Mir-540

MirGeneDB ID

Rno-Mir-540

Family name

MIR-540 (all species)

Species

Norway rat (Rattus norvegicus)

MiRBase ID

rno-mir-540

Paralogues

Orthologues

Mmu-Mir-540

Node of Origin (locus)

Muridae

Node of Origin (family)

Muridae

Genome context
(rn6)

chr6: 133706216-133706274 [+] UCSC Ensembl

Clustered miRNAs
(< 50kb from Mir-540)

Mir-770 chr6: 133682975-133683030 [+] UCSC Ensembl
Mir-673 chr6: 133691391-133691453 [+] UCSC Ensembl
Mir-493 chr6: 133699522-133699583 [+] UCSC Ensembl
Mir-337-as chr6: 133705943-133706003 [-] UCSC Ensembl
Mir-337 chr6: 133705948-133706001 [+] UCSC Ensembl
Mir-540 chr6: 133706216-133706274 [+] UCSC Ensembl
Mir-431 chr6: 133711444-133711507 [+] UCSC Ensembl
Mir-433 chr6: 133712345-133712418 [+] UCSC Ensembl
Mir-127 chr6: 133713452-133713507 [+] UCSC Ensembl
Mir-136-v2 chr6: 133716775-133716830 [+] UCSC Ensembl
Mir-136-v1 chr6: 133716775-133716830 [+] UCSC Ensembl
Mir-370 chr6: 133739928-133739984 [+] UCSC Ensembl

Seed

GGUCAGA

Precursor
(pre-Mir +30nt flank)

CCCCUGGUGGGACAUUCCCUGGGGCUGGGCCAAGGGUCACCCUCUGACUCUGUGGCCAAGGGUAGACAGGUCAGAGGUCGAUCCUGGGCCUACUCUGGGGCUUUUCCCACUGGGAUUUC

Get precursor sequence

Structure

        10           20        30        40        50         
CCCCUGGUGGGACAUUC---| UG   C      A      AC        U    GGCCA 
                    CC  GGG UGGGCC AGGGUC  CCUCUGAC CUGU     A
                    GG  CUC AUCCGG UCCUAG  GGAGACUG GACA     G
CUUUAGGGUCACCCUUUUCG^ GU   -      G      CU        -    GAUGG 
       110       100         90        80        70         60

Deep sequencing

Go to detailed chart

3' NTU

Motifs

CNNC at 3p(+17)

Tissue expression

Dr	Dr	Ad	Bi	Bi	Bi	Bi	Br	Br	Br	Br	Ce	Ce	Ce	Ce	Co	Co	Co	Co	Du	Du	Du	Du	Fa	He	He	He	Hi	Hi	Il	Il	Je	Je	Ki	Ki	Ki	Ki	Ki	La	Li	Li	Li	Li	Li	Li	Lu	Me	Me	Mu	Ov	Pa	Pa	Pa	Sk	Sm	So	So	So	So	Sp	St	St	St	St	Te	Te	Th	Ut	Wh

Star sequence

Rno-Mir-540_5p*

mirBase accession

MIMAT0017211

Sequence

0- CAAGGGUCACCCUCUGACUCUGU -23

Get sequence

Proposed targets

TargetScanVert: rno-miR-540-5p
miRDB: MIMAT0017211

Mature sequence

Rno-Mir-540_3p

mirBase accession

MIMAT0003174

Sequence

37- AGGUCAGAGGUCGAUCCUGGGC -59

Get sequence

Proposed targets

microrna.org: MIMAT0003174
TargetScanVert: rno-miR-540-3p
miRDB: MIMAT0003174