RetrogeneDB ID: retro_mmus_1709

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 18:37434242..37435113(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: Mrpl15
• Ensembl ID: ENSMUSG00000033845
• Aliases: Mrpl15, HSPC145, MRP-L7, Rpml7
• Description: mitochondrial ribosomal protein L15 [Source:MGI Symbol;Acc:MGI:1351639]

Sequence

>retro_mmus_1709
ATGGATGACGTGGTACACAGCTGCAAGTCCAACCTGGACCTGAGGTGGTCCTTGTTGTGAGTGATCCTGGAGAGCCTGAA
GCCCAACCCTAATTCCAGAAAATAGGAAAGACATCCAAGAGATTCGAGAAAACGTAGGAAATGTGGCAGAGGCCATAAAG
GAGAAAATCAGAGAGGAACACAGCCTTAGCTGGACTCTGACAGAGGGCAGACTCTATTTTACATCTGAATCCCAAAACAT
GGATTTAATGAAGAACATGGTTTCAGACACCAGTACCAGCCTTTGAGTCTCAGGGGACTACAGGATCTCGTTGATTTAAG
TCGAGTTGTTCCAACTCAATATATTGACCTAATCCAGATTATGAATGGGAGAGATGTGACCATGCCAGCACTTAAAAGCA
ATTATGGGGTCCAGCCATTTGAAGAAGGTACTGATATTTTTCAAGCAAAAGTTAATATTGAGGTGCAGTTGGCTTCAATT
GCTACAATTGAAAAAATGGTGGTTTTGTTACTACAGCCTTTTATGACCCACGAAGTATGAAGATTTGGCACAAACCTGTT
CCACTCTTTCTGTGGGGACAACACATTCCAAAACAAGTGATCCTACCTGAAGCTCTGGTGCCCTATTATACTGATGGAAA
AAATTGGGGTACCTGCCCAACCCTGCCAAGTTTCCCTAAGCAAGACTTGAACTCACCATGAAGTATGGCTATATTCTCCC
TGATATCACGAAAGATGAACTCTTCAGAATGCTCAGCACTTGGAAGGATCCAAGGCAGAGTTTCTTTGGTCTTGCTCCTG
GCCAGATGGTGAATATGGCAGATAATAAAATTCTAAAATGTACAGATGAGAATCTCAAGTATCACAGCTCC

Alignment

ORF - retro_mmus_1709 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.36 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAGTARGCGTSLDLLRSLPRVSLANLKPSPNSRKRERRPRDRRRGRKCGRGHKGERQRGTRPRLGFEGGQ
          M......C...LDL..SL..V.L..LKP.PNSRK.ER.PRD.R..RKCGRGHKGE.QRGT.P.L....GQ
Retrocopy MDDVVHSCKSNLDLRWSLL*VILESLKPNPNSRK*ERHPRDSRKRRKCGRGHKGENQRGTQP*LDSDRGQ

Parental  TPFYIRIPKYGFNEGHSFRHQYQPLSLRRLQYLIDLGRVDPTQPIDLTQLVNGRGVTIQPLKRDYGVQLV
          T.FYI.IPK.GFNE.H.FRHQYQPLSLR.LQ.L.DL.RV.PTQ.IDL.Q..NGR.VT...LK..YGVQ..
Retrocopy TLFYI*IPKHGFNEEHGFRHQYQPLSLRGLQDLVDLSRVVPTQYIDLIQIMNGRDVTMPALKSNYGVQPF

Parental  EEGADTFQAKINIEVQLASELAIAAIE-KNGGVVTTAFYDPRSLEILCKPIPFFLRGQPIPKRMLPPESL
          EEG.D.FQAK.NIEVQLAS...IA.IE.KNGG.VTTAFYDPRS..I..KP.P.FL.GQ.IPK....PE.L
Retrocopy EEGTDIFQAKVNIEVQLAS---IATIE<KNGGFVTTAFYDPRSMKIWHKPVPLFLWGQHIPKQVILPEAL

Parental  VPYYTDAKN-RGYLADPAKFPEARLELAMKFGYVLPDITKDELFRMLSARKDPRQIFFGLAPGWVVNMAD
          VPYYTD.KN..GYL..PAKFP.ARLEL.MK.GY.LPDITKDELFRMLS..KDPRQ.FFGLAPG..VNMAD
Retrocopy VPYYTDGKN<LGYLPNPAKFP*ARLELTMKYGYILPDITKDELFRMLSTWKDPRQSFFGLAPGQMVNMAD

Parental  KKILKPTDENLLKYYSS
          .KILK.TDEN.LKY.SS
Retrocopy NKILKCTDEN-LKYHSS

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain	0.12 RPM	18.29 RPM
SRP007412_cerebellum	0.48 RPM	15.63 RPM
SRP007412_heart	0.00 RPM	32.38 RPM
SRP007412_kidney	0.02 RPM	24.60 RPM
SRP007412_liver	0.00 RPM	42.66 RPM
SRP007412_testis	0.14 RPM	33.62 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1709 was not detected

EST

No EST(s) were mapped for retro_mmus_1709 retrocopy.

TSS

No TSS is located nearby retro_mmus_1709 retrocopy 5' end.

Lab

retro_mmus_1709 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1709 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001174	1 retrocopy	retro_btau_324,
Canis familiaris	ENSCAFG00000006988	2 retrocopies	retro_cfam_1573, retro_cfam_511,
Choloepus hoffmanni	ENSCHOG00000005299	3 retrocopies	retro_chof_1379, retro_chof_1719, retro_chof_746,
Callithrix jacchus	ENSCJAG00000016719	1 retrocopy	retro_cjac_2230,
Dasypus novemcinctus	ENSDNOG00000017664	1 retrocopy	retro_dnov_364,
Erinaceus europaeus	ENSEEUG00000001454	2 retrocopies	retro_eeur_128, retro_eeur_707,
Echinops telfairi	ENSETEG00000001724	1 retrocopy	retro_etel_1304,
Mustela putorius furo	ENSMPUG00000010533	1 retrocopy	retro_mputfur_149,
Mus musculus	ENSMUSG00000033845	2 retrocopies	retro_mmus_1709 , retro_mmus_3534,
Ornithorhynchus anatinus	ENSOANG00000007286	1 retrocopy	retro_oana_114,
Otolemur garnettii	ENSOGAG00000003768	1 retrocopy	retro_ogar_534,
Ochotona princeps	ENSOPRG00000000921	2 retrocopies	retro_opri_241, retro_opri_364,
Rattus norvegicus	ENSRNOG00000008566	2 retrocopies	retro_rnor_1344, retro_rnor_2785,
Sus scrofa	ENSSSCG00000030578	1 retrocopy	retro_sscr_617,
Tarsius syrichta	ENSTSYG00000014106	1 retrocopy	retro_tsyr_37,
Tursiops truncatus	ENSTTRG00000011844	2 retrocopies	retro_ttru_1139, retro_ttru_733,