RetrogeneDB ID: retro_rnor_1882

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 3:45240572..45241338(-)
• Located in intron of: ENSRNOG00000005335

Retrocopy information

• Ensembl ID: ENSRNOG00000005116
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Rps2
• Ensembl ID: ENSRNOG00000014179
• Aliases: Rps2, Rps2r1
• Description: 40S ribosomal protein S2 [Source:UniProtKB/Swiss-Prot;Acc:P27952]

Sequence

>retro_rnor_1882
GGTCACGGCCCAGGCCGTGGCCATTGTTGAGGCTATGGGGCTCATGGAGTAAATCTGAAGAGTAGTAGTAAATACCTGTC
ACCAAGCTGGGCCACCTGGTTAAGGACATGAAGATCAAGTCCCTGGAGATCTACCTGTTCTCCCTGCTCATTAAGGAGTC
TGAGATTATTGACTTTTTACAGGGTGCATCTCTAAAGGATGAGGTTCTGAAAATCATGCCAGTGCAGAAGCAGACAGATA
CTGGCCAGCAGATCCGGTTCAAGGCTTTTGTCACTATTGAGGACTGCAATGACCACATTGGTCTTGGTGTTAATTTCTCC
AAGAAGGTTGCCACTGCCATCCAAGGGGCCATAATCCTGGCCAAGTTTTCAACTTGTCCCTGTTCAGAGAGGCTACTGGG
GGAACAAGAGGGGCAAGCCCCCATAACGTTCCATGCAAGGTTACAGGCCTCTGTGGCCCTGTGCTGGTATGTCTCATCCT
TGTCCCCAGAGGCACTGGCATTGTCTCTGTTCCTGTGCCCAAGATCCTATTGATGATGGCTGGTATAGATGACTACTACA
CTTCAGCCAGGGGCTGCACTGTCACCCTAGGCAACTTTGCCAAAGCACACTTTGATGGCATCTTCAAGACCTATAGCTAC
CTGTCCCCAGACCTCTGGAAAGAGACTGTGTTCACCAAGTCTCCTTGTCAGGAATTCACTGAATATCTTGTGAAAACCCA
CACCAAAGTTTCTGTTCAGAGGACCCAGGCTCAAGCTGTGGCTACC

Alignment

ORF - retro_rnor_1882 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.99 %
• Parental protein coverage: 87.37 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GRGRGRGRGRGRGARG-GKAEDKEWIPVTKLGRLVKDMKIKSLEEIYLFSLPIKESEIIDFFLGASLKDE
          G.G.GRG...G.GA.G..K.E....IPVTKLG.LVKDMKIKSLE.IYLFSL.IKESEIIDF..GASLKDE
Retrocopy GHGPGRGHC*GYGAHG<SKSEE***IPVTKLGHLVKDMKIKSLE-IYLFSLLIKESEIIDFLQGASLKDE

Parental  VLKIMPVQKQTRAGQRTRFKAFVAIGDYNGHVGLGVKCSKEVATAIRGAIILAKLS-IVPVRRGYWGNKI
          VLKIMPVQKQT..GQ..RFKAFV.I.D.N.H.GLGV..SK.VATAI.GAIILAK.S..VPV.RGYWGNK.
Retrocopy VLKIMPVQKQTDTGQQIRFKAFVTIEDCNDHIGLGVNFSKKVATAIQGAIILAKFS>LVPVQRGYWGNKR

Parental  GKP-HTVPCKVTGRCGSVLVRLIPAPRGTGIVSAPVPKKLLMMAGIDDCYTSARGCTATLGNFAKATFDA
          GKP.H.VPCKVTG.CG.VLV.LI..PRGTGIVS.PVPK.LLMMAGIDD.YTSARGCT.TLGNFAKA.FD.
Retrocopy GKP>HNVPCKVTGLCGPVLVCLILVPRGTGIVSVPVPKILLMMAGIDDYYTSARGCTVTLGNFAKAHFDG

Parental  ISKTYSYLTPDLWKETVFTKSPYQEFTDHLVKTHTRVSVQRTQAPAVAT
          I.KTYSYL.PDLWKETVFTKSP.QEFT..LVKTHT.VSVQRTQA.AVAT
Retrocopy IFKTYSYLSPDLWKETVFTKSPCQEFTEYLVKTHTKVSVQRTQAQAVAT

