACTAAGTATTTTGATCAAAGCTTATAAAATAACTTACGGAGATTTTTGTAAGTATTGATACATTATAATAGGACTTGCCTATTTTCATTTTTAAGAAGAAAAACACCACTCATTTTATAAAATATAGTACAGCTACTATAAGGCTTGTTTGATCCCAAATGGTGCTTATCTTGATTGAACATTCAGAACAAGGATATTATTTTCAGTGATTTTGTGAGATCAGCTGAACCACTTATGATAATAATAATAAAAAAGACTGCTTTGCCCTCACGTCAGTTGTACATGGCATGGAACTTTAAAAATTTTAATATAAACTTTCATCCAGTTAGCTTCATAACTTTTACGTTCCAGAATTTTGTTTATTTTCCTGTCAATGAAAGCAATTTTTAAAGATACCAGTGGGACAGATTTGGTTTTTTAAAAATCTCATGTGTTCAAATTAACATAAATATTACACGTCAATACACTGTACATGGTGGTAATAGACTCTAAGCAATTGCCAAGATGTATTCTATTTTTATGAAGTGTATATATATTACCTTAGTGTGCATTTTCTATATAATATCTTGATGGACTCTTTTATAAAATTATTTTATAAAAAACAATGTTACACTAAAATCAGCCTAAATAAATTTTCACAACTTTTTTTCATAACCTT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000143341-HMCN1:NM_031935:106
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF126622=cEGF=PD(12.5=7.0),PF129472=EGF_3=WD(100=83.7)
A:
NA
C2:
NO
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:
CCAGTGCATCGATACACCCTG
R:
CACTGTAGGATGAGGCTCGGA
Band lengths:
353-1855
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)