SP2-AS1 (SP2 antisense RNA 1) - Rat Genome Database

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Gene: SP2-AS1 (SP2 antisense RNA 1) Homo sapiens
Analyze
Symbol: SP2-AS1
Name: SP2 antisense RNA 1
RGD ID: 9587909
HGNC Page HGNC:51341
Description: ASSOCIATED WITH genetic disease; INTERACTS WITH aflatoxin B1; benzo[a]pyrene; benzo[e]pyrene
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381747,898,386 - 47,941,404 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1747,897,330 - 47,941,410 (-)EnsemblGRCh38hg38GRCh38
GRCh371745,975,752 - 46,018,770 (-)NCBIGRCh37GRCh37hg19GRCh37
Celera1742,428,961 - 42,471,534 (-)NCBICelera
Cytogenetic Map17q21.32NCBI
HuRef1741,337,163 - 41,341,998 (-)NCBIHuRef
HuRef1741,344,319 - 41,387,436 (-)NCBIHuRef
CHM1_11746,033,557 - 46,038,392 (-)NCBICHM1_1
CHM1_11746,040,713 - 46,083,752 (-)NCBICHM1_1
T2T-CHM13v2.01748,760,176 - 48,803,194 (-)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
Additional References at PubMed
PMID:12477932   PMID:16344560  


Genomics

Variants

.
Variants in SP2-AS1
20 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
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 17q21.32(chr17:47686487-47986961)x1 copy number loss See cases [RCV000134967] Chr17:47686487..47986961 [GRCh38]
Chr17:45763853..46064327 [GRCh37]
Chr17:43118852..43419326 [NCBI36]
Chr17:17q21.32		 likely pathogenic|uncertain significance
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 17q21.31-21.33(chr17:44955325-49381173)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052480]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052480]|See cases [RCV000052480] Chr17:44955325..49381173 [GRCh38]
Chr17:43032693..47458535 [GRCh37]
Chr17:40388219..44813534 [NCBI36]
Chr17:17q21.31-21.33		 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_003110.6(SP2):c.713C>A (p.Thr238Asn) single nucleotide variant Inborn genetic diseases [RCV003248742] Chr17:47916784 [GRCh38]
Chr17:45994150 [GRCh37]
Chr17:17q21.32		 uncertain significance
NM_003110.6(SP2):c.1086G>C (p.Glu362Asp) single nucleotide variant Inborn genetic diseases [RCV003292479] Chr17:47922988 [GRCh38]
Chr17:46000354 [GRCh37]
Chr17:17q21.32		 uncertain significance
NM_003110.6(SP2):c.167C>T (p.Pro56Leu) single nucleotide variant Inborn genetic diseases [RCV003264584] Chr17:47916238 [GRCh38]
Chr17:45993604 [GRCh37]
Chr17:17q21.32		 uncertain significance
NM_003110.6(SP2):c.589G>A (p.Gly197Arg) single nucleotide variant Inborn genetic diseases [RCV002907032] Chr17:47916660 [GRCh38]
Chr17:45994026 [GRCh37]
Chr17:17q21.32		 uncertain significance
NM_003110.6(SP2):c.830T>A (p.Ile277Asn) single nucleotide variant Inborn genetic diseases [RCV002773597] Chr17:47916901 [GRCh38]
Chr17:45994267 [GRCh37]
Chr17:17q21.32		 uncertain significance
NM_003110.6(SP2):c.1610G>A (p.Arg537His) single nucleotide variant Inborn genetic diseases [RCV002861132] Chr17:47925410 [GRCh38]
Chr17:46002776 [GRCh37]
Chr17:17q21.32		 uncertain significance
NM_003110.6(SP2):c.965G>A (p.Arg322Gln) single nucleotide variant Inborn genetic diseases [RCV002774562] Chr17:47917036 [GRCh38]
Chr17:45994402 [GRCh37]
Chr17:17q21.32		 uncertain significance
NM_003110.6(SP2):c.954G>C (p.Gln318His) single nucleotide variant Inborn genetic diseases [RCV002997528] Chr17:47917025 [GRCh38]
Chr17:45994391 [GRCh37]
Chr17:17q21.32		 uncertain significance
NM_003110.6(SP2):c.823G>A (p.Asp275Asn) single nucleotide variant Inborn genetic diseases [RCV002782947] Chr17:47916894 [GRCh38]
Chr17:45994260 [GRCh37]
Chr17:17q21.32		 uncertain significance
NM_003110.6(SP2):c.1456A>G (p.Met486Val) single nucleotide variant Inborn genetic diseases [RCV002692360] Chr17:47925002 [GRCh38]
Chr17:46002368 [GRCh37]
Chr17:17q21.32		 uncertain significance
NM_003110.6(SP2):c.388A>G (p.Ile130Val) single nucleotide variant Inborn genetic diseases [RCV002822400] Chr17:47916459 [GRCh38]
Chr17:45993825 [GRCh37]
Chr17:17q21.32		 uncertain significance
NM_003110.6(SP2):c.676G>A (p.Gly226Arg) single nucleotide variant Inborn genetic diseases [RCV002854390] Chr17:47916747 [GRCh38]
Chr17:45994113 [GRCh37]
Chr17:17q21.32		 uncertain significance
NM_003110.6(SP2):c.560C>T (p.Ser187Leu) single nucleotide variant Inborn genetic diseases [RCV002804067] Chr17:47916631 [GRCh38]
Chr17:45993997 [GRCh37]
Chr17:17q21.32		 uncertain significance
NM_003110.6(SP2):c.827A>G (p.Asn276Ser) single nucleotide variant Inborn genetic diseases [RCV002929900] Chr17:47916898 [GRCh38]
Chr17:45994264 [GRCh37]
Chr17:17q21.32		 uncertain significance
NM_003110.6(SP2):c.349C>T (p.Pro117Ser) single nucleotide variant Inborn genetic diseases [RCV002955125] Chr17:47916420 [GRCh38]
Chr17:45993786 [GRCh37]
Chr17:17q21.32		 uncertain significance
NM_003110.6(SP2):c.1829C>T (p.Thr610Met) single nucleotide variant Inborn genetic diseases [RCV002987257] Chr17:47927811 [GRCh38]
Chr17:46005177 [GRCh37]
Chr17:17q21.32		 uncertain significance
NM_003110.6(SP2):c.601G>C (p.Val201Leu) single nucleotide variant Inborn genetic diseases [RCV002855011] Chr17:47916672 [GRCh38]
Chr17:45994038 [GRCh37]
Chr17:17q21.32		 uncertain significance
NM_003110.6(SP2):c.632C>T (p.Thr211Met) single nucleotide variant Inborn genetic diseases [RCV002808002] Chr17:47916703 [GRCh38]
Chr17:45994069 [GRCh37]
Chr17:17q21.32		 uncertain significance
NM_003110.6(SP2):c.579C>T (p.Pro193=) single nucleotide variant not provided [RCV003419768] Chr17:47916650 [GRCh38]
Chr17:45994016 [GRCh37]
Chr17:17q21.32		 likely benign
NM_003110.6(SP2):c.1482C>A (p.Thr494=) single nucleotide variant not provided [RCV003885658] Chr17:47925028 [GRCh38]
Chr17:46002394 [GRCh37]
Chr17:17q21.32		 likely benign
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:588
Count of miRNA genes:436
Interacting mature miRNAs:470
Transcripts:ENST00000411573, ENST00000433001, ENST00000451140, ENST00000585280
Prediction methods: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 visual system adipose tissue appendage entire extraembryonic component pharyngeal arch
High
Medium 1 1 1 30 5
Low 2012 1806 1474 370 1096 257 3228 1288 3423 352 1376 1501 127 1 1186 1912 5 2
Below cutoff 424 1139 251 253 808 207 1127 908 309 66 54 106 47 18 875 1