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	122.44 RPM
SRP017611_kidney	0.00 RPM	209.07 RPM
SRP017611_liver	0.00 RPM	159.89 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1882 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1882 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1882 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 123 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000002549	1 retrocopy	retro_acar_57,
Bos taurus	ENSBTAG00000009535	7 retrocopies	retro_btau_1236, retro_btau_1420, retro_btau_1656, retro_btau_317, retro_btau_590, retro_btau_661, retro_btau_956,
Canis familiaris	ENSCAFG00000019472	19 retrocopies	retro_cfam_1028, retro_cfam_1252, retro_cfam_1321, retro_cfam_1460, retro_cfam_1560, retro_cfam_1592, retro_cfam_1842, retro_cfam_1848, retro_cfam_1932, retro_cfam_1983, retro_cfam_2007, retro_cfam_2012, retro_cfam_2046, retro_cfam_2053, retro_cfam_2110, retro_cfam_271, retro_cfam_323, retro_cfam_490, retro_cfam_629,
Cavia porcellus	ENSCPOG00000011651	11 retrocopies	retro_cpor_1030, retro_cpor_1238, retro_cpor_1376, retro_cpor_1469, retro_cpor_1527, retro_cpor_177, retro_cpor_19, retro_cpor_437, retro_cpor_718, retro_cpor_769, retro_cpor_808,
Dipodomys ordii	ENSDORG00000007375	18 retrocopies	retro_dord_163, retro_dord_206, retro_dord_215, retro_dord_284, retro_dord_392, retro_dord_445, retro_dord_465, retro_dord_499, retro_dord_500, retro_dord_505, retro_dord_568, retro_dord_571, retro_dord_572, retro_dord_683, retro_dord_703, retro_dord_711, retro_dord_723, retro_dord_89,
Equus caballus	ENSECAG00000009065	7 retrocopies	retro_ecab_1025, retro_ecab_1105, retro_ecab_509, retro_ecab_632, retro_ecab_876, retro_ecab_892, retro_ecab_949,
Loxodonta africana	ENSLAFG00000004696	11 retrocopies	retro_lafr_1072, retro_lafr_1092, retro_lafr_1103, retro_lafr_174, retro_lafr_284, retro_lafr_327, retro_lafr_376, retro_lafr_75, retro_lafr_801, retro_lafr_812, retro_lafr_917,
Macropus eugenii	ENSMEUG00000004508	2 retrocopies	retro_meug_156, retro_meug_2103,
Monodelphis domestica	ENSMODG00000016077	1 retrocopy	retro_mdom_536,
Mus musculus	ENSMUSG00000044533	1 retrocopy	retro_mmus_148,
Procavia capensis	ENSPCAG00000002090	2 retrocopies	retro_pcap_251, retro_pcap_433,
Pteropus vampyrus	ENSPVAG00000016704	8 retrocopies	retro_pvam_1395, retro_pvam_1486, retro_pvam_221, retro_pvam_240, retro_pvam_34, retro_pvam_459, retro_pvam_521, retro_pvam_595,
Rattus norvegicus	ENSRNOG00000014179	12 retrocopies	retro_rnor_1882 , retro_rnor_2191, retro_rnor_2257, retro_rnor_2274, retro_rnor_2903, retro_rnor_438, retro_rnor_631, retro_rnor_681, retro_rnor_690, retro_rnor_809, retro_rnor_810, retro_rnor_878,
Sarcophilus harrisii	ENSSHAG00000015213	5 retrocopies	retro_shar_186, retro_shar_288, retro_shar_456, retro_shar_525, retro_shar_783,
Tursiops truncatus	ENSTTRG00000011393	12 retrocopies	retro_ttru_1341, retro_ttru_1346, retro_ttru_1414, retro_ttru_149, retro_ttru_1762, retro_ttru_1816, retro_ttru_37, retro_ttru_375, retro_ttru_419, retro_ttru_650, retro_ttru_719, retro_ttru_872,
Vicugna pacos	ENSVPAG00000006867	6 retrocopies	retro_vpac_114, retro_vpac_164, retro_vpac_220, retro_vpac_354, retro_vpac_379, retro_vpac_518,