RetrogeneDB ID: retro_ecab_861

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 5:59498980..59499527(-)
• 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_861
CAACAAACAAAGCTTCCCCATGGCTGTGGCCACCTGCTACTGAGTAAGGGGCATTTCTGTTATAGACCAAGGAGAACTGG
AGAAAGAAAGCGCAAGTCTGTTCAGGGTTGCATTGTGGATGCCAATCTGAGTGTTCTCAACTTGGTTATTGTAAACAACA
AGGAGAAGAAAATTCCTGGAGTAATTCATACTCCTGTGCCTCATTGCCTGGGGCCCAAAGGAGCACGCAGAATCCGCAAA
CTTTTCAATCTCTCCAAAGAAGATGATGCCCACCAGTATGTTGTCAGAAAGCCCCTGAACAAAGAAGGTATGAAACCCAA
GACCGAAGTCCCAAGATTCTGCATCTTGTTACTGCACGTAGCCTGTAACACAAACATCAGCATGTTGCTCTGAAGAAACA
GCATACTAAGAAAATTAAGGAAGAGGCCGCAGAATATGCTAAAATTTTGGCCAAGAGAATGAAGAAAGTTGAAGAAAAAC
GCCAGGAATAGATGCCAAAAAATGGAGGCTGTCCTCTCTTAGAGCTCCCACCTCTAAATCTGAGTCA

Alignment

ORF - retro_ecab_861 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.34 %
• Parental protein coverage: 74.4 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KQGVLTHGRVRLLLSKGHSCYRPRRTGERKRKSVRGCIVDANLSVLNLVIVKKGEAGEKDIPGLTDTTVP
          .Q..L.HG...LLLSKGH.CYRPRRTGERKRKSV.GCIVDANLSVLNLVIV......EK.IPG...T.VP
Retrocopy QQTKLPHGCGHLLLSKGHFCYRPRRTGERKRKSVQGCIVDANLSVLNLVIVNNK---EKKIPGVIHTPVP

Parental  RRLGPKRASRIRKLFNLSKEDDVRQYVVRKPLNKEGKKPRT-KAPKIQRLVTPRVLQHKRRRIALKKQRT
          ..LGPK.A.RIRKLFNLSKEDD..QYVVRKPLNKEG.KP.T...PKI..LVT.R.L.HK....ALKKQ.T
Retrocopy HCLGPKGARRIRKLFNLSKEDDAHQYVVRKPLNKEGMKPKT<RSPKILHLVTARSL*HKHQHVALKKQHT

Parental  KKNKEEAAEYAKLLAKRMKEAKEKRQEQI-AKRRRLSSLRASTSKSES
          KK.KEEAAEYAK.LAKRMK...EKRQE...AK..RLSSLRA.TSKSES
Retrocopy KKIKEEAAEYAKILAKRMKKVEEKRQE*M<AKKWRLSSLRAPTSKSES

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	1947.28 RPM
SRP021940_cerebellum	0.00 RPM	479.70 RPM
SRP021940_embryo	0.15 RPM	952.61 RPM
SRP021940_placental_villous	0.05 RPM	607.16 RPM
SRP021940_synovial_membrane	0.16 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_861 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_861 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_861 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,