RetrogeneDB ID: retro_ecab_263

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 11:23463092..23463469(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS19
• Ensembl ID: ENSECAG00000009738
• Aliases: None
• Description: ribosomal protein S19 [Source:HGNC Symbol;Acc:10402]

Sequence

>retro_ecab_263
GCTCTGGCAGCCTTTCTCAAAAAGTCCAGGAAGCTGAAAATCCCTCAATGGGTAGACACTGTGAAGCTGGCCGAGCATAA
AGAGCTTACTCCCCTCGATGAACTGGTTCTACACATGAGCTTCTTCCGCATCACAGCGCCTGTTCCTCCCTGGTAGCCCT
TGGGTTGGCTCCCTGACCAAGACCTATGGGGGATGTCAGAGAAACAACGTCATAGCAACCACTTCAGCCAAGGCTCCGAG
AGCACGGCCCACCAGGTCCTCCAAGCCCTGCAGGGCTGAAAATAGTGGAAAAGGACTAAGATGGAGGCTGCAAACTGACA
CCTCAGGGACAGAGAGGGCTGGACAGAATTGCCAGACAGGTAGCAGCTGCCAAGAAA

Alignment

ORF - retro_ecab_263 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.46 %
• Parental protein coverage: 84.67 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ALAAFLKKSGKLKVPEWVDTVKLAKHKE-LAPYDENWFYTRAASTARHLYLRGGAGVGSMTKIYGGRQRN
          ALAAFLKKS.KLK.P.WVDTVKLA.HKE.L.P...NWFYT.A.S....L.L.G...VGS.TK.YGG.QRN
Retrocopy ALAAFLKKSRKLKIPQWVDTVKLAEHKE>LLP-SMNWFYT*ASSASQRLFLPGSPWVGSLTKTYGGCQRN

Parental  GVMPS-HFSRGSKSVARRVLQALEG-LKMVEKDQDGGRKLTPQGQRDLDRIAGQVAAANK
          .V....HFS.GS.S.A..VLQAL.G.LK.VEKD.DGG.KLTPQGQR.LDRIA.QVAAA.K
Retrocopy NVIAT<HFSQGSESTAHQVLQALQG<LKIVEKD*DGGCKLTPQGQRGLDRIARQVAAAKK

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	0.30 RPM	1033.55 RPM
SRP021940_cerebellum	0.00 RPM	247.41 RPM
SRP021940_embryo	0.15 RPM	652.92 RPM
SRP021940_placental_villous	0.10 RPM	325.33 RPM
SRP021940_synovial_membrane	0.22 RPM	692.26 RPM
SRP021940_testis	0.06 RPM	219.58 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_263 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_263 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_263 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Sus scrofa	retro_sscr_308
Canis familiaris	retro_cfam_1998

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 69 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000028485	10 retrocopies	retro_cfam_1017, retro_cfam_1074, retro_cfam_1155, retro_cfam_1251, retro_cfam_1377, retro_cfam_149, retro_cfam_1998, retro_cfam_2212, retro_cfam_249, retro_cfam_499,
Callithrix jacchus	ENSCJAG00000020243	5 retrocopies	retro_cjac_1968, retro_cjac_2004, retro_cjac_2094, retro_cjac_2324, retro_cjac_3,
Dasypus novemcinctus	ENSDNOG00000002376	4 retrocopies	retro_dnov_1084, retro_dnov_1124, retro_dnov_1838, retro_dnov_2456,
Equus caballus	ENSECAG00000009738	2 retrocopies	retro_ecab_263 , retro_ecab_815,
Homo sapiens	ENSG00000105372	5 retrocopies	retro_hsap_1400, retro_hsap_2417, retro_hsap_3174, retro_hsap_3642, retro_hsap_667,
Microcebus murinus	ENSMICG00000004554	1 retrocopy	retro_mmur_1480,
Macaca mulatta	ENSMMUG00000013429	8 retrocopies	retro_mmul_1201, retro_mmul_1358, retro_mmul_1807, retro_mmul_2007, retro_mmul_2443, retro_mmul_404, retro_mmul_607, retro_mmul_691,
Monodelphis domestica	ENSMODG00000010067	3 retrocopies	retro_mdom_1531, retro_mdom_1888, retro_mdom_883,
Mustela putorius furo	ENSMPUG00000007164	4 retrocopies	retro_mputfur_1071, retro_mputfur_1148, retro_mputfur_1470, retro_mputfur_1503,
Mus musculus	ENSMUSG00000040952	15 retrocopies	retro_mmus_1206, retro_mmus_1207, retro_mmus_1528, retro_mmus_1711, retro_mmus_1713, retro_mmus_2095, retro_mmus_2295, retro_mmus_2535, retro_mmus_2850, retro_mmus_3337, retro_mmus_3499, retro_mmus_639, retro_mmus_643, retro_mmus_684, retro_mmus_899,
Otolemur garnettii	ENSOGAG00000026255	3 retrocopies	retro_ogar_1315, retro_ogar_1663, retro_ogar_2305,
Rattus norvegicus	ENSRNOG00000048199	3 retrocopies	retro_rnor_221, retro_rnor_299, retro_rnor_51,
Sus scrofa	ENSSSCG00000003042	3 retrocopies	retro_sscr_1064, retro_sscr_308, retro_sscr_58,
Ictidomys tridecemlineatus	ENSSTOG00000003502	3 retrocopies	retro_itri_256, retro_itri_751, retro_itri_872,