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000411573
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1747,898,713 - 47,941,392 (-)Ensembl
RefSeq Acc Id: ENST00000433001
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1747,899,631 - 47,941,390 (-)Ensembl
RefSeq Acc Id: ENST00000451140
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1747,898,274 - 47,941,410 (-)Ensembl
RefSeq Acc Id: ENST00000585280
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1747,897,330 - 47,941,389 (-)Ensembl
RefSeq Acc Id: NR_103856
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381747,898,386 - 47,941,404 (-)NCBI
HuRef1741,344,319 - 41,387,436 (-)NCBI
CHM1_11746,040,713 - 46,083,752 (-)NCBI
T2T-CHM13v2.01748,760,176 - 48,803,194 (-)NCBI
Sequence:
RefSeq Acc Id: NR_103857
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381747,898,386 - 47,941,404 (-)NCBI
HuRef1741,344,319 - 41,387,436 (-)NCBI
CHM1_11746,040,713 - 46,083,752 (-)NCBI
T2T-CHM13v2.01748,760,176 - 48,803,194 (-)NCBI
Sequence:
Promoters
RGD ID:15097055
Promoter ID:EPDNEWNC_H1895
Type:initiation region
Name:SP2-AS1_1
Description:SP2 antisense RNA 1 [Source:HGNC Symbol;Acc:HGNC:51341]
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
GRCh381747,941,389 - 47,941,449EPDNEWNC

Additional Information

Database Acc Id Source(s)
COSMIC SP2-AS1 COSMIC
Ensembl Genes ENSG00000234494 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000411573 ENTREZGENE
  ENST00000451140 ENTREZGENE
GTEx ENSG00000234494 GTEx
HGNC ID HGNC:51341 ENTREZGENE
Human Proteome Map SP2-AS1 Human Proteome Map
NCBI Gene SP2-AS1 ENTREZGENE
RNAcentral URS000075DDAD RNACentral
  URS000075EE8D RNACentral