LINC02909 (long intergenic non-protein coding RNA 2909) - Rat Genome Database

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Gene: LINC02909 (long intergenic non-protein coding RNA 2909) Homo sapiens
Analyze
Symbol: LINC02909
Name: long intergenic non-protein coding RNA 2909
RGD ID: 3479035
HGNC Page HGNC:27282
Description: INTERACTS WITH 4,4'-sulfonyldiphenol; benzo[a]pyrene; fulvestrant
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Previously known as: C12orf77; chromosome 12 open reading frame 77; chromosome 12 putative open reading frame 77; putative uncharacterized protein C12orf77
RGD Orthologs
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381224,993,424 - 24,997,465 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1224,993,424 - 25,006,403 (-)EnsemblGRCh38hg38GRCh38
GRCh371225,146,358 - 25,150,399 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361225,037,625 - 25,041,640 (-)NCBINCBI36Build 36hg18NCBI36
Celera1230,293,267 - 30,297,281 (-)NCBICelera
Cytogenetic Map12p12.1NCBI
HuRef1224,916,358 - 24,920,365 (-)NCBIHuRef
CHM1_11225,111,441 - 25,115,448 (-)NCBICHM1_1
T2T-CHM13v2.01224,863,524 - 24,867,561 (-)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


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:12477932  


Genomics

Comparative Map Data
LINC02909
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381224,993,424 - 24,997,465 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1224,993,424 - 25,006,403 (-)EnsemblGRCh38hg38GRCh38
GRCh371225,146,358 - 25,150,399 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361225,037,625 - 25,041,640 (-)NCBINCBI36Build 36hg18NCBI36
Celera1230,293,267 - 30,297,281 (-)NCBICelera
Cytogenetic Map12p12.1NCBI
HuRef1224,916,358 - 24,920,365 (-)NCBIHuRef
CHM1_11225,111,441 - 25,115,448 (-)NCBICHM1_1
T2T-CHM13v2.01224,863,524 - 24,867,561 (-)NCBIT2T-CHM13v2.0
Linc02909
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462475214,053,736 - 14,054,100 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 12p12.1(chr12:24638349-25193743)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000050939]|Macrocephaly [RCV000050940]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000050939]|See cases [RCV000050939] Chr12:24638349..25193743 [GRCh38]
Chr12:24791283..25346677 [GRCh37]
Chr12:12p12.1		 uncertain significance
GRCh38/hg38 12p13.33-11.22(chr12:121055-28415184)x1 copy number loss See cases [RCV000052776] Chr12:121055..28415184 [GRCh38]
Chr12:282465..28568117 [GRCh37]
Chr12:100482..28459384 [NCBI36]
Chr12:12p13.33-11.22		 pathogenic
GRCh38/hg38 12p12.3-11.23(chr12:19295848-27012560)x1 copy number loss See cases [RCV000052782] Chr12:19295848..27012560 [GRCh38]
Chr12:19448782..27165493 [GRCh37]
Chr12:19340049..27056760 [NCBI36]
Chr12:12p12.3-11.23		 pathogenic
GRCh38/hg38 12p12.1-11.21(chr12:21771052-32222232)x1 copy number loss Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052783]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052783]|See cases [RCV000052783] Chr12:21771052..32222232 [GRCh38]
Chr12:21923986..32375166 [GRCh37]
Chr12:21815253..32266433 [NCBI36]
Chr12:12p12.1-11.21		 pathogenic
GRCh38/hg38 12p13.33-11.1(chr12:77187-34380176)x3 copy number gain See cases [RCV000053660] Chr12:77187..34380176 [GRCh38]
Chr12:282465..34533111 [GRCh37]
Chr12:56614..34424378 [NCBI36]
Chr12:12p13.33-11.1		 pathogenic
GRCh38/hg38 12p13.33-12.1(chr12:80412-25470329)x3 copy number gain See cases [RCV000053662] Chr12:80412..25470329 [GRCh38]
Chr12:282465..25623263 [GRCh37]
Chr12:59839..25514530 [NCBI36]
Chr12:12p13.33-12.1		 pathogenic
GRCh38/hg38 12p13.33-11.1(chr12:212976-33926913)x4 copy number gain See cases [RCV000053666] Chr12:212976..33926913 [GRCh38]
Chr12:322142..34079848 [GRCh37]
Chr12:192403..33971115 [NCBI36]
Chr12:12p13.33-11.1		 pathogenic
GRCh38/hg38 12p12.3-12.1(chr12:18252085-25696258)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053670]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053670]|See cases [RCV000053670] Chr12:18252085..25696258 [GRCh38]
Chr12:18405019..25849192 [GRCh37]
Chr12:18296286..25740459 [NCBI36]
Chr12:12p12.3-12.1		 pathogenic
GRCh38/hg38 12p12.1(chr12:24638349-25193743)x3 copy number gain See cases [RCV000050939] Chr12:24638349..25193743 [GRCh38]
