RetrogeneDB ID: retro_ecab_976

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 8:65774148..65774523(+)
• Located in intron of: ENSECAG00000002816

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS25
• Ensembl ID: ENSECAG00000020978
• Aliases: None
• Description: ribosomal protein S25 [Source:HGNC Symbol;Acc:10413]

Sequence

>retro_ecab_976
GGCCGCAGTGGTCCCAGCTGCTGTCTGAGCTTCACGATGCCACCCAAGGACAAGAAGAAGAACATAAATGCCAGAAAGCT
GGCCAAGAAAGATAAAGACCACGCGAAGACATCCTGGGGTAAGGGCAAAAAGAAGTGGTCCAAAGCCAAAGTTTGAGACA
AGCTCAATAACCTAGTCTTGTTTGACAAAGCCTCATATGCAAAACTCTGTAAGGAAGTTCCTAACTATAGGTTTATAACC
TCAGCTGTTGTCTCTAAGAGACTGAAGATTCCCAGTTCCCTGACAAGGGTAGCCCTTCAGGAGCTCCTTAGTGAAGGACT
CATTAAAGTGGTTTCAAAGCACAGAGTTCAGATAATTTACACCAGAAGGGCAGAA

Alignment

ORF - retro_ecab_976 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.43 %
• Parental protein coverage: 91.97 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GCSGDSCCPSFAMPPKDDKKKKDAGKSAKKDKDPVNKSGGKAKKKKWSKGKVRDKLNNLVLFDKATYDKL
          G.SG.SCC.SF.MPPKD.KK...A.K.AKKDKD....S.GK.KKK.WSK.KV.DKLNNLVLFDKA.Y.KL
Retrocopy GRSGPSCCLSFTMPPKDKKKNINARKLAKKDKDHAKTSWGKGKKK-WSKAKV*DKLNNLVLFDKASYAKL

Parental  CKEVPNYKLITPAVVSERLKIRGSLARAALQELLSKGLIKLVSKHRAQVIYTRNTK
          CKEVPNY..IT.AVVS.RLKI..SL.R.ALQELLS.GLIK.VSKHR.Q.IYTR...
Retrocopy CKEVPNYRFITSAVVSKRLKIPSSLTRVALQELLSEGLIKVVSKHRVQIIYTRRAE

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	0.06 RPM	336.29 RPM
SRP021940_cerebellum	0.16 RPM	135.28 RPM
SRP021940_embryo	0.36 RPM	214.22 RPM
SRP021940_placental_villous	0.14 RPM	178.73 RPM
SRP021940_synovial_membrane	0.22 RPM	195.60 RPM
SRP021940_testis	0.00 RPM	156.85 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_976 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_976 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_976 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Sus scrofa	retro_sscr_1107

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 56 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000027772	2 retrocopies	retro_btau_203, retro_btau_9,
Callithrix jacchus	ENSCJAG00000013691	1 retrocopy	retro_cjac_208,
Dasypus novemcinctus	ENSDNOG00000007880	7 retrocopies	retro_dnov_1092, retro_dnov_1566, retro_dnov_2219, retro_dnov_2593, retro_dnov_346, retro_dnov_877, retro_dnov_973,
Equus caballus	ENSECAG00000020978	2 retrocopies	retro_ecab_89, retro_ecab_976 ,
Erinaceus europaeus	ENSEEUG00000014630	6 retrocopies	retro_eeur_250, retro_eeur_281, retro_eeur_353, retro_eeur_424, retro_eeur_519, retro_eeur_675,
Latimeria chalumnae	ENSLACG00000017531	4 retrocopies	retro_lcha_101, retro_lcha_118, retro_lcha_50, retro_lcha_72,
Macropus eugenii	ENSMEUG00000014185	3 retrocopies	retro_meug_1181, retro_meug_1562, retro_meug_174,
Mus musculus	ENSMUSG00000009927	15 retrocopies	retro_mmus_128, retro_mmus_1368, retro_mmus_1455, retro_mmus_1760, retro_mmus_1769, retro_mmus_1788, retro_mmus_2375, retro_mmus_2393, retro_mmus_2641, retro_mmus_2700, retro_mmus_2797, retro_mmus_3218, retro_mmus_336, retro_mmus_3523, retro_mmus_880,
Otolemur garnettii	ENSOGAG00000007265	3 retrocopies	retro_ogar_220, retro_ogar_257, retro_ogar_32,
Ochotona princeps	ENSOPRG00000016194	9 retrocopies	retro_opri_1099, retro_opri_1204, retro_opri_256, retro_opri_320, retro_opri_393, retro_opri_493, retro_opri_64, retro_opri_854, retro_opri_873,
Vicugna pacos	ENSVPAG00000000266	4 retrocopies	retro_vpac_106, retro_vpac_118, retro_vpac_337, retro_vpac_546,