RetrogeneDB ID: retro_ecab_282

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 13:38480155..38480594(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000018352
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPS14
• Ensembl ID: ENSECAG00000024336
• Aliases: None
• Description: ribosomal protein S14 [Source:HGNC Symbol;Acc:10387]

Sequence

>retro_ecab_282
ATGGCACTGGGCAAGGGATAGGAAAAGAAGGTAGAACAGGTCATCAGCCTCAGATCTCAGGTGGCTGAAGGAGAAAATGT
ATTTGGTTTCTGCCATATCTTTGCATCCCTCAATGACACTTTTGTCTATGTCACTCATCTTTCTGGCAAGGAAACCATCT
GCCGTATGACTGGCGGGATGAAGGTGAAGGATGACCAAGATGAATCCTCACCATACACTGGCATGTTGGCTGCCCAGGAT
GTAGCCCAGAGGTGCAAGGAGCTTGGCATCACTGCCCTCCACATCAAACTCTGGGCCACAGCAGGAAACAGGCCCAAGGG
CCAGTCAGCCCTCAAAGCCCTTCCCCACTCTGGAATGAAGATCAGGCGGATTGAGGATGTCACCCCCCATCTCTTCTGAT
AGCACCCACAGGAAAGGGGGTCACCGTGGTCGCCATCTG

Alignment

ORF - retro_ecab_282 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.97 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAPRKGKEKKEEQVISLGPQVAEGENVFGVCHIFASFNDTFVHVTDLSGKETICRVTGGMKVKADRDESS
          MA..KG.EKK.EQVISL..QVAEGENVFG.CHIFAS.NDTFV.VT.LSGKETICR.TGGMKVK.D.DESS
Retrocopy MALGKG*EKKVEQVISLRSQVAEGENVFGFCHIFASLNDTFVYVTHLSGKETICRMTGGMKVKDDQDESS

Parental  PYAAMLAAQDVAQRCKELGITALHIKLRATGGNRTKTPGPGAQSALRALARSGMKIGRIEDVT-PIPSDS
          PY..MLAAQDVAQRCKELGITALHIKL.AT.GNR.K..G..A..AL.....SGMKI.RIEDVT.PI.SDS
Retrocopy PYTGMLAAQDVAQRCKELGITALHIKLWATAGNRPK--GQSALKAL---PHSGMKIRRIEDVT>PISSDS

Parental  TRRKGGRRGRRL
          T.RKGG.RGR.L
Retrocopy THRKGGHRGRHL

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	599.86 RPM
SRP021940_cerebellum	0.05 RPM	259.40 RPM
SRP021940_embryo	0.15 RPM	423.13 RPM
SRP021940_placental_villous	0.14 RPM	279.91 RPM
SRP021940_synovial_membrane	0.14 RPM	416.53 RPM
SRP021940_testis	0.13 RPM	213.51 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_282 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_282 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_282 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 43 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004644	2 retrocopies	retro_amel_1390, retro_amel_524,
Bos taurus	ENSBTAG00000008570	2 retrocopies	retro_btau_1109, retro_btau_213,
Canis familiaris	ENSCAFG00000018094	2 retrocopies	retro_cfam_1589, retro_cfam_301,
Callithrix jacchus	ENSCJAG00000020981	1 retrocopy	retro_cjac_89,
Equus caballus	ENSECAG00000024336	3 retrocopies	retro_ecab_127, retro_ecab_282 , retro_ecab_522,
Latimeria chalumnae	ENSLACG00000016164	1 retrocopy	retro_lcha_12,
Loxodonta africana	ENSLAFG00000031195	2 retrocopies	retro_lafr_235, retro_lafr_67,
Myotis lucifugus	ENSMLUG00000013279	4 retrocopies	retro_mluc_1837, retro_mluc_205, retro_mluc_2464, retro_mluc_2485,
Macaca mulatta	ENSMMUG00000002848	5 retrocopies	retro_mmul_1921, retro_mmul_1983, retro_mmul_358, retro_mmul_570, retro_mmul_90,
Mustela putorius furo	ENSMPUG00000013776	1 retrocopy	retro_mputfur_127,
Nomascus leucogenys	ENSNLEG00000010366	1 retrocopy	retro_nleu_101,
Oryctolagus cuniculus	ENSOCUG00000011509	1 retrocopy	retro_ocun_128,
Otolemur garnettii	ENSOGAG00000000721	1 retrocopy	retro_ogar_286,
Ochotona princeps	ENSOPRG00000008422	17 retrocopies	retro_opri_1012, retro_opri_1074, retro_opri_114, retro_opri_194, retro_opri_258, retro_opri_268, retro_opri_28, retro_opri_306, retro_opri_376, retro_opri_428, retro_opri_707, retro_opri_825, retro_opri_842, retro_opri_876, retro_opri_882, retro_opri_919, retro_opri_971,