RetrogeneDB ID: retro_ecab_897

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 6:29455836..29456612(-)
• Located in intron of: ENSECAG00000024908

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL3
• Ensembl ID: ENSECAG00000020665
• Aliases: None
• Description: ribosomal protein L3 [Source:HGNC Symbol;Acc:10332]

Sequence

>retro_ecab_897
AAGCAACTGGAGAAGGACTTCAACAGCATGAAGAAGTACTGCCAGGTCATCTGTGTCATCGCCCACACCCAGATGCTCCT
GCTTCCTCTGCGCCAGAAGAAGCCCTATCTCAAGGAAATCAAAGTGAATAGAGGCACTGTGGCTGAGAAATTGGACCAGC
CCCATGGGAGGCTGGAGCAGCAGTTTCCTGTGAACCAAGTTTTTGGGCAGTATGAGATGGTCGATGCCATCGGGGTGACC
AAAGGCAAAGGCTACAAAGGGGTCACTAGCTGCGGGCACACCAAGAAGCTGCCCTGCAAGACCCACCAACGGCTGTGCAA
GGTTGCCTGTATTGGGGCATGGCATTCTGTCTGAGTGGCTTTCTCTGTGGCACGGGCTGGGCAGAAAGGCTACCATCACT
GCACCAAGATCAACAAGAAGATCTCCAAGATTGGCCAGGGCTACCTCATCAAGATGGCAAACTGATCAAGAACAGTGCCT
CCACTGATTGTGATCTGTCTGACAAGAGTATCAACCCTTTGGGTGGCTTTGTCCGCTTTGGTGAAGTGACCAATGACTTT
CTCATGCCGAAAGGCTGGGTGGTGGGAACCAAGAAGCGAGTGCTCACCCTTTGCATGTCCTTGCTGGTGCAGACAAAGTG
GTGGGCCCTGGAGAAGGTTGACCTCAAGTTCATCCATACCACCTCCAAGTTTGGCCATGGCCGCTTCTAGACAGTGGAGG
AGAAGAAAGCATTCATGGGATCACTTAAGAAAGACCGAATTGCAAAGGAAGAAGGA

Alignment

ORF - retro_ecab_897 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.46 %
• Parental protein coverage: 64.43 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KQLEKDFSSMKKYCQVIRVIAHTQMRLLPLRQKKAHLMEIQVNGGTVAEKLDWARERLEQQVPVNQVFGQ
          KQLEKDF.SMKKYCQVI.VIAHTQM.LLPLRQKK..L.EI.VN.GTVAEKLD....RLEQQ.PVNQVFGQ
Retrocopy KQLEKDFNSMKKYCQVICVIAHTQMLLLPLRQKKPYLKEIKVNRGTVAEKLDQPHGRLEQQFPVNQVFGQ

Parental  DEMIDVIGVTKGKGYKGVTSRWHTKKLPRKTHRGLRKVACIGAWHPARVAFSVARAGQKGYHHRTEINKK
          .EM.D.IGVTKGKGYKGVTS..HTKKLP.KTH..L.KVACIGAWH...VAFSVARAGQKGYHH.T.INKK
Retrocopy YEMVDAIGVTKGKGYKGVTSCGHTKKLPCKTHQRLCKVACIGAWHSV*VAFSVARAGQKGYHHCTKINKK

Parental  IYKIGQGYLIK-DGKLIKNNASTDYDLSDKSINPLGGFVHYGEVTNDFVMLKGCVVGTKKRVLTLRKSLL
          I.KIGQGYLIK.DGKLIKN.ASTD.DLSDKSINPLGGFV..GEVTNDF.M.KG.VVGTKKRVLTL..SLL
Retrocopy ISKIGQGYLIK<DGKLIKNSASTDCDLSDKSINPLGGFVRFGEVTNDFLMPKGWVVGTKKRVLTLCMSLL

