SEMA6A-AS1 (SEMA6A antisense RNA 1) - Rat Genome Database

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Gene: SEMA6A-AS1 (SEMA6A antisense RNA 1) Homo sapiens
Analyze
Symbol: SEMA6A-AS1
Name: SEMA6A antisense RNA 1
RGD ID: 8695026
HGNC Page HGNC:51110
Description: ASSOCIATED WITH Autism; autistic disorder; INTERACTS WITH acrylamide; aflatoxin B1; aristolochic acid A
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Previously known as: CTB-118N6.3
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh385116,447,498 - 116,471,673 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl5116,447,547 - 116,508,276 (+)EnsemblGRCh38hg38GRCh38
GRCh375115,783,194 - 115,807,369 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map5q23.1NCBI
HuRef5110,964,385 - 110,988,540 (+)NCBIHuRef
CHM1_15115,216,120 - 115,231,620 (+)NCBICHM1_1
T2T-CHM13v2.05116,959,951 - 116,984,105 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Phenotype Annotations     Click to see Annotation Detail View

Human Phenotype
Autism  (IAGP)
References

Genomics

Variants

.
Variants in SEMA6A-AS1
5 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 5q21.3-23.1(chr5:108585264-116815075)x1 copy number loss See cases [RCV000133813] Chr5:108585264..116815075 [GRCh38]
Chr5:107920965..116150771 [GRCh37]
Chr5:107948864..116178670 [NCBI36]
Chr5:5q21.3-23.1		 pathogenic
GRCh38/hg38 5q22.3-23.2(chr5:114707561-126507744)x1 copy number loss See cases [RCV000134895] Chr5:114707561..126507744 [GRCh38]
Chr5:114043258..125843436 [GRCh37]
Chr5:114071157..125871335 [NCBI36]
Chr5:5q22.3-23.2		 pathogenic
GRCh38/hg38 5q21.3-23.1(chr5:107002209-118025316)x1 copy number loss See cases [RCV000135699] Chr5:107002209..118025316 [GRCh38]
Chr5:106337910..117361011 [GRCh37]
Chr5:106365809..117388910 [NCBI36]
Chr5:5q21.3-23.1		 pathogenic
GRCh38/hg38 5q22.1-23.2(chr5:111463016-127193038)x1 copy number loss See cases [RCV000135549] Chr5:111463016..127193038 [GRCh38]
Chr5:110798714..126528730 [GRCh37]
Chr5:110826613..126556629 [NCBI36]
Chr5:5q22.1-23.2		 pathogenic
GRCh38/hg38 5q22.1-23.3(chr5:110687442-130103838)x1 copy number loss See cases [RCV000139235] Chr5:110687442..130103838 [GRCh38]
Chr5:110023143..129439531 [GRCh37]
Chr5:110051042..129467430 [NCBI36]
Chr5:5q22.1-23.3		 pathogenic|uncertain significance
GRCh38/hg38 5q14.3-23.3(chr5:90374606-128076423)x1 copy number loss See cases [RCV000139893] Chr5:90374606..128076423 [GRCh38]
Chr5:89670423..127412115 [GRCh37]
Chr5:89706179..127440014 [NCBI36]
Chr5:5q14.3-23.3		 pathogenic
GRCh38/hg38 5q14.3-23.1(chr5:92899734-119614119)x1 copy number loss See cases [RCV000141252] Chr5:92899734..119614119 [GRCh38]
Chr5:92235441..118949814 [GRCh37]
Chr5:92261197..118977713 [NCBI36]
Chr5:5q14.3-23.1		 pathogenic
GRCh38/hg38 5q22.2-23.1(chr5:112323517-117773507)x1 copy number loss See cases [RCV000140791] Chr5:112323517..117773507 [GRCh38]
Chr5:111659214..117109202 [GRCh37]
Chr5:111687113..117137101 [NCBI36]
Chr5:5q22.2-23.1		 pathogenic
GRCh38/hg38 5q21.3-23.2(chr5:108308463-125777797)x1 copy number loss See cases [RCV000143326] Chr5:108308463..125777797 [GRCh38]
Chr5:107644164..125113490 [GRCh37]
Chr5:107672063..125141389 [NCBI36]
Chr5:5q21.3-23.2		 pathogenic
GRCh38/hg38 5q14.3-31.1(chr5:91411708-131319563)x1 copy number loss See cases [RCV000143746] Chr5:91411708..131319563 [GRCh38]
Chr5:90707525..130655256 [GRCh37]
Chr5:90743281..130683155 [NCBI36]
Chr5:5q14.3-31.1		 pathogenic
GRCh38/hg38 5q21.3-33.2(chr5:106619588-156124387)x1 copy number loss See cases [RCV000053524] Chr5:106619588..156124387 [GRCh38]
Chr5:105955289..155551397 [GRCh37]
Chr5:105983188..155483975 [NCBI36]
Chr5:5q21.3-33.2		 pathogenic
Single allele duplication Autism [RCV000754292] Chr5:114046360..118610426 [GRCh38]
Chr5:5q22.3-23.1		 likely pathogenic
NM_020796.5(SEMA6A):c.1926C>A (p.His642Gln) single nucleotide variant not specified [RCV004300465] Chr5:116447780 [GRCh38]
Chr5:115783476 [GRCh37]
Chr5:5q23.1		 uncertain significance
NM_020796.5(SEMA6A):c.1816T>C (p.Trp606Arg) single nucleotide variant not specified [RCV004190714] Chr5:116467661 [GRCh38]
Chr5:115803357 [GRCh37]
Chr5:5q23.1		 uncertain significance
NM_020796.5(SEMA6A):c.1772C>T (p.Ser591Leu) single nucleotide variant not specified [RCV004088803] Chr5:116467705 [GRCh38]
Chr5:115803401 [GRCh37]
Chr5:5q23.1		 uncertain significance
NM_020796.5(SEMA6A):c.2086C>T (p.Arg696Trp) single nucleotide variant not specified [RCV004321921] Chr5:116447620 [GRCh38]
Chr5:115783316 [GRCh37]
Chr5:5q23.1		 uncertain significance
NM_020796.5(SEMA6A):c.1853C>A (p.Pro618His) single nucleotide variant not specified [RCV004336588] Chr5:116467624 [GRCh38]
Chr5:115803320 [GRCh37]
Chr5:5q23.1		 uncertain significance
NM_020796.5(SEMA6A):c.1897G>C (p.Val633Leu) single nucleotide variant not specified [RCV004450719] Chr5:116447809 [GRCh38]
Chr5:115783505 [GRCh37]
Chr5:5q23.1		 uncertain significance
NM_020796.5(SEMA6A):c.2030G>A (p.Arg677Gln) single nucleotide variant not specified [RCV004450720] Chr5:116447676 [GRCh38]
Chr5:115783372 [GRCh37]
Chr5:5q23.1		 uncertain significance
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:742
Count of miRNA genes:529
Interacting mature miRNAs:589
Transcripts:ENST00000507558, ENST00000508424, ENST00000508640, ENST00000510682, ENST00000512128, ENST00000514214
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system sensory system adipose tissue appendage entire extraembryonic component
High
Medium 2 1 25 1 14 2 18 4
Low 2233 1872 1575 487 1159 332 3858 1588 2363 306 1315 1443 159 1184 2361 4
Below cutoff 192 1091 137 126 737 123 479 603 1341 105 108 150 11 20 427

