RetrogeneDB ID: retro_btau_1388

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 5:70650321..70650810(+)
• Located in intron of: ENSBTAG00000010149

Retrocopy information

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

Parental gene information

• Parental gene symbol: BT.65634
• Ensembl ID: ENSBTAG00000015285
• Aliases: None
• Description: 40S ribosomal protein S8 [Source:UniProtKB/Swiss-Prot;Acc:Q5E958]

Sequence

>retro_btau_1388
GGAGCAAGAAAGCCCTACCACAGGAAGCAGAAGTATGAGCTGAGAATCCCTGCTGCCAACACTAAGATTGATGCTGGCCT
CATACACACAGTCCATGTGCAGGGAGGCAACAAGAAATACCGTATCTTGAGGCTGGACATGGACATGGGGAAATTTTACT
GAGGCTTGGAGTGTTGTATGTGCAAAGCAAGGATTAAAGATGTTGTTCACAGTGCATCCAACGATGAGCTGGTCAGTACC
AAGACCCTAGTGAAGAACTGCATCTTGCTCACTGACAGCACACTATTCTGAGAGAAGTAGGGGTCCCACTATGCACTGCC
TCTGGGCTGCAAGAATGGAGCCAAGCTGACTCTCAAGGAAGAAGGGATTTTAAACAACAACAATAAAAAATGACCTAAGA
AAATTCAGAAGAAATATGATGAAAAGGAGAATGCTCAAATCAGCAGTTTTCTGAAGGAGCAGTTCCAGGAGCGAAAGCTT
CTTGCATGC

Alignment

ORF - retro_btau_1388 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.68 %
• Parental protein coverage: 76.81 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GKRKPYHKKRKYELGRPAANTKIGPRRIHTVRVRGGNKKYRALRLDV--GNFSWGSECCTRKTRIIDVVY
          G.RKPYH.K.KYEL..PAANTKI....IHTV.V.GGNKKYR.LRLD...G.F..G.ECC..K.RI.DVV.
Retrocopy GARKPYHRKQKYELRIPAANTKIDAGLIHTVHVQGGNKKYRILRLDMDMGKFY*GLECCMCKARIKDVVH

Parental  NASNNELVRTKTLVKNCIVLIDSTPYRQWYESHYALPLGRKKGAKLTPEEEEILN---KKRSKKIQKKYD
          .ASN.ELV.TKTLVKNCI.L.DST.......SHYALPLG.K.GAKLT..EE.ILN...KK..KKIQKKYD
Retrocopy SASNDELVSTKTLVKNCILLTDSTLF*EK*GSHYALPLGCKNGAKLTLKEEGILNNNNKK*PKKIQKKYD

Parental  ERKKNAKISSLLEEQFQQGKLLAC
          E.K.NA.ISS.L.EQFQ..KLLAC
Retrocopy E-KENAQISSFLKEQFQERKLLAC

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	301.00 RPM
ERP005899_muscle	0.11 RPM	2211.18 RPM
SRP017611_brain	0.00 RPM	199.85 RPM
SRP017611_kidney	0.00 RPM	421.48 RPM
SRP017611_liver	0.00 RPM	265.64 RPM
SRP030211_testis	0.09 RPM	185.16 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1388 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1388 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1388 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 92 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000015285	2 retrocopies	retro_btau_1388 , retro_btau_1593,
Canis familiaris	ENSCAFG00000004745	8 retrocopies	retro_cfam_1336, retro_cfam_1662, retro_cfam_1730, retro_cfam_2139, retro_cfam_2177, retro_cfam_261, retro_cfam_589, retro_cfam_791,
Callithrix jacchus	ENSCJAG00000004197	5 retrocopies	retro_cjac_1068, retro_cjac_181, retro_cjac_3138, retro_cjac_6, retro_cjac_951,
Cavia porcellus	ENSCPOG00000000723	3 retrocopies	retro_cpor_1099, retro_cpor_335, retro_cpor_621,
Dipodomys ordii	ENSDORG00000009287	1 retrocopy	retro_dord_429,
Felis catus	ENSFCAG00000022996	4 retrocopies	retro_fcat_1222, retro_fcat_200, retro_fcat_456, retro_fcat_962,
Gorilla gorilla	ENSGGOG00000005645	5 retrocopies	retro_ggor_1127, retro_ggor_1170, retro_ggor_1357, retro_ggor_1465, retro_ggor_556,
Myotis lucifugus	ENSMLUG00000001559	30 retrocopies	retro_mluc_1114, retro_mluc_1132, retro_mluc_1165, retro_mluc_1277, retro_mluc_1288, retro_mluc_1418, retro_mluc_1467, retro_mluc_1476, retro_mluc_1486, retro_mluc_1634, retro_mluc_1656, retro_mluc_1689, retro_mluc_1808, retro_mluc_1911, retro_mluc_1938, retro_mluc_2043, retro_mluc_2055, retro_mluc_2085, retro_mluc_2111, retro_mluc_2153, retro_mluc_2182, retro_mluc_2209, retro_mluc_2414, retro_mluc_460, retro_mluc_662, retro_mluc_730, retro_mluc_773, retro_mluc_820, retro_mluc_821, retro_mluc_906,
Macaca mulatta	ENSMMUG00000015270	2 retrocopies	retro_mmul_275, retro_mmul_70,
Nomascus leucogenys	ENSNLEG00000014147	1 retrocopy	retro_nleu_34,
Oryctolagus cuniculus	ENSOCUG00000012476	1 retrocopy	retro_ocun_168,
Otolemur garnettii	ENSOGAG00000006922	16 retrocopies	retro_ogar_1156, retro_ogar_1746, retro_ogar_1895, retro_ogar_2501, retro_ogar_2529, retro_ogar_2556, retro_ogar_2699, retro_ogar_2723, retro_ogar_2947, retro_ogar_308, retro_ogar_3291, retro_ogar_3436, retro_ogar_394, retro_ogar_521, retro_ogar_730, retro_ogar_805,
Pongo abelii	ENSPPYG00000001426	1 retrocopy	retro_pabe_147,
Pan troglodytes	ENSPTRG00000000659	1 retrocopy	retro_ptro_30,
Pteropus vampyrus	ENSPVAG00000009859	10 retrocopies	retro_pvam_1285, retro_pvam_1315, retro_pvam_1345, retro_pvam_403, retro_pvam_419, retro_pvam_463, retro_pvam_514, retro_pvam_578, retro_pvam_685, retro_pvam_991,
Rattus norvegicus	ENSRNOG00000018768	2 retrocopies	retro_rnor_222, retro_rnor_235,