LINC01554 (long intergenic non-protein coding RNA 1554) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models   new Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Gene: LINC01554 (long intergenic non-protein coding RNA 1554) Homo sapiens
Analyze
Symbol: LINC01554
Name: long intergenic non-protein coding RNA 1554
RGD ID: 2303887
HGNC Page HGNC:24687
Description: INTERACTS WITH (+)-catechin; 2-hydroxypropanoic acid; 3-isobutyl-1-methyl-7H-xanthine
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Previously known as: C5orf27; FIS; FLJ38821; MGC126626
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38595,852,232 - 95,860,133 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl595,838,245 - 95,860,141 (+)EnsemblGRCh38hg38GRCh38
GRCh37595,187,936 - 95,195,837 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36595,213,695 - 95,221,593 (+)NCBINCBI36Build 36hg18NCBI36
Celera591,066,688 - 91,074,592 (+)NCBICelera
Cytogenetic Map5q15NCBI
HuRef590,378,496 - 90,386,399 (+)NCBIHuRef
CHM1_1594,620,728 - 94,628,633 (+)NCBICHM1_1
T2T-CHM13v2.0596,353,459 - 96,361,362 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


References

References - curated
# Reference Title Reference Citation
1. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932   PMID:14702039   PMID:28028307   PMID:30809309   PMID:32231743   PMID:33000250   PMID:33378013   PMID:34422133   PMID:35845928   PMID:35988928  


Genomics


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 5q14.3-21.1(chr5:85966055-101335711)x1 copy number loss See cases [RCV000135748] Chr5:85966055..101335711 [GRCh38]
Chr5:85261873..100671415 [GRCh37]
Chr5:85297629..100699314 [NCBI36]
Chr5:5q14.3-21.1		 pathogenic
GRCh38/hg38 5q15(chr5:94902711-95930059)x3 copy number gain See cases [RCV000139042] Chr5:94902711..95930059 [GRCh38]
Chr5:94238416..95265763 [GRCh37]
Chr5:94264172..95291519 [NCBI36]
Chr5:5q15		 likely benign
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 5q14.3-22.1(chr5:84603580-111435081)x1 copy number loss See cases [RCV000139656] Chr5:84603580..111435081 [GRCh38]
Chr5:83899398..110770779 [GRCh37]
Chr5:83935154..110798678 [NCBI36]
Chr5:5q14.3-22.1		 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 5q15-22.2(chr5:93193104-113287795)x1 copy number loss See cases [RCV000143249] Chr5:93193104..113287795 [GRCh38]
Chr5:92528810..112623492 [GRCh37]
Chr5:92554566..112651391 [NCBI36]
Chr5:5q15-22.2		 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 5q14.3-21.1(chr5:87376883-101524443)x1 copy number loss See cases [RCV000050945] Chr5:87376883..101524443 [GRCh38]
Chr5:86672700..100860147 [GRCh37]
Chr5:86708456..100888046 [NCBI36]
Chr5:5q14.3-21.1		 pathogenic
GRCh38/hg38 5q13.3-22.1(chr5:74163186-110809453)x3 copy number gain See cases [RCV000051839] Chr5:74163186..110809453 [GRCh38]
Chr5:73459011..110145153 [GRCh37]
Chr5:73494767..110173052 [NCBI36]
Chr5:5q13.3-22.1		 pathogenic
GRCh38/hg38 5q14.3-21.2(chr5:89081352-104687248)x1 copy number loss See cases [RCV000053516] Chr5:89081352..104687248 [GRCh38]
Chr5:88377169..104022949 [GRCh37]
Chr5:88412925..104050848 [NCBI36]
Chr5:5q14.3-21.2		 pathogenic
GRCh38/hg38 5q14.3-15(chr5:91386552-98365880)x1 copy number loss See cases [RCV000053519] Chr5:91386552..98365880 [GRCh38]
Chr5:90682369..97701584 [GRCh37]
Chr5:90718125..97729488 [NCBI36]
Chr5:5q14.3-15		 pathogenic
GRCh38/hg38 5q15(chr5:93405010-97716265)x3 copy number gain See cases [RCV000053285] Chr5:93405010..97716265 [GRCh38]
Chr5:92740716..97051969 [GRCh37]
Chr5:92766472..97077725 [NCBI36]
Chr5:5q15		 uncertain significance
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:608
Count of miRNA genes:471
Interacting mature miRNAs:505
Transcripts:ENST00000357880, ENST00000436592
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.

