MIR3677HG (MIR3677 and MIR940 host gene) - 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: MIR3677HG (MIR3677 and MIR940 host gene) Homo sapiens
Analyze
Symbol: MIR3677HG
Name: MIR3677 and MIR940 host gene
RGD ID: 16562932
HGNC Page HGNC:55382
Description: Predicted to be involved in miRNA-mediated post-transcriptional gene silencing. Predicted to be part of RISC complex.
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Previously known as: AC009065.4; AC009065.5; LOC106660606; uncharacterized LOC106660606
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38.p14 Ensembl - Human Genome Assembly GRCh38 Ensembl
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38162,268,663 - 2,273,072 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl162,268,155 - 2,273,418 (+)EnsemblGRCh38hg38GRCh38
GRCh37162,318,664 - 2,323,073 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map16p13.3NCBI
CHM1_1162,318,621 - 2,323,030 (+)NCBICHM1_1
T2T-CHM13v2.0162,291,109 - 2,295,518 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
RISC complex  (IEA)

Phenotype Annotations     Click to see Annotation Detail View

Human Phenotype
References
Additional References at PubMed
PMID:16341674  


Genomics


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 16p13.3(chr16:46766-3214623)x3 copy number gain See cases [RCV000052370] Chr16:46766..3214623 [GRCh38]
Chr16:96766..3264623 [GRCh37]
Chr16:36766..3204624 [NCBI36]
Chr16:16p13.3		 pathogenic
NC_000016.10:g.2077605_2284389dup duplication Endometrial carcinoma [RCV000588521] Chr16:2077605..2284389 [GRCh38]
Chr16:2127606..2334390 [GRCh37]
Chr16:16p13.3		 uncertain significance
GRCh38/hg38 16p13.3-13.12(chr16:43732-13326806)x3 copy number gain See cases [RCV000139166] Chr16:43732..13326806 [GRCh38]
Chr16:93732..13420663 [GRCh37]
Chr16:33732..13328164 [NCBI36]
Chr16:16p13.3-13.12		 pathogenic
GRCh38/hg38 16p13.3-13.11(chr16:666662-15743104)x3 copy number gain See cases [RCV000143710] Chr16:666662..15743104 [GRCh38]
Chr16:716662..15836961 [GRCh37]
Chr16:656663..15744462 [NCBI36]
Chr16:16p13.3-13.11		 pathogenic
GRCh38/hg38 16p13.3-13.13(chr16:23141-11296695)x3 copy number gain See cases [RCV000052367] Chr16:23141..11296695 [GRCh38]
Chr16:73141..11390552 [GRCh37]
Chr16:13141..11298053 [NCBI36]
Chr16:16p13.3-13.13		 pathogenic
GRCh38/hg38 16p13.3(chr16:46766-4247185)x3 copy number gain See cases [RCV000136687] Chr16:46766..4247185 [GRCh38]
Chr16:96766..4297186 [GRCh37]
Chr16:36766..4237187 [NCBI36]
Chr16:16p13.3		 pathogenic
GRCh38/hg38 16p13.3(chr16:29941-2560460)x3 copy number gain See cases [RCV000052368] Chr16:29941..2560460 [GRCh38]
Chr16:79941..2610461 [GRCh37]
Chr16:19941..2550462 [NCBI36]
Chr16:16p13.3		 pathogenic
GRCh38/hg38 16p13.3-13.13(chr16:46766-11525516)x3 copy number gain See cases [RCV000133780] Chr16:46766..11525516 [GRCh38]
Chr16:96766..11619372 [GRCh37]
Chr16:36766..11526873 [NCBI36]
Chr16:16p13.3-13.13		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:873
Count of miRNA genes:520
Interacting mature miRNAs:559
Transcripts:ENST00000562838, ENST00000563734, ENST00000567888
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 2 48 1 7 1 17 1 46 94
Low 2409 2275 1564 511 1565 353 4120 1744 3678 409 1394 1489 170 1173 2574 4
Below cutoff 21 683 108 107 321 107 227 442 13 8 8 23 30 209

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000562838
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl162,268,663 - 2,273,124 (+)Ensembl
RefSeq Acc Id: ENST00000563734
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl162,268,155 - 2,273,418 (+)Ensembl
RefSeq Acc Id: ENST00000567888
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl162,268,623 - 2,273,039 (+)Ensembl
RefSeq Acc Id: NR_132988
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38162,268,663 - 2,273,072 (+)NCBI
T2T-CHM13v2.0162,291,109 - 2,295,518 (+)NCBI
Sequence:

Additional Information

Database Acc Id Source(s)
COSMIC MIR3677HG COSMIC
Ensembl Genes ENSG00000260778 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000562838 ENTREZGENE
GTEx ENSG00000260778 GTEx
HGNC ID HGNC:55382 ENTREZGENE
Human Proteome Map MIR3677HG Human Proteome Map
NCBI Gene LOC106660606 ENTREZGENE
RNAcentral URS00008E3982 RNACentral


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2020-12-14 MIR3677HG  MIR3677 and MIR940 host gene  AC009065.4  novel transcript  Symbol and/or name change 19259463 PROVISIONAL
2020-08-20 AC009065.4  novel transcript  AC009065.5  novel transcript  Symbol and/or name change 19259462 PROVISIONAL
2020-06-25 AC009065.5  novel transcript  LOC106660606  uncharacterized LOC106660606  Symbol and/or name change 19259462 PROVISIONAL
2020-06-18 LOC106660606  uncharacterized LOC106660606  AC009065.5  novel transcript  Symbol and/or name change 5135510 APPROVED
2020-02-07 AC009065.5  novel transcript  AC009065.4  novel transcript  Symbol and/or name change 19259462 PROVISIONAL