RetrogeneDB ID: retro_rnor_2582

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 8:86211328..86211667(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Mrpl51
• Ensembl ID: ENSRNOG00000019165
• Aliases: None
• Description: 39S ribosomal protein L51, mitochondrial [Source:RefSeq peptide;Acc:NP_001100091]

Sequence

>retro_rnor_2582
CTATGGGGCTGGATGTACTTGACACACAGAAACTTTTCTCTAGGTGTTCCTCTATTGGCCCATGTAAGACTTACTCTTCC
TCCTCCTAGAGCTGTTGATCATGGGAATAAGAAAGGGGTTCTCTTTGGTGTATACAACAATATTGGAATCCTGGAGAAAT
TTAAAAGATATCCAAAAGAACTAATCAAAGGCCTAGTATGACTTCAAGCCTGGAGAGGAAATGGATTGTAGCATTGTATC
TGAAAGAAGAAAATGGTTGAAATGCTCATTGAGGACTTTCACAGTCTTAACAAATGGGTCAACTAGCTCTACAAACACTT
TAACCAACATGGAAAGTAT

Alignment

ORF - retro_rnor_2582 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.22 %
• Parental protein coverage: 89.84 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LWGSMLSACRSFSLGVPLLARVRLTLPPPRVIDRWNEKRALFGVYDNIGILGDFEKHPKELIKGPVWLRG
          LWG.M....R.FSLGVPLLA.VRLTLPPPR..D..N.K..LFGVY.NIGIL..F...PKELIKG.V.L..
Retrocopy LWGWMYLTHRNFSLGVPLLAHVRLTLPPPRAVDHGNKKGVLFGVYNNIGILEKFKRYPKELIKGLV*LQA

Parental  WRGNELQRCIRKKKMVGNRMFTEDLHNLNKRISYLYKHFNRHGKY
          WRGN.L..CI.KKKMV...M..ED.H.LNK....LYKHFN.HGKY
Retrocopy WRGNGL*HCI*KKKMV--EMLIEDFHSLNKWVN*LYKHFNQHGKY

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
SRP017611_brain	0.00 RPM	33.72 RPM
SRP017611_kidney	0.00 RPM	25.05 RPM
SRP017611_liver	0.00 RPM	24.81 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2582 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2582 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2582 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,