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000507558
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl5116,471,190 - 116,472,638 (+)Ensembl
RefSeq Acc Id: ENST00000508424
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl5116,447,603 - 116,471,673 (+)Ensembl
RefSeq Acc Id: ENST00000508640
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl5116,449,628 - 116,496,121 (+)Ensembl
RefSeq Acc Id: ENST00000510682
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl5116,449,624 - 116,508,276 (+)Ensembl
RefSeq Acc Id: ENST00000512128
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl5116,447,547 - 116,449,861 (+)Ensembl
RefSeq Acc Id: ENST00000514214
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl5116,449,730 - 116,499,154 (+)Ensembl
RefSeq Acc Id: NR_109879
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh385116,447,498 - 116,471,673 (+)NCBI
HuRef5110,964,385 - 110,988,540 (+)NCBI
CHM1_15115,215,901 - 115,240,059 (+)NCBI
T2T-CHM13v2.05116,959,951 - 116,984,105 (+)NCBI
Sequence:
Promoters
RGD ID:15095930
Promoter ID:EPDNEWNC_H773
Type:initiation region
Name:SEMA6A-AS1_1
Description:SEMA6A antisense RNA 1 [Source:HGNC Symbol;Acc:HGNC:51110]
SO ACC ID:SO:0000170
Source:EPDNEWNC (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.; Paired-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh385116,447,522 - 116,447,582EPDNEWNC

Additional Information

Database Acc Id Source(s)
COSMIC SEMA6A-AS1 COSMIC
Ensembl Genes ENSG00000248445 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000508424 ENTREZGENE
GTEx ENSG00000248445 GTEx
HGNC ID HGNC:51110 ENTREZGENE
Human Proteome Map SEMA6A-AS1 Human Proteome Map
NCBI Gene SEMA6A-AS1 ENTREZGENE
RNAcentral URS000075CF29 RNACentral