MIR616 (microRNA 616) - Rat Genome Database

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Gene: MIR616 (microRNA 616) Homo sapiens
Analyze
Symbol: MIR616
Name: microRNA 616
RGD ID: 1602936
HGNC Page HGNC:32872
Description: Predicted to be involved in miRNA-mediated post-transcriptional gene silencing.
Type: ncrna (Ensembl: miRNA)
RefSeq Status: PROVISIONAL
Previously known as: hsa-mir-616; MIRN616
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381257,519,163 - 57,519,259 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1257,519,163 - 57,519,259 (-)EnsemblGRCh38hg38GRCh38
GRCh371257,912,946 - 57,913,042 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361256,199,212 - 56,199,308 (-)NCBINCBI36Build 36hg18NCBI36
Celera1257,568,779 - 57,568,875 (-)NCBICelera
Cytogenetic Map12q13.3NCBI
HuRef1254,950,944 - 54,951,040 (-)NCBIHuRef
CHM1_11257,880,802 - 57,880,898 (-)NCBICHM1_1
T2T-CHM13v2.01257,487,391 - 57,487,487 (-)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Phenotype Annotations     Click to see Annotation Detail View

Human Phenotype
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:16381832   PMID:16505370   PMID:17604727   PMID:21224345   PMID:23497787   PMID:26499912   PMID:27615006   PMID:29271996   PMID:29658596   PMID:29777710   PMID:30028057   PMID:31200002  
PMID:31350524   PMID:31502810   PMID:31537542   PMID:31747371   PMID:32439362   PMID:32668286   PMID:37493101   PMID:37685841   PMID:38042032  


Genomics


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 12q13.3-14.2(chr12:57013355-63042498)x1 copy number loss See cases [RCV000052813] Chr12:57013355..63042498 [GRCh38]
Chr12:57407139..63436278 [GRCh37]
Chr12:55693406..61722545 [NCBI36]
Chr12:12q13.3-14.2		 pathogenic
GRCh38/hg38 12q13.3-14.1(chr12:57041158-60273934)x1 copy number loss See cases [RCV000052814] Chr12:57041158..60273934 [GRCh38]
Chr12:57434942..60667715 [GRCh37]
Chr12:55721209..58953982 [NCBI36]
Chr12:12q13.3-14.1		 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
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-q24.33(chr12:173787-133777902)x3 copy number gain See cases [RCV000510482] Chr12:173787..133777902 [GRCh37]
Chr12:12p13.33-q24.33		 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-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-q24.33(chr12:191619-133777645)x3 copy number gain not provided [RCV000750246] Chr12:191619..133777645 [GRCh37]
Chr12:12p13.33-q24.33		 pathogenic
GRCh37/hg19 12q13.3-14.1(chr12:57582163-59031979)x1 copy number loss not provided [RCV001006506] Chr12:57582163..59031979 [GRCh37]
Chr12:12q13.3-14.1		 likely pathogenic
GRCh37/hg19 12q13.2-14.1(chr12:55552371-62126304)x3 copy number gain not provided [RCV001006505] Chr12:55552371..62126304 [GRCh37]
Chr12:12q13.2-14.1		 pathogenic
NC_000012.11:g.(?_57881874)_(58190366_?)dup duplication not provided [RCV001916382] Chr12:57881874..58190366 [GRCh37]
Chr12:12q13.3-14.1		 uncertain significance
NC_000012.11:g.(?_57906514)_(57976962_?)dup duplication Severe early-onset pulmonary alveolar proteinosis due to MARS deficiency [RCV003113624]|Spastic paraplegia [RCV003113625] Chr12:57906514..57976962 [GRCh37]
Chr12:12q13.3		 uncertain significance
NC_000012.11:g.(?_57534470)_(58190366_?)dup duplication Familial melanoma [RCV003119257] Chr12:57534470..58190366 [GRCh37]
Chr12:12q13.3-14.1		 uncertain significance
GRCh37/hg19 12q13.3-14.1(chr12:57631073-58236597)x1 copy number loss not provided [RCV002474565] Chr12:57631073..58236597 [GRCh37]
Chr12:12q13.3-14.1		 likely pathogenic
GRCh37/hg19 12q13.3-14.1(chr12:57064059-59314016)x1 copy number loss not provided [RCV003222783] Chr12:57064059..59314016 [GRCh37]
Chr12:12q13.3-14.1		 likely pathogenic
miRNA Target Status

Confirmed Targets
Gene TargetMature miRNAMethod NameResult TypeData TypeSupport TypePMID
ATP7Bhsa-miR-616-5pMirtarbaseexternal_infoCLASHFunctional MTI (Weak)23622248
TFPI2hsa-miR-616-3pMirtarbaseexternal_infoIn situ hybridization//Luciferase reporter assay//Functional MTI21224345
PON1hsa-miR-616-3pMirtarbaseexternal_infoLuciferase reporter assayFunctional MTI23497787
TFPI2hsa-miR-616-3pTarbaseexternal_infoMicroarrayPOSITIVE
TFPI2hsa-miR-616-3pOncomiRDBexternal_infoNANA21224345

Predicted Targets
Summary Value
Count of predictions:31848
Count of gene targets:11383
Count of transcripts:22455
Interacting mature miRNAs:hsa-miR-616-3p, hsa-miR-616-5p
Prediction methods:Microtar, Miranda, Pita, Rnahybrid, Targetscan
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 64 11 102 59 273 64 73 36 41 39 86 142 3 4 2
Low 1066 1396 1026 273 901 203 2384 673 1111 298 694 1031 77 746 1357 2
Below cutoff 488 567 241 101 256 77 628 561 710 28 168 146 24 196 457

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000385293
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1257,519,163 - 57,519,259 (-)Ensembl
RefSeq Acc Id: NR_030346
RefSeq Status: PROVISIONAL
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381257,519,163 - 57,519,259 (-)NCBI
GRCh371257,912,946 - 57,913,042 (-)RGD
Celera1257,568,779 - 57,568,875 (-)RGD
HuRef1254,950,944 - 54,951,040 (-)ENTREZGENE
CHM1_11257,880,802 - 57,880,898 (-)NCBI
T2T-CHM13v2.01257,487,391 - 57,487,487 (-)NCBI
Sequence:
Promoters
RGD ID:6790007
Promoter ID:HG_KWN:15980
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:CD4+TCell,   CD4+TCell_12Hour,   HeLa_S3,   Jurkat,   Lymphoblastoid,   NB4
Transcripts:ENST00000385293
Position:
Human AssemblyChrPosition (strand)Source
Build 361256,199,221 - 56,199,977 (-)MPROMDB

Additional Information

Database Acc Id Source(s)
COSMIC MIR616 COSMIC
Ensembl Genes ENSG00000208028 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000385293 ENTREZGENE
GTEx ENSG00000208028 GTEx
HGNC ID HGNC:32872 ENTREZGENE
Human Proteome Map MIR616 Human Proteome Map
miRBase MI0003629 ENTREZGENE
NCBI Gene 693201 ENTREZGENE
OMIM 614489 OMIM
PharmGKB PA164722912 PharmGKB
RNAcentral URS00005D986D RNACentral
  URS00005E3F32 RNACentral
  URS00006DC233 RNACentral