RetrogeneDB ID: retro_ecab_559

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 20:56388583..56388945(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSECAG00000021116
• Aliases: None
• Description: Profilin [Source:UniProtKB/TrEMBL;Acc:F6UJ33]

Sequence

>retro_ecab_559
GGGATCTGTCAGGACAAGACTATTCTGGGCTATAAGGACTCAACCTCTGGTCTGGGCCATCGTCCAGGCAAAACCTTCAT
CAACATCACGCCAGCTGAGGTTGGCGTCCTGGTTGGCAAAGACTGGTCAAGTGTTCCCGTGAATGGGCTGACACTTGGGG
GCTAGAAATATTATGTGATGTGGGGCTCGCTGCCGCAGGGCGGGGAATTTACCCTCCATCTTCCTACCAGGAGCACGAGC
GGAGCCTCCACTTCACCATCATTGTCACCATGACTGCCAAGACGTTAGCCCTGCTGATGGGCAATGCAAGTGTCCATGGT
GGTATGATCGACAACAAGTGATATGAGATGGGCTCCTGCCTG

Alignment

ORF - retro_ecab_559 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.35 %
• Parental protein coverage: 86.43 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GTCQDAAIVGYKDS-PSVWAAV-PGKTFVNITPAEVGVLVGKDRSSFFVNGLTLGGQKCSVIRDSLLQDG
          G.CQD..I.GYKDS.P.VWA.V.PGKTF.NITPAEVGVLVGKD.SS..VNGLTLGG.K..V...SL.Q.G
Retrocopy GICQDKTILGYKDS>PLVWAIV<PGKTFINITPAEVGVLVGKDWSSVPVNGLTLGG*KYYVMWGSLPQGG

Parental  EFTMDLRTKSTGGAPT-FNITVTMTAKTLVLLMGKEGVHGGMINKKCYEMASHL
          EFT..L.T.ST.GA.T.F.I.VTMTAKTL.LLMG...VHGGMI..K.YEM.S.L
Retrocopy EFTLHLPTRSTSGAST<FTIIVTMTAKTLALLMGNASVHGGMIDNK*YEMGSCL

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	0.00 RPM	34.71 RPM
SRP021940_cerebellum	0.00 RPM	60.09 RPM
SRP021940_embryo	0.08 RPM	145.53 RPM
SRP021940_placental_villous	0.05 RPM	161.12 RPM
SRP021940_synovial_membrane	0.08 RPM	176.43 RPM
SRP021940_testis	0.00 RPM	72.90 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_559 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_559 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_559 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 52 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006193	2 retrocopies	retro_amel_1712, retro_amel_1781,
Callithrix jacchus	ENSCJAG00000011719	2 retrocopies	retro_cjac_1023, retro_cjac_1641,
Cavia porcellus	ENSCPOG00000013136	1 retrocopy	retro_cpor_1216,
Dasypus novemcinctus	ENSDNOG00000011649	2 retrocopies	retro_dnov_1762, retro_dnov_485,
Equus caballus	ENSECAG00000021116	3 retrocopies	retro_ecab_171, retro_ecab_28, retro_ecab_559 ,
Homo sapiens	ENSG00000108518	10 retrocopies	retro_hsap_214, retro_hsap_215, retro_hsap_221, retro_hsap_223, retro_hsap_224, retro_hsap_352, retro_hsap_446, retro_hsap_447, retro_hsap_450, retro_hsap_451,
Gorilla gorilla	ENSGGOG00000022394	3 retrocopies	retro_ggor_285, retro_ggor_289, retro_ggor_366,
Macaca mulatta	ENSMMUG00000002772	5 retrocopies	retro_mmul_407, retro_mmul_527, retro_mmul_528, retro_mmul_574, retro_mmul_732,
Mus musculus	ENSMUSG00000018293	1 retrocopy	retro_mmus_1326,
Nomascus leucogenys	ENSNLEG00000017446	6 retrocopies	retro_nleu_16, retro_nleu_1870, retro_nleu_2425, retro_nleu_2429, retro_nleu_848, retro_nleu_886,
Otolemur garnettii	ENSOGAG00000031395	3 retrocopies	retro_ogar_1680, retro_ogar_2143, retro_ogar_3351,
Procavia capensis	ENSPCAG00000000291	1 retrocopy	retro_pcap_27,
Pelodiscus sinensis	ENSPSIG00000004124	1 retrocopy	retro_psin_8,
Pan troglodytes	ENSPTRG00000008616	5 retrocopies	retro_ptro_185, retro_ptro_196, retro_ptro_276, retro_ptro_332, retro_ptro_333,
Rattus norvegicus	ENSRNOG00000003975	1 retrocopy	retro_rnor_1623,
Sus scrofa	ENSSSCG00000017905	1 retrocopy	retro_sscr_275,
Ictidomys tridecemlineatus	ENSSTOG00000028950	1 retrocopy	retro_itri_129,
Tursiops truncatus	ENSTTRG00000001299	1 retrocopy	retro_ttru_14,
Vicugna pacos	ENSVPAG00000005327	3 retrocopies	retro_vpac_389, retro_vpac_395, retro_vpac_457,