LYNX1-SLURP2 (LYNX1-SLURP2 readthrough) - Rat Genome Database

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Gene: LYNX1-SLURP2 (LYNX1-SLURP2 readthrough) Homo sapiens
Analyze
No known orthologs.
Symbol: LYNX1-SLURP2
Name: LYNX1-SLURP2 readthrough
RGD ID: 13438473
HGNC Page HGNC
Description: Exhibits acetylcholine receptor binding activity and acetylcholine receptor regulator activity. Involved in regulation of neurotransmitter receptor activity. Predicted to localize to anchored component of membrane and plasma membrane.
Type: protein-coding
RefSeq Status: REVIEWED
Also known as: LYNX1-SLURP2 protein
RGD Orthologs
Alliance Genes
More Info homologs ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl8142,764,334 - 142,778,224 (-)EnsemblGRCh38hg38GRCh38
GRCh388142,764,338 - 142,777,872 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh378143,845,756 - 143,859,288 (-)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map8q24.3NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

References
Additional References at PubMed
PMID:11181995   PMID:12477932   PMID:26033490  


Genomics


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 appendage entire extraembryonic component pharyngeal arch
High
Medium 11 25 138 104 2 106 84 8 95 84 132 97 3 1 1
Low 112 6 150 126 119 126 184 33 84 208 180 214 9 2 2 2
Below cutoff 50 19 24 19 194 20 20 18 24 22 43 47 2

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000523332   ⟹   ENSP00000428713
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl8142,764,334 - 142,776,021 (-)Ensembl
RefSeq Acc Id: ENST00000615007   ⟹   ENSP00000479586
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl8142,764,338 - 142,778,224 (-)Ensembl
RefSeq Acc Id: NM_023946   ⟹   NP_076435
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh388142,764,338 - 142,777,872 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_076435 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AEE61023 (Get FASTA)   NCBI Sequence Viewer  
  EAW82299 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_076435   ⟸   NM_023946
- Peptide Label: precursor
- UniProtKB: P0DP58 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSP00000479586   ⟸   ENST00000615007
RefSeq Acc Id: ENSP00000428713   ⟸   ENST00000523332
Protein Domains
UPAR/Ly6

Promoters
RGD ID:7214317
Promoter ID:EPDNEW_H12897
Type:initiation region
Name:LYNX1_4
Description:Ly6/neurotoxin 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H12898  EPDNEW_H12900  EPDNEW_H12901  
Experiment Methods:Single-end sequencing.; Paired-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh388142,774,149 - 142,774,209EPDNEW
RGD ID:7214303
Promoter ID:EPDNEW_H12898
Type:initiation region
Name:LYNX1_1
Description:Ly6/neurotoxin 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H12900  EPDNEW_H12901  EPDNEW_H12897  
Experiment Methods:Single-end sequencing.; Paired-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh388142,777,202 - 142,777,262EPDNEW
RGD ID:7214305
Promoter ID:EPDNEW_H12899
Type:initiation region
Name:LYNX1-SLURP2_1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh388142,777,845 - 142,777,905EPDNEW
RGD ID:7214309
Promoter ID:EPDNEW_H12901
Type:initiation region
Name:LYNX1_3
Description:Ly6/neurotoxin 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H12898  EPDNEW_H12900  EPDNEW_H12897  
Experiment Methods:Single-end sequencing.; Paired-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh388142,777,862 - 142,777,922EPDNEW

