RetrogeneDB ID: retro_rnor_1372

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 18:82951724..82952769(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Rpf1
• Ensembl ID: ENSRNOG00000015969
• Aliases: Rpf1, Bxdc5
• Description: ribosome production factor 1 [Source:RefSeq peptide;Acc:NP_001094264]

Sequence

>retro_rnor_1372
ATGGCAAAGGCCGGCAAGAAAAGTGGCAGTGGTAGCAAGCGAGGCTTGAAGAGGGAAGTCGCTGCTAAAGAGCCCTAAGA
GGCTGCGATCAAGAGCAATGGGAAGGCTGCGAGGGTCGGGGGATTGCTGTCCGTGAAAGCCGCTCAACCCACCCTGGGCT
TCAGTATCTTGGAGATTAAGAACAAGTAGCCACAATACTTGCTGTTCACACAGTGGAAACAGCAGCAGGAGAAAGAAAAG
TTGGCAGCTAAGGAAAAACTTAAGAGAGAAAGGCTCTTGGTAAAAGGTTCCACCAAAGCCTGTCCCCAAGACCATTGACC
AGCAACTCCTTATGATGAGCCCTCATTAGACCCCAATGAAGAAGAGGTGGCTTATGAGGAAGCTACAGATGAATTTGTTT
CTTACTTCATCAACAGAGACGTCTCCTAAGATTCTTATCATAACGTCAGAGAGACCTCATGGGAGAACAGTATGACTCTG
TGAGCAGCTCTCAACAGTTATACCAGATCCAAATGTATATTACAGAAGAGGACTGGCTCTGAAAAAATTATCCCACAGTG
CATTGCAAGAGATTTCACAGGCCTGATCATTATTTAATGAAGATCTTAATACACCAAATGGACTTATTCTGAGTTAGTTG
CCAAATGGTCCAAGTACTCATTTTAAAATGAGTAGTGTTCCTCTTCATAAAGAAATTAGGCAATGAGGCAAACACCCCAC
AGAACATGTACCCGAGATAATTCTAAATAACTGTACCACATGAATAGGTCATTCTATCAGACGTATGTTCGCTTCTCTAT
TTCCTCATATTCTCCAATTTATTGGAAGACAAGTTGCCACGTTCCACAATCAGCAGTAATACATCCTCAGGTTTCACAGA
TACATATTCAAGAGTGAAAAGAAGGTGGAAATTCAGGAACATGGACAATGTTTTACCTTGAAATTATGATTTCTCCATAA
GGGAAAGTTTGATTCTAAGTATGGAGAGTATGAATGGGTCCACAAGCCATGGGAAATGGATATAAGTCAAAGTAAATGCC
ATATA

Alignment

ORF - retro_rnor_1372 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.63 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 8
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MAKAGEKSGGGGKRGLKRKAPAEEPQETAVASDGTAE--SGVQSAKAAAFPPGFSISEIKNKQRRHLMFT
          MAKAG.KSG.G.KRGLKR...A.EP.E.A..S.G.A....G..S.KAA....GFSI.EIKNK....L.FT
Retrocopy MAKAGKKSGSGSKRGLKREVAAKEP*EAAIKSNGKAARVGGLLSVKAAQPTLGFSILEIKNK*PQYLLFT

Parental  RWKQQQRKEKLAAKKKLKREREALGDKAPPKPVP-KTIDNQRV-YDETTVDPNDEEVAYDEATDEFASYF
          .WKQQQ.KEKLAAK.KLKRER..L..K...K..P.KTID.Q...YDE...DPN.EEVAY.EATDEF.SYF
Retrocopy QWKQQQEKEKLAAKEKLKRER--LLVKGSTKACP>KTIDQQLL<YDEPSLDPNEEEVAYEEATDEFVSYF

Parental  -NRQTSPKILITTSDRPHGRTVRLCEQLSTVIPDSHVYYRRGLALK-KIIPQCIARDFTDLIVI-NEDRK
          ....TSPKILI.TS.RPHGRTV.LCEQLSTVIPD..VYYRRGLALK.KIIPQCIARDFT.LI.I.NED..
Retrocopy >STETSPKILIITSERPHGRTV*LCEQLSTVIPDPNVYYRRGLALK<KIIPQCIARDFTGLIII>NEDLN

Parental  TPNGLILSHLPNGPTAHFKMSSVRLRKEIKRRGKDPTEHVPEIILNNFTTRLGHSIGRMFASLFPHNPQF
          TPNGLILS.LPNGP..HFKMSSV.L.KEI...GK.PTEHVPEIILNN.TT..GHSI.RMFASLFPH..QF
Retrocopy TPNGLILS*LPNGPSTHFKMSSVPLHKEIRQ*GKHPTEHVPEIILNNCTT*IGHSIRRMFASLFPHILQF

Parental  IGRQVATFHNQRDYIFFRFHRYIFKSEKKVGIQELGPRFTLKLRSLQKGTFDSKYGEYEWVHKPREMDTS
          IGRQVATFHNQ..YI..RFHRYIFKSEKKV.IQE.G..FTLKL..L.KG.FDSKYGEYEWVHKP.EMD.S
Retrocopy IGRQVATFHNQQ*YI-LRFHRYIFKSEKKVEIQEHGQCFTLKL*FLHKGKFDSKYGEYEWVHKPWEMDIS

Parental  RRKFHL
          ..K.H.
Retrocopy QSKCHI

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	10.28 RPM
SRP017611_kidney	0.00 RPM	15.42 RPM
SRP017611_liver	0.00 RPM	8.81 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1372 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1372 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1372 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000001097	1 retrocopy	retro_eeur_17,
Myotis lucifugus	ENSMLUG00000016028	2 retrocopies	retro_mluc_681, retro_mluc_942,
Mus musculus	ENSMUSG00000028187	1 retrocopy	retro_mmus_3026,
Oryctolagus cuniculus	ENSOCUG00000014803	1 retrocopy	retro_ocun_1133,
Pteropus vampyrus	ENSPVAG00000003729	1 retrocopy	retro_pvam_1489,
Rattus norvegicus	ENSRNOG00000015969	1 retrocopy	retro_rnor_1372 ,
Tupaia belangeri	ENSTBEG00000013600	4 retrocopies	retro_tbel_1027, retro_tbel_2204, retro_tbel_2279, retro_tbel_63,