LINC00304 (long intergenic non-protein coding RNA 304) - Rat Genome Database

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Gene: LINC00304 (long intergenic non-protein coding RNA 304) Homo sapiens
Analyze
Symbol: LINC00304
Name: long intergenic non-protein coding RNA 304
RGD ID: 1605831
HGNC Page HGNC:26713
Description: ASSOCIATED WITH KBG syndrome; INTERACTS WITH aflatoxin B1; Aflatoxin B2 alpha; antirheumatic drug
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Previously known as: C16orf81; FLJ36701; NCRNA00304
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381689,159,220 - 89,163,675 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1689,159,146 - 89,164,245 (+)EnsemblGRCh38hg38GRCh38
GRCh371689,225,628 - 89,230,083 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361687,753,129 - 87,754,268 (+)NCBINCBI36Build 36hg18NCBI36
Celera1674,291,250 - 74,295,695 (+)NCBICelera
Cytogenetic Map16q24.3NCBI
HuRef1674,924,634 - 74,929,020 (+)NCBIHuRef
CHM1_11690,636,917 - 90,641,372 (+)NCBICHM1_1
T2T-CHM13v2.01695,239,246 - 95,243,609 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
KBG syndrome  (IAGP)

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
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:14702039   PMID:31012142  


Genomics


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 16q23.3-24.3(chr16:83988570-90081985)x3 copy number gain See cases [RCV000135659] Chr16:83988570..90081985 [GRCh38]
Chr16:84022175..90148393 [GRCh37]
Chr16:82579676..88675894 [NCBI36]
Chr16:16q23.3-24.3		 likely pathogenic
GRCh38/hg38 16q23.2-24.3(chr16:80946659-90081985)x3 copy number gain See cases [RCV000136898] Chr16:80946659..90081985 [GRCh38]
Chr16:80980556..90148393 [GRCh37]
Chr16:79538057..88675894 [NCBI36]
Chr16:16q23.2-24.3		 pathogenic|likely pathogenic
GRCh38/hg38 16q22.1-24.3(chr16:70749398-90096995)x3 copy number gain See cases [RCV000137495] Chr16:70749398..90096995 [GRCh38]
Chr16:70783301..90163403 [GRCh37]
Chr16:69340802..88690904 [NCBI36]
Chr16:16q22.1-24.3		 pathogenic
GRCh38/hg38 16q24.2-24.3(chr16:87848216-90096995)x3 copy number gain See cases [RCV000138161] Chr16:87848216..90096995 [GRCh38]
Chr16:87881822..90163403 [GRCh37]
Chr16:86439323..88690904 [NCBI36]
Chr16:16q24.2-24.3		 likely pathogenic
GRCh38/hg38 16q23.3-24.3(chr16:83478453-89932910)x3 copy number gain See cases [RCV000137980] Chr16:83478453..89932910 [GRCh38]
Chr16:83512058..89999318 [GRCh37]
Chr16:82069559..88526819 [NCBI36]
Chr16:16q23.3-24.3		 likely pathogenic
GRCh38/hg38 16q21-24.3(chr16:65511483-90096995)x3 copy number gain See cases [RCV000139426] Chr16:65511483..90096995 [GRCh38]
Chr16:65545386..90163403 [GRCh37]
Chr16:64102887..88690904 [NCBI36]
Chr16:16q21-24.3		 pathogenic
GRCh38/hg38 16q23.1-24.3(chr16:75377981-90081992)x3 copy number gain See cases [RCV000139302] Chr16:75377981..90081992 [GRCh38]
Chr16:75411879..90148400 [GRCh37]
Chr16:73969380..88675901 [NCBI36]
Chr16:16q23.1-24.3		 pathogenic
GRCh38/hg38 16q24.3(chr16:89079074-89287677)x3 copy number gain See cases [RCV000139882] Chr16:89079074..89287677 [GRCh38]
Chr16:89145482..89354085 [GRCh37]
Chr16:87672983..87881586 [NCBI36]
Chr16:16q24.3		 uncertain significance
GRCh38/hg38 16q24.1-24.3(chr16:85552976-90096995)x3 copy number gain See cases [RCV000139658] Chr16:85552976..90096995 [GRCh38]
Chr16:85586582..90163403 [GRCh37]
Chr16:84144083..88690904 [NCBI36]
Chr16:16q24.1-24.3		 pathogenic
GRCh38/hg38 16q23.2-24.3(chr16:80717291-90096662)x3 copy number gain See cases [RCV000141128] Chr16:80717291..90096662 [GRCh38]
Chr16:80751188..90163070 [GRCh37]
Chr16:79308689..88690571 [NCBI36]
Chr16:16q23.2-24.3		 pathogenic
GRCh38/hg38 16q23.1-24.3(chr16:76336203-90088654)x3 copy number gain See cases [RCV000141700] Chr16:76336203..90088654 [GRCh38]
Chr16:76370100..90155062 [GRCh37]
Chr16:74927601..88682563 [NCBI36]
Chr16:16q23.1-24.3		 pathogenic
GRCh38/hg38 16q23.2-24.3(chr16:80067315-90057871)x3 copy number gain See cases [RCV000142698] Chr16:80067315..90057871 [GRCh38]
Chr16:80101212..90124279 [GRCh37]
Chr16:78658713..88651780 [NCBI36]
Chr16:16q23.2-24.3		 pathogenic
GRCh38/hg38 16q21-24.3(chr16:64389378-90081985)x3 copy number gain See cases [RCV000142578] Chr16:64389378..90081985 [GRCh38]
Chr16:64423281..90148393 [GRCh37]
Chr16:62980782..88675894 [NCBI36]