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 8q21.3-24.3(chr8:87931152-145068712)x3 copy number gain See cases [RCV000138551] Chr8:87931152..145068712 [GRCh38]
Chr8:88943380..146294098 [GRCh37]
Chr8:89012496..146264902 [NCBI36]
Chr8:8q21.3-24.3
pathogenic
GRCh38/hg38 8q24.3(chr8:142763122-142880038)x3 copy number gain See cases [RCV000140669] Chr8:142763122..142880038 [GRCh38]
Chr8:143844540..143961454 [GRCh37]
Chr8:143841542..143958456 [NCBI36]
Chr8:8q24.3
likely benign
GRCh38/hg38 8q22.1-24.3(chr8:94682154-145068656)x3 copy number gain See cases [RCV000134353] Chr8:94682154..145068656 [GRCh38]
Chr8:95694382..146294042 [GRCh37]
Chr8:95763558..146264846 [NCBI36]
Chr8:8q22.1-24.3
pathogenic
GRCh38/hg38 8q24.21-24.3(chr8:128220912-145049449)x3 copy number gain See cases [RCV000050830] Chr8:128220912..145049449 [GRCh38]
Chr8:129233158..146274835 [GRCh37]
Chr8:129302340..146245639 [NCBI36]
Chr8:8q24.21-24.3
pathogenic
GRCh38/hg38 8q22.1-24.3(chr8:97382873-145070385)x3 copy number gain See cases [RCV000140447] Chr8:97382873..145070385 [GRCh38]
Chr8:98395101..146295771 [GRCh37]
Chr8:98464277..146266575 [NCBI36]
Chr8:8q22.1-24.3
pathogenic
GRCh38/hg38 8q24.3(chr8:139004218-145049449)x3 copy number gain See cases [RCV000137340] Chr8:139004218..145049449 [GRCh38]
Chr8:140016461..146274835 [GRCh37]
Chr8:140085643..146245639 [NCBI36]
Chr8:8q24.3
likely pathogenic
GRCh38/hg38 8p23.3-q24.3(chr8:241530-145049449)x3 copy number gain See cases [RCV000051206] Chr8:241530..145049449 [GRCh38]
Chr8:191530..146274835 [GRCh37]
Chr8:181530..146245639 [NCBI36]
Chr8:8p23.3-q24.3
pathogenic
GRCh38/hg38 8q23.3-24.3(chr8:113580402-145054634)x3 copy number gain See cases [RCV000050638] Chr8:113580402..145054634 [GRCh38]
Chr8:114592631..146280020 [GRCh37]
Chr8:114661807..146250824 [NCBI36]
Chr8:8q23.3-24.3
pathogenic
GRCh38/hg38 8p23.3-q24.3(chr8:208048-145070385)x3 copy number gain See cases [RCV000141808] Chr8:208048..145070385 [GRCh38]
Chr8:158048..146295771 [GRCh37]
Chr8:148048..146266575 [NCBI36]
Chr8:8p23.3-q24.3
pathogenic
GRCh38/hg38 8q21.13-24.3(chr8:78614077-145054634)x3 copy number gain See cases [RCV000142597] Chr8:78614077..145054634 [GRCh38]
Chr8:79526312..146280020 [GRCh37]
Chr8:79688867..146250824 [NCBI36]
Chr8:8q21.13-24.3
pathogenic
GRCh38/hg38 8q24.3(chr8:142201468-144002730)x1 copy number loss See cases [RCV000135981] Chr8:142201468..144002730 [GRCh38]
Chr8:143282829..145076898 [GRCh37]
Chr8:143280736..145148886 [NCBI36]
Chr8:8q24.3
pathogenic
GRCh38/hg38 8q24.3(chr8:139236824-145068712)x3 copy number gain See cases [RCV000137466] Chr8:139236824..145068712 [GRCh38]
Chr8:140249067..146294098 [GRCh37]
Chr8:140318249..146264902 [NCBI36]
Chr8:8q24.3
likely pathogenic
GRCh38/hg38 8q21.2-24.3(chr8:85765999-145070385)x3 copy number gain See cases [RCV000143659] Chr8:85765999..145070385 [GRCh38]
Chr8:86778228..146295771 [GRCh37]
Chr8:86863079..146266575 [NCBI36]
Chr8:8q21.2-24.3
pathogenic
GRCh38/hg38 8q24.13-24.3(chr8:124498498-145068712)x3 copy number gain See cases [RCV000137346] Chr8:124498498..145068712 [GRCh38]
Chr8:125510739..146294098 [GRCh37]
Chr8:125579920..146264902 [NCBI36]
Chr8:8q24.13-24.3
pathogenic
GRCh38/hg38 8q24.22-24.3(chr8:130639182-145068712)x3 copy number gain See cases [RCV000137644] Chr8:130639182..145068712 [GRCh38]
Chr8:131651428..146294098 [GRCh37]
Chr8:131720610..146264902 [NCBI36]
Chr8:8q24.22-24.3
pathogenic|conflicting data from submitters
GRCh38/hg38 8p23.3-q24.3(chr8:241530-145054634)x3 copy number gain See cases [RCV000053602] Chr8:241530..145054634 [GRCh38]
Chr8:191530..146280020 [GRCh37]
Chr8:181530..146250824 [NCBI36]
Chr8:8p23.3-q24.3
pathogenic
GRCh38/hg38 8q21.13-24.3(chr8:77480050-145068712)x3 copy number gain See cases [RCV000139036] Chr8:77480050..145068712 [GRCh38]
Chr8:78392286..146294098 [GRCh37]
Chr8:78554841..146264902 [NCBI36]
Chr8:8q21.13-24.3
pathogenic
GRCh38/hg38 8q24.3(chr8:141738068-144140607)x1 copy number loss See cases [RCV000140913] Chr8:141738068..144140607 [GRCh38]
Chr8:142764538..145195510 [GRCh37]
Chr8:142823655..145267498 [NCBI36]
Chr8:8q24.3
pathogenic
GRCh38/hg38 8p21.3-q24.3(chr8:21291522-145070385)x3 copy number gain See cases [RCV000142021] Chr8:21291522..145070385 [GRCh38]
Chr8:21149033..146295771 [GRCh37]
Chr8:21193313..146266575 [NCBI36]
Chr8:8p21.3-q24.3
pathogenic
GRCh38/hg38 8p23.3-q24.3(chr8:226452-145068712)x3 copy number gain See cases [RCV000142858] Chr8:226452..145068712 [GRCh38]
Chr8:176452..146294098 [GRCh37]
Chr8:166452..146264902 [NCBI36]
Chr8:8p23.3-q24.3
pathogenic
GRCh38/hg38 8q22.3-24.3(chr8:100867343-145070385)x3 copy number gain See cases [RCV000141694] Chr8:100867343..145070385 [GRCh38]
Chr8:101879571..146295771 [GRCh37]
Chr8:101948747..146266575 [NCBI36]
Chr8:8q22.3-24.3
pathogenic
GRCh38/hg38 8q22.3-24.3(chr8:103306336-145068712)x3 copy number gain See cases [RCV000142810] Chr8:103306336..145068712 [GRCh38]
Chr8:104318564..146294098 [GRCh37]
Chr8:104387740..146264902 [NCBI36]
Chr8:8q22.3-24.3
pathogenic|likely pathogenic
GRCh38/hg38 8p23.3-q24.3(chr8:241605-145054781)x3 copy number gain See cases [RCV000138643] Chr8:241605..145054781 [GRCh38]
Chr8:191605..146280167 [GRCh37]
Chr8:181605..146250971 [NCBI36]
Chr8:8p23.3-q24.3
pathogenic
GRCh38/hg38 8q24.13-24.3(chr8:124514090-145054634)x3 copy number gain See cases [RCV000053678] Chr8:124514090..145054634 [GRCh38]
Chr8:125526331..146280020 [GRCh37]
Chr8:125595512..146250824 [NCBI36]
Chr8:8q24.13-24.3
pathogenic
NM_177458.3(SLURP2):c.258C>T (p.Ile86=) single nucleotide variant not provided [RCV000925073] Chr8:142764641 [GRCh38]
Chr8:143846059 [GRCh37]
Chr8:8q24.3
benign