Chr12:24791283..25346677 [GRCh37]
Chr12:24682550..25237944 [NCBI36]
Chr12:12p12.1		 uncertain significance
GRCh38/hg38 12p12.1(chr12:24784088-25101275)x3 copy number gain See cases [RCV000135386] Chr12:24784088..25101275 [GRCh38]
Chr12:24937022..25254209 [GRCh37]
Chr12:24828289..25145476 [NCBI36]
Chr12:12p12.1		 uncertain significance
GRCh38/hg38 12p12.3-12.1(chr12:19265334-25482589)x1 copy number loss See cases [RCV000135588] Chr12:19265334..25482589 [GRCh38]
Chr12:19418268..25635523 [GRCh37]
Chr12:19309535..25526790 [NCBI36]
Chr12:12p12.3-12.1		 likely pathogenic
GRCh38/hg38 12p13.33-11.1(chr12:121255-34603274)x3 copy number gain See cases [RCV000136611] Chr12:121255..34603274 [GRCh38]
Chr12:282465..34756209 [GRCh37]
Chr12:100682..34647476 [NCBI36]
Chr12:12p13.33-11.1		 pathogenic
GRCh38/hg38 12p13.33-11.1(chr12:121271-34603261)x3 copy number gain See cases [RCV000139052] Chr12:121271..34603261 [GRCh38]
Chr12:282465..34756196 [GRCh37]
Chr12:100698..34647463 [NCBI36]
Chr12:12p13.33-11.1		 pathogenic
GRCh38/hg38 12p13.33-q24.33(chr12:121271-133196807)x3 copy number gain See cases [RCV000139555] Chr12:121271..133196807 [GRCh38]
Chr12:282465..133773393 [GRCh37]
Chr12:100698..132283466 [NCBI36]
Chr12:12p13.33-q24.33		 pathogenic
GRCh38/hg38 12p13.33-11.1(chr12:54427-34608071)x4 copy number gain See cases [RCV000139787] Chr12:54427..34608071 [GRCh38]
Chr12:282465..34761006 [GRCh37]
Chr12:33854..34652273 [NCBI36]
Chr12:12p13.33-11.1		 pathogenic
GRCh38/hg38 12p13.33-11.1(chr12:64620-34682902)x4 copy number gain See cases [RCV000142149] Chr12:64620..34682902 [GRCh38]
Chr12:173786..34835837 [GRCh37]
Chr12:44047..34727104 [NCBI36]
Chr12:12p13.33-11.1		 pathogenic
GRCh38/hg38 12p12.1(chr12:24552217-25193743)x3 copy number gain See cases [RCV000143315] Chr12:24552217..25193743 [GRCh38]
Chr12:24705151..25346677 [GRCh37]
Chr12:24596418..25237944 [NCBI36]
Chr12:12p12.1		 uncertain significance
GRCh37/hg19 12p13.33-11.1(chr12:148034-34178799)x4 copy number gain See cases [RCV000240164] Chr12:148034..34178799 [GRCh37]
Chr12:12p13.33-11.1		 pathogenic
GRCh37/hg19 12p13.33-q24.33(chr12:1-133851895)x3 copy number gain See cases [RCV000258805] Chr12:1..133851895 [GRCh37]
Chr12:12p13.33-q24.33		 pathogenic|likely pathogenic
GRCh37/hg19 12p13.33-11.1(chr12:89061-34178799)x3 copy number gain See cases [RCV000240487] Chr12:89061..34178799 [GRCh37]
Chr12:12p13.33-11.1		 pathogenic
GRCh37/hg19 12p12.1(chr12:24970786-25307280)x3 copy number gain not provided [RCV000585303] Chr12:24970786..25307280 [GRCh37]
Chr12:12p12.1		 likely benign
GRCh37/hg19 12p12.1(chr12:24686645-25353987)x3 copy number gain See cases [RCV000449381] Chr12:24686645..25353987 [GRCh37]
Chr12:12p12.1		 uncertain significance
GRCh37/hg19 12p12.1(chr12:24965813-25225609)x3 copy number gain See cases [RCV000449101] Chr12:24965813..25225609 [GRCh37]
Chr12:12p12.1		 benign
GRCh37/hg19 12p13.33-q11(chr12:173786-37869301)x3 copy number gain See cases [RCV000449191] Chr12:173786..37869301 [GRCh37]
Chr12:12p13.33-q11		 pathogenic
GRCh37/hg19 12p13.33-12.1(chr12:173786-25286865)x3 copy number gain See cases [RCV000449287] Chr12:173786..25286865 [GRCh37]
Chr12:12p13.33-12.1		 pathogenic
GRCh37/hg19 12p13.33-11.1(chr12:173786-34835837)x3 copy number gain See cases [RCV000447551] Chr12:173786..34835837 [GRCh37]
Chr12:12p13.33-11.1		 pathogenic
GRCh37/hg19 12p12.3-11.23(chr12:18037107-26681362)x3 copy number gain See cases [RCV000446008] Chr12:18037107..26681362 [GRCh37]
Chr12:12p12.3-11.23		 pathogenic
GRCh37/hg19 12p13.33-11.1(chr12:189578-34756150) copy number gain See cases [RCV000446017] Chr12:189578..34756150 [GRCh37]
Chr12:12p13.33-11.1		 pathogenic
GRCh37/hg19 12p12.1(chr12:25097583-25225609)x3 copy number gain See cases [RCV000448318] Chr12:25097583..25225609 [GRCh37]
Chr12:12p12.1		 benign
GRCh37/hg19 12p13.33-q24.33(chr12:173787-133777902)x3 copy number gain See cases [RCV000510482] Chr12:173787..133777902 [GRCh37]
Chr12:12p13.33-q24.33		 pathogenic
GRCh37/hg19 12p12.1(chr12:24687132-25353987)x3 copy number gain See cases [RCV000510169] Chr12:24687132..25353987 [GRCh37]
Chr12:12p12.1		 likely benign
GRCh37/hg19 12p13.33-11.1(chr12:565369-34835837)x3 copy number gain See cases [RCV000511580] Chr12:565369..34835837 [GRCh37]
