RetrogeneDB ID: retro_rnor_558

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 1:3420206..3420710(-)
• Located in intron of: ENSRNOG00000014303

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS6
• Ensembl ID: ENSRNOG00000007663
• Aliases: None
• Description: 40S ribosomal protein S6 [Source:UniProtKB/Swiss-Prot;Acc:P62755]

Sequence

>retro_rnor_558
ATGGAGCTGAACGTCTCCTTCTCTGCAACTGGCTGTCAGAGCCTCACAGAGGTGGGTGATAGACGCAAGCTTCACGCTCT
CTATGAGAAGCGCCTAGTCACAGAAGCAGCGGCCGCCGCTGAGTGAGGAATACATGGGCTATGTGTTCGGAAGCAGGGGT
GAGAATGACAAACAAGGTTTCCCCATGAAGTGTGAGGTGTCCTGACCCATGACACAGTGCGCCTGCTGCTGAGTAAGGGG
CAGTCTCATTACAGACCAAGGATAACTGGAGAGAGGAAGCCCATGTCTGTTCAAGGATGCATTGTGGGTGCCGTCTGAGC
GTTCTCAAACTTATATTCTTGCTTATTGTTAAAAGTGGGGGAAGGATATTCCTGGACCGACGAATATCACTGTGCCTCAG
TGGTTAGTGTACAAAAGAGCTAGGAGAACCTGAAGGTTTTTGATCTCTCTAAGGAAGACGATGTCCACCAACATGCTGCT
TGAAAGCCCTCAAAGAAGGTAGGA

Alignment

ORF - retro_rnor_558 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.14 %
• Parental protein coverage: 66.67 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MKLNISFPATGCQKLIEVDDERKLRTFYEKRMATEVAADA-LGEEWKGYVVRISGGNDKQG-FPMKQ-GV
          M.LN.SF.ATGCQ.L.EV.D.RKL...YEKR..TE.AA.A.L.EE..GYV....G.NDKQG.FP....GV
Retrocopy MELNVSFSATGCQSLTEVGDRRKLHALYEKRLVTE-AAAA>LSEEYMGYVFGSRGENDKQG<FPHEV*GV

Parental  LTHGRVRLLLSKGHSCYRPRRTGERKRKSVRGCIVDA-NLSVLNLV---IVKKG-EKDIPGLTDTTVPRR
          LTH..VRLLLSKG.S.YRPR.TGERK..SV.GCIV.A..LSVL.L....IVK.G..KDIPG.T..TVP..
Retrocopy LTHDTVRLLLSKGQSHYRPRITGERKPMSVQGCIVGA<RLSVLKLIFLLIVKSG<GKDIPGPTNITVPQW

Parental  LGPKRASRI-RKLFNLSKEDDVRQYVVRKPLNKEG
          L..KRA.R...K.F.LSKEDDV.Q....KP..K.G
Retrocopy LVYKRARRT<LKVFDLSKEDDVHQHAA*KPSKKVG

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	0.43 RPM	0.14 RPM
SRP017611_kidney	0.00 RPM	0.00 RPM
SRP017611_liver	0.07 RPM	0.07 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_558 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_558 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_558 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Mus musculus	retro_mmus_617

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 132 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000017634	1 retrocopy	retro_acar_20,
Cavia porcellus	ENSCPOG00000003750	4 retrocopies	retro_cpor_1244, retro_cpor_22, retro_cpor_317, retro_cpor_486,
Echinops telfairi	ENSETEG00000001584	18 retrocopies	retro_etel_1143, retro_etel_1281, retro_etel_1410, retro_etel_1430, retro_etel_1575, retro_etel_167, retro_etel_1822, retro_etel_188, retro_etel_1964, retro_etel_2004, retro_etel_2041, retro_etel_2194, retro_etel_263, retro_etel_337, retro_etel_378, retro_etel_541, retro_etel_809, retro_etel_825,
Ficedula albicollis	ENSFALG00000003078	1 retrocopy	retro_falb_24,
Homo sapiens	ENSG00000137154	16 retrocopies	retro_hsap_1009, retro_hsap_1067, retro_hsap_1231, retro_hsap_1310, retro_hsap_1967, retro_hsap_2184, retro_hsap_2298, retro_hsap_3045, retro_hsap_3996, retro_hsap_4122, retro_hsap_4235, retro_hsap_4279, retro_hsap_4860, retro_hsap_731, retro_hsap_818, retro_hsap_966,
Loxodonta africana	ENSLAFG00000010766	4 retrocopies	retro_lafr_1021, retro_lafr_1239, retro_lafr_59, retro_lafr_667,
Myotis lucifugus	ENSMLUG00000007588	27 retrocopies	retro_mluc_1041, retro_mluc_1146, retro_mluc_1169, retro_mluc_1393, retro_mluc_1411, retro_mluc_1448, retro_mluc_1472, retro_mluc_1532, retro_mluc_1566, retro_mluc_1593, retro_mluc_1629, retro_mluc_1635, retro_mluc_1723, retro_mluc_1799, retro_mluc_1909, retro_mluc_1928, retro_mluc_1933, retro_mluc_2110, retro_mluc_2129, retro_mluc_490, retro_mluc_493, retro_mluc_514, retro_mluc_557, retro_mluc_652, retro_mluc_678, retro_mluc_722, retro_mluc_830,
Monodelphis domestica	ENSMODG00000004095	1 retrocopy	retro_mdom_301,
Ochotona princeps	ENSOPRG00000012290	5 retrocopies	retro_opri_123, retro_opri_642, retro_opri_78, retro_opri_862, retro_opri_895,
Pan troglodytes	ENSPTRG00000039153	19 retrocopies	retro_ptro_1313, retro_ptro_1442, retro_ptro_1627, retro_ptro_1662, retro_ptro_1994, retro_ptro_2442, retro_ptro_2713, retro_ptro_2799, retro_ptro_2878, retro_ptro_2902, retro_ptro_2938, retro_ptro_3235, retro_ptro_519, retro_ptro_569, retro_ptro_669, retro_ptro_749, retro_ptro_785, retro_ptro_799, retro_ptro_845,
Rattus norvegicus	ENSRNOG00000007663	21 retrocopies	retro_rnor_1092, retro_rnor_1093, retro_rnor_1269, retro_rnor_1484, retro_rnor_1556, retro_rnor_1564, retro_rnor_1845, retro_rnor_1901, retro_rnor_1991, retro_rnor_2071, retro_rnor_2073, retro_rnor_2187, retro_rnor_2332, retro_rnor_2447, retro_rnor_2781, retro_rnor_2790, retro_rnor_558 , retro_rnor_756, retro_rnor_896, retro_rnor_942, retro_rnor_943,
Rattus norvegicus	ENSRNOG00000049025	8 retrocopies	retro_rnor_1008, retro_rnor_1189, retro_rnor_1988, retro_rnor_1990, retro_rnor_2085, retro_rnor_2635, retro_rnor_479, retro_rnor_718,
Sorex araneus	ENSSARG00000006549	6 retrocopies	retro_sara_284, retro_sara_369, retro_sara_392, retro_sara_436, retro_sara_512, retro_sara_710,
Sarcophilus harrisii	ENSSHAG00000005486	1 retrocopy	retro_shar_549,