Chr16:16q21-24.3		 pathogenic|likely pathogenic
GRCh38/hg38 16q12.2-24.3(chr16:52899183-90088654)x3 copy number gain See cases [RCV000143425] Chr16:52899183..90088654 [GRCh38]
Chr16:52933095..90155062 [GRCh37]
Chr16:51490596..88682563 [NCBI36]
Chr16:16q12.2-24.3		 pathogenic
GRCh38/hg38 16q24.1-24.3(chr16:86950106-89335814)x1 copy number loss See cases [RCV000143624] Chr16:86950106..89335814 [GRCh38]
Chr16:86983712..89402222 [GRCh37]
Chr16:85541213..87929723 [NCBI36]
Chr16:16q24.1-24.3		 pathogenic
GRCh38/hg38 16q24.3(chr16:88818756-89413158)x1 copy number loss See cases [RCV000050963] Chr16:88818756..89413158 [GRCh38]
Chr16:88885164..89479566 [GRCh37]
Chr16:87412665..88007067 [NCBI36]
Chr16:16q24.3		 pathogenic
GRCh38/hg38 16q23.1-24.3(chr16:78816291-90081985)x3 copy number gain See cases [RCV000050840] Chr16:78816291..90081985 [GRCh38]
Chr16:78850188..90148393 [GRCh37]
Chr16:77407689..88675894 [NCBI36]
Chr16:16q23.1-24.3		 pathogenic
GRCh38/hg38 16q21-24.3(chr16:65313395-90081985)x3 copy number gain See cases [RCV000052421] Chr16:65313395..90081985 [GRCh38]
Chr16:65347298..90148393 [GRCh37]
Chr16:63904799..88675894 [NCBI36]
Chr16:16q21-24.3		 pathogenic
GRCh38/hg38 16q22.1-24.3(chr16:70514631-90081985)x3 copy number gain See cases [RCV000052422] Chr16:70514631..90081985 [GRCh38]
Chr16:70548534..90148393 [GRCh37]
Chr16:69106035..88675894 [NCBI36]
Chr16:16q22.1-24.3		 pathogenic
GRCh38/hg38 16q23.1-24.3(chr16:76873569-90081985)x3 copy number gain See cases [RCV000052423] Chr16:76873569..90081985 [GRCh38]
Chr16:76907466..90148393 [GRCh37]
Chr16:75464967..88675894 [NCBI36]
Chr16:16q23.1-24.3		 pathogenic
GRCh38/hg38 16q23.3-24.3(chr16:82173150-90081985)x3 copy number gain See cases [RCV000052424] Chr16:82173150..90081985 [GRCh38]
Chr16:82206755..90148393 [GRCh37]
Chr16:80764256..88675894 [NCBI36]
Chr16:16q23.3-24.3		 pathogenic
GRCh38/hg38 16q24.1-24.3(chr16:84707538-90081985)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052425]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052425]|See cases [RCV000052425] Chr16:84707538..90081985 [GRCh38]
Chr16:84741144..90148393 [GRCh37]
Chr16:83298645..88675894 [NCBI36]
Chr16:16q24.1-24.3		 pathogenic
GRCh38/hg38 16q24.2-24.3(chr16:87853401-90081985)x3 copy number gain See cases [RCV000052428] Chr16:87853401..90081985 [GRCh38]
Chr16:87887007..90148393 [GRCh37]
Chr16:86444508..88675894 [NCBI36]
Chr16:16q24.2-24.3		 pathogenic
GRCh38/hg38 16q24.2-24.3(chr16:87306529-89269079)x1 copy number loss See cases [RCV000053362] Chr16:87306529..89269079 [GRCh38]
Chr16:87340135..89335487 [GRCh37]
Chr16:85897636..87862988 [NCBI36]
Chr16:16q24.2-24.3		 pathogenic
GRCh38/hg38 16q24.2-24.3(chr16:88159660-89506042)x1 copy number loss See cases [RCV000053363] Chr16:88159660..89506042 [GRCh38]
Chr16:88193266..89572450 [GRCh37]
Chr16:86750767..88099951 [NCBI36]
Chr16:16q24.2-24.3		 pathogenic
GRCh38/hg38 16q24.2-24.3(chr16:88640116-89530475)x1 copy number loss See cases [RCV000053380] Chr16:88640116..89530475 [GRCh38]
Chr16:88706524..89596883 [GRCh37]
Chr16:87234025..88124384 [NCBI36]
Chr16:16q24.2-24.3		 pathogenic
GRCh38/hg38 16q24.2-24.3(chr16:88662702-89454555)x1 copy number loss See cases [RCV000053381] Chr16:88662702..89454555 [GRCh38]
Chr16:88729110..89520963 [GRCh37]
Chr16:87256611..88048464 [NCBI36]
Chr16:16q24.2-24.3		 pathogenic
GRCh38/hg38 16q24.3(chr16:89154317-89195486)x1 copy number loss See cases [RCV000053382] Chr16:89154317..89195486 [GRCh38]
Chr16:89220725..89261894 [GRCh37]
Chr16:87748226..87789395 [NCBI36]
Chr16:16q24.3		 pathogenic
Single allele deletion KBG syndrome [RCV003388954] Chr16:88197484..89331695 [GRCh38]
Chr16:16q24.2-24.3		 pathogenic
Single allele deletion KBG syndrome [RCV003388955] Chr16:88621654..89376245 [GRCh38]
Chr16:16q24.2-24.3		 pathogenic
Single allele deletion KBG syndrome [RCV003388953] Chr16:87169884..89487487 [GRCh38]
Chr16:16q24.2-24.3		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:900
Count of miRNA genes:621
Interacting mature miRNAs:722
Transcripts:ENST00000321214, ENST00000562248, ENST00000565008
Prediction methods: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 1 1 10 1 1 361 3 1
Low 1688 853 459 26 557 17 1637 1142 1606 76 1121 626 9 352 1311
Below cutoff 626 2086 1091 464 957 312 2660 1039 1705 194 190 827 156 850 1473 2