Chr12:12p13.33-11.1		 likely pathogenic
GRCh37/hg19 12p13.33-q24.33(chr12:173787-133777902) copy number gain See cases [RCV000511643] Chr12:173787..133777902 [GRCh37]
Chr12:12p13.33-q24.33		 pathogenic
GRCh37/hg19 12p13.33-11.22(chr12:173786-28219229)x3 copy number gain See cases [RCV000510961] Chr12:173786..28219229 [GRCh37]
Chr12:12p13.33-11.22		 pathogenic
GRCh37/hg19 12p13.33-11.1(chr12:173786-34835837)x2,3 copy number gain not provided [RCV000683478] Chr12:173786..34835837 [GRCh37]
Chr12:12p13.33-11.1		 pathogenic
GRCh37/hg19 12p13.33-q11(chr12:173786-37869107)x3 copy number gain not provided [RCV000683480] Chr12:173786..37869107 [GRCh37]
Chr12:12p13.33-q11		 pathogenic
GRCh37/hg19 12p13.33-11.1(chr12:173786-34835837)x3 copy number gain not provided [RCV000683479] Chr12:173786..34835837 [GRCh37]
Chr12:12p13.33-11.1		 pathogenic
GRCh37/hg19 12p13.33-q24.33(chr12:191619-133777645)x3 copy number gain not provided [RCV000750246] Chr12:191619..133777645 [GRCh37]
Chr12:12p13.33-q24.33		 pathogenic
GRCh37/hg19 12p13.33-q24.33(chr12:621220-133779118)x3 copy number gain not provided [RCV000750253] Chr12:621220..133779118 [GRCh37]
Chr12:12p13.33-q24.33		 pathogenic
GRCh37/hg19 12p13.33-11.21(chr12:191619-31733044)x3 copy number gain not provided [RCV000750245] Chr12:191619..31733044 [GRCh37]
Chr12:12p13.33-11.21		 pathogenic
GRCh37/hg19 12p12.1(chr12:24690628-25356709)x3 copy number gain not provided [RCV000750337] Chr12:24690628..25356709 [GRCh37]
Chr12:12p12.1		 likely benign
GRCh37/hg19 12p13.33-q11(chr12:274676-37869301)x4 copy number gain not provided [RCV001006470] Chr12:274676..37869301 [GRCh37]
Chr12:12p13.33-q11		 pathogenic
GRCh37/hg19 12p12.1(chr12:22602778-25225668)x1 copy number loss Lamb-Shaffer syndrome [RCV000856634] Chr12:22602778..25225668 [GRCh37]
Chr12:12p12.1		 pathogenic
GRCh37/hg19 12p12.1(chr12:24692382-25353945)x3 copy number gain not provided [RCV000849877] Chr12:24692382..25353945 [GRCh37]
Chr12:12p12.1		 uncertain significance
GRCh37/hg19 12p12.3-11.23(chr12:16141429-27733325)x1 copy number loss not provided [RCV000849815] Chr12:16141429..27733325 [GRCh37]
Chr12:12p12.3-11.23		 pathogenic
GRCh37/hg19 12p13.33-11.1(chr12:173786-34496628)x3 copy number gain not provided [RCV000847209] Chr12:173786..34496628 [GRCh37]
Chr12:12p13.33-11.1		 pathogenic
GRCh37/hg19 12p12.1(chr12:23457173-25177321)x1 copy number loss Lamb-Shaffer syndrome [RCV000857286] Chr12:23457173..25177321 [GRCh37]
Chr12:12p12.1		 pathogenic
GRCh37/hg19 12p13.33-12.1(chr12:173786-25286865) copy number gain not specified [RCV002052955] Chr12:173786..25286865 [GRCh37]
Chr12:12p13.33-12.1		 pathogenic
GRCh37/hg19 12p13.33-11.1(chr12:173786-34835837) copy number gain not specified [RCV002052957] Chr12:173786..34835837 [GRCh37]
Chr12:12p13.33-11.1		 pathogenic
GRCh37/hg19 12p12.3-11.23(chr12:17884992-26704895) copy number gain not specified [RCV002052974] Chr12:17884992..26704895 [GRCh37]
Chr12:12p12.3-11.23		 pathogenic
GRCh37/hg19 12p13.33-q11(chr12:173786-37869301) copy number gain not specified [RCV002052958] Chr12:173786..37869301 [GRCh37]
Chr12:12p13.33-q11		 pathogenic
GRCh37/hg19 12p12.1(chr12:24686645-25353987) copy number gain not specified [RCV002052984] Chr12:24686645..25353987 [GRCh37]
Chr12:12p12.1		 uncertain significance
GRCh37/hg19 12p12.1-11.22(chr12:23693737-29545102)x1 copy number loss not provided [RCV001827630] Chr12:23693737..29545102 [GRCh37]
Chr12:12p12.1-11.22		 pathogenic
GRCh37/hg19 12p13.33-11.1(chr12:176047-34179852)x4 copy number gain Pallister-Killian syndrome [RCV003154827] Chr12:176047..34179852 [GRCh37]
Chr12:12p13.33-11.1		 pathogenic
Single allele duplication not provided [RCV003448692] Chr12:188053..34856694 [GRCh37]
Chr12:12p13.33-11.1		 pathogenic
GRCh37/hg19 12p13.33-11.1(chr12:173786-34835641)x3 copy number gain not specified [RCV003986979] Chr12:173786..34835641 [GRCh37]
Chr12:12p13.33-11.1		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:758
Count of miRNA genes:552
Interacting mature miRNAs:589
Transcripts:ENST00000434912, ENST00000549262, ENST00000549828
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 92
Low 60 3 24 14 597 16 171 43 60 48 71 167 8 11 1
Below cutoff 429 463 202 94 496 40 1081 140 357 95 416 276 57 97 525 2

