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

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Gene: SCOC-AS1 (SCOC antisense RNA 1) Homo sapiens
Analyze
Symbol: SCOC-AS1
Name: SCOC antisense RNA 1
RGD ID: 8656920
HGNC Page HGNC:50601
Description: INTERACTS WITH 4,4'-sulfonyldiphenol; dorsomorphin; lipopolysaccharide
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
GRCh384140,283,726 - 140,373,392 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl4140,283,724 - 140,373,409 (-)EnsemblGRCh38hg38GRCh38
GRCh374141,204,880 - 141,294,546 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 364141,424,328 - 141,513,964 (-)NCBINCBI36Build 36hg18NCBI36
Celera4138,534,900 - 138,624,544 (-)NCBICelera
Cytogenetic Map4q31.1NCBI
HuRef4136,934,754 - 137,025,191 (-)NCBIHuRef
CHM1_14141,182,154 - 141,271,900 (-)NCBICHM1_1
T2T-CHM13v2.04143,603,486 - 143,693,170 (-)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
References
Additional References at PubMed
PMID:14702039   PMID:32393512   PMID:34855149  


Genomics

Variants

.
Variants in SCOC-AS1
2 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 4q31.1-35.2(chr4:138510532-189963195)x3 copy number gain See cases [RCV000136810] Chr4:138510532..189963195 [GRCh38]
Chr4:139431686..190828225 [GRCh37]
Chr4:139651136..191121344 [NCBI36]
Chr4:4q31.1-35.2		 pathogenic
GRCh38/hg38 4q28.3-35.2(chr4:131985253-190095391)x3 copy number gain See cases [RCV000137721] Chr4:131985253..190095391 [GRCh38]
Chr4:132906408..190828225 [GRCh37]
Chr4:133125858..191250527 [NCBI36]
Chr4:4q28.3-35.2		 pathogenic|likely benign
GRCh38/hg38 4q28.1-35.1(chr4:125432943-185761887)x3 copy number gain See cases [RCV000138578] Chr4:125432943..185761887 [GRCh38]
Chr4:126354098..186683041 [GRCh37]
Chr4:126573548..186920035 [NCBI36]
Chr4:4q28.1-35.1		 pathogenic|likely benign
GRCh38/hg38 4q28.3-35.2(chr4:134935616-190036318)x3 copy number gain See cases [RCV000143559] Chr4:134935616..190036318 [GRCh38]
Chr4:135856771..190957473 [GRCh37]
Chr4:136076221..191194467 [NCBI36]
Chr4:4q28.3-35.2		 pathogenic
GRCh38/hg38 4q27-35.2(chr4:121518223-190062270)x3 copy number gain See cases [RCV000051786] Chr4:121518223..190062270 [GRCh38]
Chr4:122439378..190828225 [GRCh37]
Chr4:122658828..191220419 [NCBI36]
Chr4:4q27-35.2		 pathogenic
GRCh38/hg38 4q22.2-32.3(chr4:92913386-165299707)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051775]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051775]|See cases [RCV000051775] Chr4:92913386..165299707 [GRCh38]
Chr4:93834537..166220859 [GRCh37]
Chr4:94053560..166440309 [NCBI36]
Chr4:4q22.2-32.3		 pathogenic
GRCh38/hg38 4q26-35.2(chr4:118065569-190042639)x3 copy number gain See cases [RCV000051785] Chr4:118065569..190042639 [GRCh38]
Chr4:118986724..190828225 [GRCh37]
Chr4:119206172..191200788 [NCBI36]
Chr4:4q26-35.2		 pathogenic
GRCh38/hg38 4q28.2-31.21(chr4:128119872-142431375)x1 copy number loss See cases [RCV000051056] Chr4:128119872..142431375 [GRCh38]
Chr4:129041027..143352528 [GRCh37]
Chr4:129260477..143571978 [NCBI36]
Chr4:4q28.2-31.21		 pathogenic
GRCh38/hg38 4q26-31.21(chr4:116630862-145429900)x1 copy number loss See cases [RCV000053321] Chr4:116630862..145429900 [GRCh38]
Chr4:117552018..146351052 [GRCh37]
Chr4:117771466..146570502 [NCBI36]
Chr4:4q26-31.21		 pathogenic
NM_001153585.1(SCOC):c.23A>C (p.Glu8Ala) single nucleotide variant not specified [RCV004105106] Chr4:140343661 [GRCh38]
Chr4:141264815 [GRCh37]
Chr4:4q31.1		 uncertain significance
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:331
Count of miRNA genes:298
Interacting mature miRNAs:311
Transcripts:ENST00000512692, ENST00000608178, ENST00000609616
Prediction methods:Microtar, Miranda, Rnahybrid
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 12 1
Low 1329 1368 1439 299 1099 208 2752 1026 3529 327 1116 1423 99 958 1463 3
Below cutoff 1087 1516 283 322 738 255 1596 1161 179 91 313 177 71 245 1321 1

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000512692
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl4140,283,724 - 140,373,384 (-)Ensembl
RefSeq Acc Id: ENST00000608178
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl4140,360,682 - 140,373,409 (-)Ensembl
RefSeq Acc Id: ENST00000609616
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl4140,360,812 - 140,373,354 (-)Ensembl
RefSeq Acc Id: ENST00000658255
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl4140,284,795 - 140,373,403 (-)Ensembl
RefSeq Acc Id: ENST00000664103
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl4140,284,823 - 140,373,360 (-)Ensembl
RefSeq Acc Id: ENST00000693274
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl4140,368,296 - 140,373,393 (-)Ensembl
RefSeq Acc Id: NR_033939
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh384140,283,726 - 140,373,392 (-)NCBI
HuRef4136,934,754 - 137,025,191 (-)NCBI
CHM1_14141,182,154 - 141,271,900 (-)NCBI
T2T-CHM13v2.04143,603,486 - 143,693,170 (-)NCBI
Sequence:
Protein Sequences
GenBank Protein BAC04571 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences

Promoters
RGD ID:15095807
Promoter ID:EPDNEWNC_H647
Type:initiation region
Name:SCOC-AS1_1
Description:SCOC antisense RNA 1 [Source:HGNC Symbol;Acc:HGNC:50601]
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
GRCh384140,373,360 - 140,373,420EPDNEWNC

Additional Information

Database Acc Id Source(s)
COSMIC SCOC-AS1 COSMIC
Ensembl Genes ENSG00000196951 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000512692 ENTREZGENE
GTEx ENSG00000196951 GTEx
HGNC ID HGNC:50601 ENTREZGENE
Human Proteome Map SCOC-AS1 Human Proteome Map
NCBI Gene SCOC-AS1 ENTREZGENE
RNAcentral URS000075D09A RNACentral