Mir-542-P1c

MirGeneDB ID

Rno-Mir-542-P1c

Family name

MIR-542 (all species)

Seed

GUGACAG

Species

Norway rat (Rattus norvegicus)

MiRBase ID

rno-mir-542-2

Paralogues

Rno-Mir-542-P1a Rno-Mir-542-P1b

Orthologues

Bta-Mir-542 Cja-Mir-542 Cpo-Mir-542 Ete-Mir-542 Laf-Mir-542 Mmu-Mir-542 Pab-Mir-542

Node of Origin (locus)

R. norvegicus

Node of Origin (family)

Eutheria

Genome context
(rn6)

chrX: 158152156-158152216 [+] UCSC Ensembl

Clustered miRNAs
(< 50kb from Mir-542-P1c)

Mir-15-P1c4 chrX: 158148183-158148240 [+] UCSC Ensembl
Mir-15-P2c4 chrX: 158148481-158148543 [+] UCSC Ensembl
Mir-351-P1b chrX: 158149221-158149280 [+] UCSC Ensembl
Mir-542-P1c chrX: 158152156-158152216 [+] UCSC Ensembl
Mir-450-P1b chrX: 158153261-158153317 [+] UCSC Ensembl
Mir-450-P2b chrX: 158153394-158153450 [+] UCSC Ensembl
Mir-542-P1b chrX: 158158895-158158955 [+] UCSC Ensembl

Precursor
(pre-Mir +30nt flank)

UGAAGUUCCACAUGCAAGGAUCUCAGACGUCUCGGGGAUCAUCAUGUCACGAGAUACCACUGCGCACUUGUGACAGAUUGAUAACUGAAAGGUCUGGGAGCCACUCCUCUUCCUAAGAAUA

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Structure

        10          20        30        40        50          
UGAAGUUCCACAUGCAA--| A        GUC    GG    UCA         AUACCA 
                   GG UCUCAGAC   UCGG  AUCA   UGUCACGAG      \
                   CC AGGGUCUG   AGUC  UAGU   ACAGUGUUC      C
AUAAGAAUCCUUCUCCUCA^ G        GAA    AA    UAG         ACGCGU 
 .       110       100        90        80        70

Deep sequencing

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Comment

The Drosha cut in murids is -1 and they do not express the second variant at relatively high levels relative to the other mammals.

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-542-P1c_5p*

mirBase accession

MIMAT0003178

Sequence

0- CUCGGGGAUCAUCAUGUCACGAG -23

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Mature sequence

Rno-Mir-542-P1c_3p

mirBase accession

MIMAT0003179

Sequence

38- UGUGACAGAUUGAUAACUGAAAG -61

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