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000434912
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1224,995,670 - 24,996,919 (-)Ensembl
RefSeq Acc Id: ENST00000549262
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1224,995,063 - 25,006,403 (-)Ensembl
RefSeq Acc Id: ENST00000623395
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1224,993,424 - 24,997,439 (-)Ensembl
RefSeq Acc Id: NR_171024
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381224,993,424 - 24,997,465 (-)NCBI
T2T-CHM13v2.01224,863,524 - 24,867,561 (-)NCBI
Sequence:
Protein Sequences
GenBank Protein EAW96500 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences

Promoters
RGD ID:6789778
Promoter ID:HG_KWN:15213
Type:Non-CpG
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:K562,   Lymphoblastoid
Transcripts:NM_001101339,   UC009ZJB.1
Position:
Human AssemblyChrPosition (strand)Source
Build 361225,041,636 - 25,042,457 (-)MPROMDB

Additional Information

Database Acc Id Source(s)
COSMIC LINC02909 COSMIC
Ensembl Genes ENSG00000226397 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000623395 ENTREZGENE
GTEx ENSG00000226397 GTEx
HGNC ID HGNC:27282 ENTREZGENE
Human Proteome Map LINC02909 Human Proteome Map
NCBI Gene 196415 ENTREZGENE
RNAcentral URS00021231BA RNACentral


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-02-22 LINC02909  long intergenic non-protein coding RNA 2909  C12orf77  chromosome 12 putative open reading frame 77  Symbol and/or name change 19259463 PROVISIONAL
2020-08-10 C12orf77  chromosome 12 putative open reading frame 77  C12orf77  chromosome 12 open reading frame 77  Symbol and/or name change 19259463 PROVISIONAL