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000321214
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1689,159,220 - 89,163,675 (+)Ensembl
RefSeq Acc Id: ENST00000562248
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1689,159,146 - 89,160,562 (+)Ensembl
RefSeq Acc Id: ENST00000565008
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1689,162,382 - 89,164,245 (+)Ensembl
RefSeq Acc Id: NR_024347
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381689,159,220 - 89,163,675 (+)NCBI
GRCh371689,225,628 - 89,230,083 (+)RGD
Celera1674,291,250 - 74,295,695 (+)RGD
HuRef1674,924,634 - 74,929,020 (+)ENTREZGENE
CHM1_11690,636,917 - 90,641,372 (+)NCBI
T2T-CHM13v2.01695,239,246 - 95,243,609 (+)NCBI
Sequence:
Protein Sequences
GenBank Protein BAC04270 (Get FASTA)   NCBI Sequence Viewer  
  Q8N9R0 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q8N9R0-F1-model_v2 AlphaFold Q8N9R0 1-145 view protein structure

Promoters
RGD ID:15097013
Promoter ID:EPDNEWNC_H1856
Type:initiation region
Name:LINC00304_1
Description:long intergenic non-protein coding RNA 304 [Source:HGNCSymbol;Acc:HGNC:26713]
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
GRCh381689,162,353 - 89,162,413EPDNEWNC

Additional Information

Database Acc Id Source(s)
COSMIC LINC00304 COSMIC
Ensembl Genes ENSG00000180422 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000321214 ENTREZGENE
GTEx ENSG00000180422 GTEx
HGNC ID HGNC:26713 ENTREZGENE
Human Proteome Map LINC00304 Human Proteome Map
NCBI Gene 283860 ENTREZGENE
PharmGKB PA162378401 PharmGKB
RNAcentral URS00001AE523 RNACentral
UniProt CP081_HUMAN UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2011-09-01 LINC00304  long intergenic non-protein coding RNA 304  NCRNA00304  non-protein coding RNA 304  Symbol and/or name change 5135510 APPROVED
2011-07-27 NCRNA00304  non-protein coding RNA 304  C16orf81  chromosome 16 open reading frame 81  Symbol and/or name change 5135510 APPROVED