RetrogeneDB ID: retro_btau_1609

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 8:46381618..46381967(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL51
• Ensembl ID: ENSBTAG00000014729
• Aliases: MRPL51, L51mt, MRP-L51
• Description: 39S ribosomal protein L51, mitochondrial [Source:UniProtKB/Swiss-Prot;Acc:P0C2B6]

Sequence

>retro_btau_1609
ATGGCAGGGAACCTCTCTTGGGTGGCAGGCTGTAATCTATGGGACCAGTGCCTCTGGCCTGCAGAAGTTTCTCTTTGGGT
GTTCCCAGATTGTTCCATGTAATGGTCACCCTCCTGCCCCCAAAGTGGCTGACCATTGGAAAGAGAAGAGGGCCATGCTT
GGGGTATATGACAGTATCAGGATCCTGGGCAACTTTGAAAAGCACTCCAAAGAACTGATCAAGGGCCCCATATGATTTTG
AGGCTGGAAGGAGAATTAATTGCAGTGTTGTATCCAAAAGAAGATATTGGTTAGAAACAGAATGTTCACTGATGAACTGC
ACAACCTTAGCAGACTCATCAGCTATCTC

Alignment

ORF - retro_btau_1609 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.43 %
• Parental protein coverage: 91.41 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAGSLSWVAGRRLW-GLVPLACRSFFLGVPRLFHVRVTL-PPPKVIDRWNQKRAMFGVYDNIGILGNFEK
          MAG.LSWVAG..LW.G.VPLACRSF.LGVPRLFHV.VTL.P.PKV.D.W..KRAM.GVYD.I.ILGNFEK
Retrocopy MAGNLSWVAGCNLW<GPVPLACRSFSLGVPRLFHVMVTL<PAPKVADHWKEKRAMLGVYDSIRILGNFEK

Parental  HPKELIKGPVWLRGWKGNELQRCIRKKRMVGNRMFIDDLHNLNKRISFL
          H.KELIKGP....GWK.N.LQ.CI.KK..V.NRMF.D.LHNL...IS.L
Retrocopy HSKELIKGPI*F*GWKEN*LQCCIQKKILVRNRMFTDELHNLSRLISYL

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
ERP005899_liver	0.00 RPM	35.98 RPM
ERP005899_muscle	0.00 RPM	48.35 RPM
SRP017611_brain	0.00 RPM	41.84 RPM
SRP017611_kidney	0.00 RPM	64.78 RPM
SRP017611_liver	0.00 RPM	24.54 RPM
SRP030211_testis	0.00 RPM	28.15 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1609 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1609 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1609 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014729	1 retrocopy	retro_btau_1609 ,
Callithrix jacchus	ENSCJAG00000018232	1 retrocopy	retro_cjac_548,
Cavia porcellus	ENSCPOG00000008478	1 retrocopy	retro_cpor_1082,
Loxodonta africana	ENSLAFG00000002106	2 retrocopies	retro_lafr_1157, retro_lafr_845,
Mus musculus	ENSMUSG00000030335	2 retrocopies	retro_mmus_1967, retro_mmus_2607,
Pteropus vampyrus	ENSPVAG00000012566	1 retrocopy	retro_pvam_534,
Rattus norvegicus	ENSRNOG00000019165	2 retrocopies	retro_rnor_2582, retro_rnor_926,
Tupaia belangeri	ENSTBEG00000000936	2 retrocopies	retro_tbel_3219, retro_tbel_3408,