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:52291 AgrOrtholog
COSMIC LYNX1-SLURP2 COSMIC
Ensembl Genes ENSG00000180155 UniProtKB/Swiss-Prot
  ENSG00000284505 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSP00000428713 UniProtKB/TrEMBL
  ENSP00000477648 UniProtKB/Swiss-Prot
  ENSP00000478390 UniProtKB/Swiss-Prot
  ENSP00000478402 UniProtKB/Swiss-Prot
  ENSP00000479586 ENTREZGENE
  ENSP00000498325 UniProtKB/Swiss-Prot
Ensembl Transcript ENST00000523332 UniProtKB/TrEMBL
  ENST00000614491 UniProtKB/Swiss-Prot
  ENST00000615007 ENTREZGENE
  ENST00000620006 UniProtKB/Swiss-Prot
  ENST00000621401 UniProtKB/Swiss-Prot
  ENST00000652477 UniProtKB/Swiss-Prot
GTEx ENSG00000180155 GTEx
  ENSG00000284505 GTEx
HGNC ID HGNC:52291 ENTREZGENE
Human Proteome Map LYNX1-SLURP2 Human Proteome Map
InterPro LY6_UPA_recep-like UniProtKB/Swiss-Prot
  Toxin/TOLIP UniProtKB/Swiss-Prot
KEGG Report hsa:111188157 UniProtKB/Swiss-Prot
  hsa:66004 UniProtKB/Swiss-Prot
NCBI Gene LYNX1-SLURP2 ENTREZGENE
Pfam Toxin_TOLIP UniProtKB/Swiss-Prot
SMART SM00134 UniProtKB/Swiss-Prot
UniProt G3V0Z9_HUMAN UniProtKB/TrEMBL
  LYNX1_HUMAN UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary A0A140VJN6 UniProtKB/Swiss-Prot
  D3DWI7 UniProtKB/Swiss-Prot
  G3XAC2 UniProtKB/Swiss-Prot
  Q86SR0 UniProtKB/Swiss-Prot
  Q9BZG9 UniProtKB/Swiss-Prot