RetrogeneDB ID: retro_btau_1728

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: X:8751310..8751710(+)
• Located in intron of: ENSBTAG00000018819

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL32
• Ensembl ID: ENSBTAG00000015283
• Aliases: None
• Description: 60S ribosomal protein L32 [Source:UniProtKB/Swiss-Prot;Acc:Q3SZQ6]

Sequence

>retro_btau_1728
GTGGCTGCCCTCAGACCCCTTGTGAAGCCCAAGATTATCAAAAAGAGGACCAAGAAGTTCATCCAGCACCAGTCAGAATG
ACACGTCAAAATTAAGTGGAACTGGCGGAAACCAGAGGCATTGACAACAGGGTCTGTAGATTCAAAGGCCAAATCTGGAT
GCCAACATCAGTTACAGGAGCAACAAGGAAACAAAGCACATGCTGCCCAGTGGCTTCTGGAATTTTTTGGTTCACAATGT
CAAGGAGCTTGAAGCGCTGCTGATGTGCAACAAATCTTACTGTGCTGAGATTGCTCACAAAGTCCTCTCCAAGAGCCGCA
AAACCCTTGTGGACAGAGCAGCCCACTTGGGCATCAGAATTAGCAATACCAATGCCAGGTTGTGCAGGGAAGAAAAGGAA

Alignment

ORF - retro_btau_1728 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.37 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAALRPLVKPKIVKKRTKKFIRHQSDRYVKIKRNWRKP-RGIDNRVRRRFKGQILMP-NIGYGSNKKTKH
          .AALRPLVKPKI.KKRTKKFI.HQS...VKIK.NWRKP.RGIDNRV.R.FKGQI.MP.NI.Y.SNK.TKH
Retrocopy VAALRPLVKPKIIKKRTKKFIQHQSE*HVKIKWNWRKP<RGIDNRVCR-FKGQIWMP<NISYRSNKETKH

Parental  MLPSGFRKFLVHNVKELEVLLMCNKSYCAEIAHNVSSKNRKAIVERAAQLAIRITNPNARLRSEENE
          MLPSGF..FLVHNVKELE.LLMCNKSYCAEIAH.V.SK.RK..V.RAA.L.IRI.N.NARL..EE.E
Retrocopy MLPSGFWNFLVHNVKELEALLMCNKSYCAEIAHKVLSKSRKTLVDRAAHLGIRISNTNARLCREEKE