Markers in Region
A004D35  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37595,195,618 - 95,195,813UniSTSGRCh37
Build 36595,221,374 - 95,221,569RGDNCBI36
Celera591,074,373 - 91,074,568RGD
Cytogenetic Map5q15UniSTS
HuRef590,386,180 - 90,386,375UniSTS
GeneMap99-GB4 RH Map5417.6UniSTS
FIS__6724  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37595,195,162 - 95,195,836UniSTSGRCh37
Build 36595,220,918 - 95,221,592RGDNCBI36
Celera591,073,914 - 91,074,591RGD
HuRef590,385,721 - 90,386,398UniSTS


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 14 91 311 423 5 310 939 441 151 26 7 2 112 23 769
Low 1454 1828 895 140 709 97 2866 883 3004 252 1061 1123 49 1131 1760 2
Below cutoff 931 1051 513 58 912 56 519 862 566 130 354 462 10 50 256 3

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000357880
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl595,852,232 - 95,860,133 (+)Ensembl
RefSeq Acc Id: ENST00000436592
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl595,852,232 - 95,860,133 (+)Ensembl
RefSeq Acc Id: ENST00000620167
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl595,856,869 - 95,860,133 (+)Ensembl
RefSeq Acc Id: ENST00000656444
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl595,838,245 - 95,860,085 (+)Ensembl
RefSeq Acc Id: ENST00000702482
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl595,852,232 - 95,860,141 (+)Ensembl
RefSeq Acc Id: NR_026936
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38595,852,232 - 95,860,133 (+)NCBI
GRCh37595,187,936 - 95,195,837 (+)RGD
Celera591,066,688 - 91,074,592 (+)RGD
HuRef590,378,496 - 90,386,399 (+)ENTREZGENE
CHM1_1594,620,728 - 94,628,633 (+)NCBI
T2T-CHM13v2.0596,353,459 - 96,361,362 (+)NCBI
Sequence:
Protein Sequences
GenBank Protein AAO25675 (Get FASTA)   NCBI Sequence Viewer  
  BAG37278 (Get FASTA)   NCBI Sequence Viewer  
  EAW96058 (Get FASTA)   NCBI Sequence Viewer  
  EAW96059 (Get FASTA)   NCBI Sequence Viewer  
  Q52M75 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q52M75-F1-model_v2 AlphaFold Q52M75 1-96 view protein structure

Promoters
RGD ID:15095925
Promoter ID:EPDNEWNC_H758
Type:single initiation site
Name:LINC01554_1
Description:long intergenic non-protein coding RNA 1554 [Source:HGNCSymbol;Acc:HGNC:24687]
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
GRCh38595,852,232 - 95,852,292EPDNEWNC

Additional Information

Database Acc Id Source(s)
COSMIC LINC01554 COSMIC
Ensembl Genes ENSG00000236882 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000357880 ENTREZGENE
GTEx ENSG00000236882 GTEx
HGNC ID HGNC:24687 ENTREZGENE
Human Proteome Map LINC01554 Human Proteome Map
NCBI Gene 202299 ENTREZGENE
RNAcentral URS000075DFD6 RNACentral
UniProt CE027_HUMAN UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary B2RBN1 UniProtKB/Swiss-Prot
  Q86YS4 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2014-10-07 LINC01554  long intergenic non-protein coding RNA 1554  C5orf27  chromosome 5 open reading frame 27  Symbol and/or name change 5135510 APPROVED