RetrogeneDB ID: retro_ecab_175

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 1:82330334..82330730(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS6
• Ensembl ID: ENSECAG00000016190
• Aliases: None
• Description: ribosomal protein S6 [Source:HGNC Symbol;Acc:10429]

Sequence

>retro_ecab_175
GGGCAGGGGGAGATTTCTGGATGGATTGATACTGCCATGCCTGTGGCCTGAGGCCCAAAAGAGCTGGAAGAATCTGCAAA
CTTTCAATCTCCTAAAGAAGATGATGCCCACCAGTGTGTTGTGAGAAAGCCCCTGAACAAAGAAGGTAAGAAACCCAGAA
CCAAAGCGCCCAAGATTCAGCGTCCTGTTACTCCACCTGTCCTGCAACATACATGTCAGCATATTGCCCTGAAGAAACAG
CATACTCAGAAAAATAAAGAAGGGCACACAAAATATGCTCAACTTTAGGCCAAGAGAATGAAGGAGGCCAAAGAAAAATG
CCAGGAGCAGATTGCCAAGAGATGGAGGCTGTCGTCTCTGAGAGCTTCCGCCTCTGAGTCTGAGTCCGGTCAAAAA

Alignment

ORF - retro_ecab_175 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.32 %
• Parental protein coverage: 53.2 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GEKDIPGLTDTTVPRRLGPK-RASRIRKL-FNL-SKEDDVRQYVVRKPLNKEGKKPRTKAPKIQRLVTPR
          G...I.G..DT..P...GPK.RA.RI.KL.FNL..KEDD..Q.VVRKPLNKEGKKPRTKAPKIQR.VTP.
Retrocopy GQGEISGWIDTAMPVA*GPK<RAGRICKL<FNL<PKEDDAHQCVVRKPLNKEGKKPRTKAPKIQRPVTPP

Parental  VLQHKRRRIALKKQRTKKNKEEAAEYAKLLAKRMKEAKEKRQEQIAKRRRLSSLRASTSKSESSQK
          VLQH....IALKKQ.T.KNKE....YA.L.AKRMKEAKEK.QEQIAKR.RLSSLRAS.S.SES.QK
Retrocopy VLQHTCQHIALKKQHTQKNKEGHTKYAQL*AKRMKEAKEKCQEQIAKRWRLSSLRASASESESGQK

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	1947.28 RPM
SRP021940_cerebellum	0.00 RPM	479.70 RPM
SRP021940_embryo	0.03 RPM	952.61 RPM
SRP021940_placental_villous	0.00 RPM	607.16 RPM
SRP021940_synovial_membrane	0.03 RPM	878.82 RPM
SRP021940_testis	0.00 RPM	289.09 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_175 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_175 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_175 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 99 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000017634	1 retrocopy	retro_acar_20,
Ailuropoda melanoleuca	ENSAMEG00000002925	14 retrocopies	retro_amel_1040, retro_amel_1250, retro_amel_1384, retro_amel_1526, retro_amel_1646, retro_amel_1676, retro_amel_189, retro_amel_312, retro_amel_334, retro_amel_382, retro_amel_510, retro_amel_568, retro_amel_657, retro_amel_841,
Canis familiaris	ENSCAFG00000001615	4 retrocopies	retro_cfam_184, retro_cfam_1936, retro_cfam_48, retro_cfam_87,
Callithrix jacchus	ENSCJAG00000020612	6 retrocopies	retro_cjac_1246, retro_cjac_18, retro_cjac_180, retro_cjac_190, retro_cjac_2982, retro_cjac_59,
Cavia porcellus	ENSCPOG00000003750	4 retrocopies	retro_cpor_1244, retro_cpor_22, retro_cpor_317, retro_cpor_486,
Dasypus novemcinctus	ENSDNOG00000007241	1 retrocopy	retro_dnov_1192,
Equus caballus	ENSECAG00000016190	5 retrocopies	retro_ecab_175 , retro_ecab_312, retro_ecab_603, retro_ecab_771, retro_ecab_861,
Felis catus	ENSFCAG00000002541	26 retrocopies	retro_fcat_1082, retro_fcat_1108, retro_fcat_1154, retro_fcat_1262, retro_fcat_1373, retro_fcat_1642, retro_fcat_1679, retro_fcat_1760, retro_fcat_1791, retro_fcat_1934, retro_fcat_1937, retro_fcat_1963, retro_fcat_198, retro_fcat_238, retro_fcat_328, retro_fcat_358, retro_fcat_380, retro_fcat_392, retro_fcat_493, retro_fcat_659, retro_fcat_738, retro_fcat_750, retro_fcat_850, retro_fcat_894, retro_fcat_912, retro_fcat_968,
Gorilla gorilla	ENSGGOG00000002652	13 retrocopies	retro_ggor_1430, retro_ggor_1703, retro_ggor_2097, retro_ggor_2358, retro_ggor_2439, retro_ggor_2769, retro_ggor_2863, retro_ggor_2864, retro_ggor_616, retro_ggor_670, retro_ggor_777, retro_ggor_896, retro_ggor_965,
Loxodonta africana	ENSLAFG00000010766	4 retrocopies	retro_lafr_1021, retro_lafr_1239, retro_lafr_59, retro_lafr_667,
Macaca mulatta	ENSMMUG00000003412	1 retrocopy	retro_mmul_263,
Monodelphis domestica	ENSMODG00000004095	1 retrocopy	retro_mdom_301,
Ochotona princeps	ENSOPRG00000012290	5 retrocopies	retro_opri_123, retro_opri_642, retro_opri_78, retro_opri_862, retro_opri_895,
Rattus norvegicus	ENSRNOG00000049025	8 retrocopies	retro_rnor_1008, retro_rnor_1189, retro_rnor_1988, retro_rnor_1990, retro_rnor_2085, retro_rnor_2635, retro_rnor_479, retro_rnor_718,
Sus scrofa	ENSSSCG00000005169	6 retrocopies	retro_sscr_187, retro_sscr_425, retro_sscr_645, retro_sscr_856, retro_sscr_940, retro_sscr_983,