Parental  VQTKRRALEKVDLKFIDTTSKFGHGRFQTVEEKKAFMGPLKKDRIAKEEG
          VQTK..ALEKVDLKFI.TTSKFGHGRF.TVEEKKAFMG.LKKDRIAKEEG
Retrocopy VQTKWWALEKVDLKFIHTTSKFGHGRF*TVEEKKAFMGSLKKDRIAKEEG

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
SRP021940_articular_cartilage	0.24 RPM	2429.67 RPM
SRP021940_cerebellum	0.31 RPM	953.12 RPM
SRP021940_embryo	1.13 RPM	1675.57 RPM
SRP021940_placental_villous	0.67 RPM	868.45 RPM
SRP021940_synovial_membrane	0.85 RPM	1754.87 RPM
SRP021940_testis	0.19 RPM	563.98 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_897 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_897 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_897 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 82 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003228	3 retrocopies	retro_btau_1644, retro_btau_281, retro_btau_341,
Canis familiaris	ENSCAFG00000001346	1 retrocopy	retro_cfam_97,
Callithrix jacchus	ENSCJAG00000016276	6 retrocopies	retro_cjac_1198, retro_cjac_1972, retro_cjac_2157, retro_cjac_2264, retro_cjac_3079, retro_cjac_823,
Equus caballus	ENSECAG00000020665	1 retrocopy	retro_ecab_897 ,
Gorilla gorilla	ENSGGOG00000002326	10 retrocopies	retro_ggor_1043, retro_ggor_1295, retro_ggor_1582, retro_ggor_1822, retro_ggor_2329, retro_ggor_2616, retro_ggor_2713, retro_ggor_2736, retro_ggor_2955, retro_ggor_36,
Macropus eugenii	ENSMEUG00000009789	26 retrocopies	retro_meug_1045, retro_meug_118, retro_meug_1210, retro_meug_1403, retro_meug_1452, retro_meug_1492, retro_meug_1516, retro_meug_1554, retro_meug_1589, retro_meug_1604, retro_meug_1698, retro_meug_1856, retro_meug_2150, retro_meug_2151, retro_meug_221, retro_meug_367, retro_meug_412, retro_meug_461, retro_meug_592, retro_meug_677, retro_meug_683, retro_meug_831, retro_meug_851, retro_meug_886, retro_meug_889, retro_meug_898,
Macaca mulatta	ENSMMUG00000010029	4 retrocopies	retro_mmul_1170, retro_mmul_149, retro_mmul_2334, retro_mmul_973,
Monodelphis domestica	ENSMODG00000009539	2 retrocopies	retro_mdom_380, retro_mdom_408,
Nomascus leucogenys	ENSNLEG00000015234	2 retrocopies	retro_nleu_1038, retro_nleu_1449,
Oryctolagus cuniculus	ENSOCUG00000027712	4 retrocopies	retro_ocun_105, retro_ocun_179, retro_ocun_1893, retro_ocun_558,
Otolemur garnettii	ENSOGAG00000000032	7 retrocopies	retro_ogar_1264, retro_ogar_1679, retro_ogar_2096, retro_ogar_2122, retro_ogar_2448, retro_ogar_3431, retro_ogar_960,
Pongo abelii	ENSPPYG00000011837	10 retrocopies	retro_pabe_1113, retro_pabe_1861, retro_pabe_2167, retro_pabe_2743, retro_pabe_2985, retro_pabe_3170, retro_pabe_3318, retro_pabe_3349, retro_pabe_3696, retro_pabe_3761,
Rattus norvegicus	ENSRNOG00000016896	2 retrocopies	retro_rnor_1333, retro_rnor_731,
Sarcophilus harrisii	ENSSHAG00000003212	2 retrocopies	retro_shar_154, retro_shar_662,
Tursiops truncatus	ENSTTRG00000010880	2 retrocopies	retro_ttru_1266, retro_ttru_1518,