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	69.50 RPM
ERP005899_muscle	0.00 RPM	1096.54 RPM
SRP017611_brain	0.00 RPM	108.17 RPM
SRP017611_kidney	0.00 RPM	229.50 RPM
SRP017611_liver	0.00 RPM	143.69 RPM
SRP030211_testis	0.00 RPM	205.08 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1728 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1728 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1728 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 208 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000014763	3 retrocopies	retro_acar_104, retro_acar_125, retro_acar_67,
Ailuropoda melanoleuca	ENSAMEG00000004583	26 retrocopies	retro_amel_1004, retro_amel_1041, retro_amel_1059, retro_amel_112, retro_amel_1274, retro_amel_1284, retro_amel_13, retro_amel_1394, retro_amel_1450, retro_amel_150, retro_amel_1651, retro_amel_168, retro_amel_1766, retro_amel_1827, retro_amel_1897, retro_amel_274, retro_amel_275, retro_amel_44, retro_amel_573, retro_amel_658, retro_amel_71, retro_amel_776, retro_amel_781, retro_amel_871, retro_amel_892, retro_amel_923,
Bos taurus	ENSBTAG00000015283	10 retrocopies	retro_btau_1102, retro_btau_1391, retro_btau_1568, retro_btau_1645, retro_btau_1728 , retro_btau_1764, retro_btau_377, retro_btau_623, retro_btau_631, retro_btau_654,
Choloepus hoffmanni	ENSCHOG00000013534	27 retrocopies	retro_chof_1131, retro_chof_1164, retro_chof_1181, retro_chof_1234, retro_chof_1461, retro_chof_152, retro_chof_1821, retro_chof_1957, retro_chof_2022, retro_chof_205, retro_chof_2090, retro_chof_2146, retro_chof_2242, retro_chof_2265, retro_chof_2301, retro_chof_2410, retro_chof_2509, retro_chof_2527, retro_chof_2606, retro_chof_276, retro_chof_286, retro_chof_313, retro_chof_554, retro_chof_585, retro_chof_607, retro_chof_758, retro_chof_913,
Cavia porcellus	ENSCPOG00000019967	2 retrocopies	retro_cpor_1241, retro_cpor_608,
Equus caballus	ENSECAG00000007201	4 retrocopies	retro_ecab_1115, retro_ecab_26, retro_ecab_369, retro_ecab_698,
Felis catus	ENSFCAG00000030450	38 retrocopies	retro_fcat_1014, retro_fcat_1063, retro_fcat_1173, retro_fcat_1185, retro_fcat_1186, retro_fcat_1340, retro_fcat_1402, retro_fcat_144, retro_fcat_1515, retro_fcat_1526, retro_fcat_16, retro_fcat_1600, retro_fcat_1620, retro_fcat_1665, retro_fcat_1674, retro_fcat_1779, retro_fcat_1819, retro_fcat_1847, retro_fcat_1857, retro_fcat_1863, retro_fcat_191, retro_fcat_1912, retro_fcat_1981, retro_fcat_319, retro_fcat_357, retro_fcat_412, retro_fcat_435, retro_fcat_438, retro_fcat_499, retro_fcat_510, retro_fcat_660, retro_fcat_740, retro_fcat_745, retro_fcat_893, retro_fcat_936, retro_fcat_95, retro_fcat_979, retro_fcat_997,
Loxodonta africana	ENSLAFG00000032737	1 retrocopy	retro_lafr_14,
Myotis lucifugus	ENSMLUG00000022528	6 retrocopies	retro_mluc_100, retro_mluc_1283, retro_mluc_173, retro_mluc_2224, retro_mluc_2256, retro_mluc_48,
Macaca mulatta	ENSMMUG00000001340	6 retrocopies	retro_mmul_106, retro_mmul_117, retro_mmul_126, retro_mmul_79, retro_mmul_93, retro_mmul_95,
Mustela putorius furo	ENSMPUG00000017189	4 retrocopies	retro_mputfur_121, retro_mputfur_76, retro_mputfur_8, retro_mputfur_85,
Mus musculus	ENSMUSG00000057841	16 retrocopies	retro_mmus_1132, retro_mmus_1142, retro_mmus_1746, retro_mmus_2010, retro_mmus_2263, retro_mmus_2316, retro_mmus_2341, retro_mmus_2699, retro_mmus_3099, retro_mmus_3378, retro_mmus_3605, retro_mmus_385, retro_mmus_442, retro_mmus_496, retro_mmus_533, retro_mmus_985,
Nomascus leucogenys	ENSNLEG00000004789	12 retrocopies	retro_nleu_1109, retro_nleu_125, retro_nleu_1452, retro_nleu_1642, retro_nleu_193, retro_nleu_224, retro_nleu_2808, retro_nleu_2809, retro_nleu_442, retro_nleu_497, retro_nleu_56, retro_nleu_603,
Otolemur garnettii	ENSOGAG00000028498	24 retrocopies	retro_ogar_129, retro_ogar_1321, retro_ogar_1340, retro_ogar_1360, retro_ogar_1425, retro_ogar_1524, retro_ogar_160, retro_ogar_1683, retro_ogar_1766, retro_ogar_1833, retro_ogar_2032, retro_ogar_2412, retro_ogar_2416, retro_ogar_2515, retro_ogar_3247, retro_ogar_3384, retro_ogar_545, retro_ogar_56, retro_ogar_571, retro_ogar_776, retro_ogar_870, retro_ogar_891, retro_ogar_924, retro_ogar_973,
Pongo abelii	ENSPPYG00000013391	2 retrocopies	retro_pabe_135, retro_pabe_98,
Rattus norvegicus	ENSRNOG00000010746	4 retrocopies	retro_rnor_179, retro_rnor_27, retro_rnor_278, retro_rnor_327,
Sarcophilus harrisii	ENSSHAG00000012782	1 retrocopy	retro_shar_580,
Sus scrofa	ENSSSCG00000027637	9 retrocopies	retro_sscr_1001, retro_sscr_1054, retro_sscr_107, retro_sscr_1081, retro_sscr_165, retro_sscr_76, retro_sscr_793, retro_sscr_957, retro_sscr_989,
Ictidomys tridecemlineatus	ENSSTOG00000026505	9 retrocopies	retro_itri_1294, retro_itri_1322, retro_itri_1465, retro_itri_1639, retro_itri_1715, retro_itri_1748, retro_itri_370, retro_itri_885, retro_itri_948,
Tupaia belangeri	ENSTBEG00000012875	3 retrocopies	retro_tbel_3304, retro_tbel_47, retro_tbel_51,
Vicugna pacos	ENSVPAG00000002594	1 retrocopy	retro_vpac_17,