SEPTIN4-AS1 (SEPTIN4 antisense RNA 1) - Rat Genome Database

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Gene: SEPTIN4-AS1 (SEPTIN4 antisense RNA 1) Homo sapiens
Analyze
Symbol: SEPTIN4-AS1
Name: SEPTIN4 antisense RNA 1
RGD ID: 9587927
HGNC Page HGNC:51345
Description: ASSOCIATED WITH genetic disease; INTERACTS WITH propofol; silicon dioxide
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Previously known as: SEPT4 antisense RNA 1; SEPT4-AS1
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381758,519,837 - 58,556,925 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1758,519,837 - 58,557,799 (+)EnsemblGRCh38hg38GRCh38
GRCh371756,597,198 - 56,634,286 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map17q22NCBI
HuRef1751,963,373 - 51,994,574 (+)NCBIHuRef
CHM1_11756,668,629 - 56,699,815 (+)NCBICHM1_1
T2T-CHM13v2.01759,387,708 - 59,424,795 (+)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
References

References - curated
# Reference Title Reference Citation
1. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
Additional References at PubMed
PMID:15851553   PMID:23666239   PMID:23666240  


Genomics

Variants

.
Variants in SEPTIN4-AS1
23 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
NM_001038704.2(C17orf47):c.1088C>T (p.Ser363Phe) single nucleotide variant Malignant melanoma [RCV000071585] Chr17:58543099 [GRCh38]
Chr17:56620460 [GRCh37]
Chr17:53975459 [NCBI36]
Chr17:17q22		 not provided
GRCh38/hg38 17q23.1-25.1(chr17:36449220-75053130)x3 copy number gain See cases [RCV000137437] Chr17:36449220..75053130 [GRCh38]
Chr17:57595736..73049225 [GRCh37]
Chr17:54950518..70560820 [NCBI36]
Chr17:17q23.1-25.1		 pathogenic
GRCh38/hg38 17q22-23.1(chr17:57418806-59735464)x1 copy number loss See cases [RCV000140211] Chr17:57418806..59735464 [GRCh38]
Chr17:55496167..57812825 [GRCh37]
Chr17:52851166..55167607 [NCBI36]
Chr17:17q22-23.1		 pathogenic
GRCh38/hg38 17q21.33-24.2(chr17:36449220-68170214)x3 copy number gain See cases [RCV000050957] Chr17:36449220..68170214 [GRCh38]
Chr17:48563237..65936105 [GRCh37]
Chr17:45918236..63677950 [NCBI36]
Chr17:17q21.33-24.2		 pathogenic
GRCh38/hg38 17q23.2-25.3(chr17:36449220-83086677)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052483]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052483]|See cases [RCV000052483] Chr17:36449220..83086677 [GRCh38]
Chr17:58617905..81044553 [GRCh37]
Chr17:55972687..78637842 [NCBI36]
Chr17:17q23.2-25.3		 pathogenic
NM_001368771.2(SEPTIN4):c.2073G>A (p.Arg691=) single nucleotide variant not provided [RCV000916988] Chr17:58525714 [GRCh38]
Chr17:56603075 [GRCh37]
Chr17:17q22		 likely benign
NM_001368771.2(SEPTIN4):c.2929G>A (p.Glu977Lys) single nucleotide variant not provided [RCV000959190] Chr17:58520745 [GRCh38]
Chr17:56598106 [GRCh37]
Chr17:17q22		 benign
NM_001368771.2(SEPTIN4):c.1622G>A (p.Arg541His) single nucleotide variant Inborn genetic diseases [RCV003248792] Chr17:58526971 [GRCh38]
Chr17:56604332 [GRCh37]
Chr17:17q22		 uncertain significance
NM_001368771.2(SEPTIN4):c.1921G>C (p.Glu641Gln) single nucleotide variant Inborn genetic diseases [RCV003292530] Chr17:58526304 [GRCh38]
Chr17:56603665 [GRCh37]
Chr17:17q22		 uncertain significance
NM_001368771.2(SEPTIN4):c.2132T>C (p.Val711Ala) single nucleotide variant Inborn genetic diseases [RCV003304721] Chr17:58525162 [GRCh38]
Chr17:56602523 [GRCh37]
Chr17:17q22		 uncertain significance
NM_001368771.2(SEPTIN4):c.2762A>G (p.His921Arg) single nucleotide variant Inborn genetic diseases [RCV003280425] Chr17:58521067 [GRCh38]
Chr17:56598428 [GRCh37]
Chr17:17q22		 uncertain significance
NM_001368771.2(SEPTIN4):c.571C>T (p.Arg191Cys) single nucleotide variant Inborn genetic diseases [RCV002986470] Chr17:58543616 [GRCh38]
Chr17:56620977 [GRCh37]
Chr17:17q22		 uncertain significance
NM_001368771.2(SEPTIN4):c.760G>A (p.Gly254Ser) single nucleotide variant Inborn genetic diseases [RCV002649209] Chr17:58543427 [GRCh38]
Chr17:56620788 [GRCh37]
Chr17:17q22		 likely benign
NM_001368771.2(SEPTIN4):c.317G>A (p.Ser106Asn) single nucleotide variant Inborn genetic diseases [RCV002719159] Chr17:58543870 [GRCh38]
Chr17:56621231 [GRCh37]
Chr17:17q22		 likely benign
NM_001368771.2(SEPTIN4):c.2500A>G (p.Lys834Glu) single nucleotide variant Inborn genetic diseases [RCV003174453] Chr17:58521616 [GRCh38]
Chr17:56598977 [GRCh37]
Chr17:17q22		 uncertain significance
NM_001368771.2(SEPTIN4):c.2230G>A (p.Ala744Thr) single nucleotide variant Inborn genetic diseases [RCV003211205] Chr17:58522088 [GRCh38]
Chr17:56599449 [GRCh37]
Chr17:17q22		 uncertain significance
NM_001368771.2(SEPTIN4):c.2686T>C (p.Cys896Arg) single nucleotide variant Inborn genetic diseases [RCV003219778] Chr17:58521143 [GRCh38]
Chr17:56598504 [GRCh37]
Chr17:17q22		 uncertain significance
NM_001368771.2(SEPTIN4):c.2173G>T (p.Val725Leu) single nucleotide variant Inborn genetic diseases [RCV003263818] Chr17:58525121 [GRCh38]
Chr17:56602482 [GRCh37]
Chr17:17q22		 uncertain significance
NM_001368771.2(SEPTIN4):c.2065C>T (p.Arg689Trp) single nucleotide variant Inborn genetic diseases [RCV003341400] Chr17:58525722 [GRCh38]
Chr17:56603083 [GRCh37]
Chr17:17q22		 uncertain significance
NM_001368771.2(SEPTIN4):c.1793C>A (p.Pro598His) single nucleotide variant Inborn genetic diseases [RCV003381333] Chr17:58526800 [GRCh38]
Chr17:56604161 [GRCh37]
Chr17:17q22		 uncertain significance
NM_001368771.2(SEPTIN4):c.1640C>T (p.Thr547Met) single nucleotide variant Inborn genetic diseases [RCV003363424] Chr17:58526953 [GRCh38]
Chr17:56604314 [GRCh37]
Chr17:17q22		 uncertain significance
NM_001368771.2(SEPTIN4):c.2915G>A (p.Arg972Gln) single nucleotide variant Inborn genetic diseases [RCV003367643] Chr17:58520759 [GRCh38]
Chr17:56598120 [GRCh37]
Chr17:17q22		 uncertain significance
NM_001368771.2(SEPTIN4):c.2680G>T (p.Gly894Trp) single nucleotide variant Inborn genetic diseases [RCV003384388] Chr17:58521149 [GRCh38]
Chr17:56598510 [GRCh37]
Chr17:17q22		 uncertain significance
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:315
Count of miRNA genes:230
Interacting mature miRNAs:241
Transcripts:ENST00000578022, ENST00000580589, ENST00000580769
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 1 2 1
Low 770 916 1339 318 452 275 938 172 1637 209 863 1275 46 502 642 3
Below cutoff 1433 1375 368 284 547 178 2534 1467 1926 186 510 285 112 645 1583 1

