RetrogeneDB ID: retro_ecab_388

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 16:75978104..75978677(-)
• Located in intron of: ENSECAG00000019885

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL13A
• Ensembl ID: ENSECAG00000015832
• Aliases: None
• Description: ribosomal protein L13a [Source:HGNC Symbol;Acc:10304]

Sequence

>retro_ecab_388
ATGGTGGAGGGGCAGGTCCTGGTTCTAGATGGCTGAGGCCTTCTCTGGGGCCACGTGGCAGTCACTGTACCCAAGCAAGG
GCTGCTGGACCAGAGGTGGTGGTTGTGCAATGTGAGGGCACCAACATTTCTGGCAATTTCTACAGAAACAAGTTGAAGCA
CCTGGCTTTCCTCCAAAAGCAGATGGACACAACCCATCCCGTGGCTCCTACCACTTCCGAGGCCCCAGCTGTATCTCTTG
GCGAACCATGCGAGGCACACTGCCCCACAGGCACAAGTGAGGTCACACGGCCCAGGACCTCCCCAAGGTACCTGATGGCA
TCCCACCACCCTACAACAAGAAAGAGCGAATGGTGGCTCCCACTGCCCTCAAGGTTGTATGTCTGAAGCCTGCACGAAAG
CCTGCCTCCCTGGGGCACCTGGCTCTTGAGGTGGGCTGGAAGCACCAGGCAGTTACAGCCACTCAGAGGAGAAGAGGAAG
GAGGAGGCCAAGATCCATTACCAGAAGAAATAACAGCTCATCAGACCATGGAAACAGGCTGAAGAGAACATGGAGAGGAA
AACTGACAAATAC

Alignment

ORF - retro_ecab_388 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.74 %
• Parental protein coverage: 94.58 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAEGQVLVLDGRGHLLGRLAAIVAKQVLL-GRKVVVVRCEGINISGNFYRNKLKYLAFLRKRMNT-NPSR
          M.EGQVLVLDG.G.L.G..A..V.KQ.LL.G..VVVV.CEG.NISGNFYRNKLK.LAFL.K.M.T.NPSR
Retrocopy MVEGQVLVLDG*GLLWGHVAVTVPKQGLL<GPEVVVVQCEGTNISGNFYRNKLKHLAFLQKQMDT<NPSR

Parental  GPYHFRAPSRIFWRTVRGMLPHKTKRGQAALDRLKVFDGIPPPYDKKKRMVVPAALKVVRLKPTRKFAYL
          G.YHFR.PS.I.WRT.RG.LPH..K.G..A.D..KV.DGIPPPY.KK.RMV.P.ALKVV.LKP.RK.A.L
Retrocopy GSYHFRGPSCISWRTMRGTLPHRHK*GHTAQDLPKVPDGIPPPYNKKERMVAPTALKVVCLKPARKPASL

Parental  GRLAHEVGWKYQAVTAT-LEEKRKEKAKIHYRKKKQLTRLRKQAEKNVEKKIDRY
          G.LA.EVGWK.QAVTAT..EEKRKE.AKIHY.KK.QL.R..KQAE.N.E.K.D.Y
Retrocopy GHLALEVGWKHQAVTAT<SEEKRKEEAKIHYQKK*QLIRPWKQAEENMERKTDKY

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	0.18 RPM	1340.63 RPM
SRP021940_cerebellum	0.21 RPM	377.08 RPM
SRP021940_embryo	0.56 RPM	895.50 RPM
SRP021940_placental_villous	0.29 RPM	582.96 RPM
SRP021940_synovial_membrane	0.85 RPM	852.14 RPM
SRP021940_testis	0.06 RPM	357.57 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_388 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_388 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_388 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 93 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005296	3 retrocopies	retro_btau_1251, retro_btau_719, retro_btau_789,
Canis familiaris	ENSCAFG00000029892	3 retrocopies	retro_cfam_1772, retro_cfam_924, retro_cfam_976,
Callithrix jacchus	ENSCJAG00000000072	16 retrocopies	retro_cjac_1130, retro_cjac_1706, retro_cjac_182, retro_cjac_197, retro_cjac_1997, retro_cjac_2170, retro_cjac_2322, retro_cjac_2467, retro_cjac_2468, retro_cjac_2665, retro_cjac_2699, retro_cjac_2755, retro_cjac_3009, retro_cjac_664, retro_cjac_941, retro_cjac_972,
Equus caballus	ENSECAG00000015832	3 retrocopies	retro_ecab_388 , retro_ecab_653, retro_ecab_773,
Echinops telfairi	ENSETEG00000017076	2 retrocopies	retro_etel_46, retro_etel_853,
Gorilla gorilla	ENSGGOG00000002932	11 retrocopies	retro_ggor_12, retro_ggor_1739, retro_ggor_214, retro_ggor_2271, retro_ggor_2737, retro_ggor_334, retro_ggor_6, retro_ggor_615, retro_ggor_627, retro_ggor_846, retro_ggor_869,
Loxodonta africana	ENSLAFG00000016213	3 retrocopies	retro_lafr_1160, retro_lafr_576, retro_lafr_810,
Macaca mulatta	ENSMMUG00000007551	14 retrocopies	retro_mmul_1100, retro_mmul_1256, retro_mmul_1638, retro_mmul_1756, retro_mmul_2179, retro_mmul_2249, retro_mmul_2352, retro_mmul_2399, retro_mmul_296, retro_mmul_500, retro_mmul_520, retro_mmul_547, retro_mmul_837, retro_mmul_924,
Mus musculus	ENSMUSG00000074129	3 retrocopies	retro_mmus_1129, retro_mmus_1334, retro_mmus_20,
Oryctolagus cuniculus	ENSOCUG00000025258	9 retrocopies	retro_ocun_1038, retro_ocun_1077, retro_ocun_1392, retro_ocun_1462, retro_ocun_304, retro_ocun_674, retro_ocun_756, retro_ocun_786, retro_ocun_972,
Otolemur garnettii	ENSOGAG00000004625	7 retrocopies	retro_ogar_1496, retro_ogar_211, retro_ogar_2254, retro_ogar_3148, retro_ogar_54, retro_ogar_596, retro_ogar_612,
Pongo abelii	ENSPPYG00000010251	1 retrocopy	retro_pabe_148,
Pan troglodytes	ENSPTRG00000011298	1 retrocopy	retro_ptro_31,
Pteropus vampyrus	ENSPVAG00000010958	3 retrocopies	retro_pvam_129, retro_pvam_625, retro_pvam_771,
Rattus norvegicus	ENSRNOG00000020618	10 retrocopies	retro_rnor_1073, retro_rnor_1112, retro_rnor_1212, retro_rnor_1292, retro_rnor_1357, retro_rnor_1742, retro_rnor_564, retro_rnor_593, retro_rnor_665, retro_rnor_988,
Sus scrofa	ENSSSCG00000003166	4 retrocopies	retro_sscr_290, retro_sscr_300, retro_sscr_392, retro_sscr_743,