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000578022
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1758,525,460 - 58,557,799 (+)Ensembl
RefSeq Acc Id: ENST00000580589
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1758,519,837 - 58,556,925 (+)Ensembl
RefSeq Acc Id: ENST00000580769
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1758,525,669 - 58,544,307 (+)Ensembl
RefSeq Acc Id: NR_110810
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381758,519,837 - 58,556,925 (+)NCBI
CHM1_11756,662,772 - 56,699,854 (+)NCBI
T2T-CHM13v2.01759,387,708 - 59,424,795 (+)NCBI
Sequence:
Promoters
RGD ID:15097066
Promoter ID:EPDNEWNC_H1908
Type:initiation region
Name:SEPT4-AS1_1
Description:SEPT4 antisense RNA 1 [Source:HGNC Symbol;Acc:HGNC:51345]
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
GRCh381758,525,501 - 58,525,561EPDNEWNC
RGD ID:15097067
Promoter ID:EPDNEWNC_H1909
Type:initiation region
Name:SEPT4-AS1_2
Description:SEPT4 antisense RNA 1 [Source:HGNC Symbol;Acc:HGNC:51345]
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
GRCh381758,525,677 - 58,525,737EPDNEWNC

Additional Information

Database Acc Id Source(s)
COSMIC SEPTIN4-AS1 COSMIC
Ensembl Genes ENSG00000264672 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000580589 ENTREZGENE
GTEx ENSG00000264672 GTEx
HGNC ID HGNC:51345 ENTREZGENE
Human Proteome Map SEPTIN4-AS1 Human Proteome Map
NCBI Gene SEPT4-AS1 ENTREZGENE
RNAcentral URS000015693D RNACentral


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2019-12-18 SEPTIN4-AS1  SEPTIN4 antisense RNA 1  SEPTIN4-AS1  SEPT4 antisense RNA 1  Symbol and/or name change 5135510 APPROVED
2019-04-09 SEPTIN4-AS1  SEPT4 antisense RNA 1  SEPT4-AS1    Symbol and/or name change 5135510 APPROVED