RetrogeneDB ID: retro_ecab_809

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 4:45454402..45454559(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LSM5
• Ensembl ID: ENSECAG00000018445
• Aliases: None
• Description: LSM5 homolog, U6 small nuclear RNA associated (S. cerevisiae) [Source:HGNC Symbol;Acc:17162]

Sequence

>retro_ecab_809
ACACTTCTAGGATTTAATGAATTTGTCAATATGTTACTGGAAATGCCAATGAATTTACAACCTCTTTGGAAAGAGGGATA
ATTGCCAGTTAAAGTATATTTGGCCAAGTGGAAATAACATGACAATGCTGGTTCCCAGGGAATAAGGACCTGAGGTG

Alignment

ORF - retro_ecab_809 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.73 %
• Parental protein coverage: 58.24 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TLLGFDDFVNMVLE-DVTEFEITPEGRRIT-KLDQILLNGNNITMLVPGGEGPEV
          TLLGF..FVNM.LE....EF....E...I...L..I...GNN.TMLVP...GPEV
Retrocopy TLLGFNEFVNMLLE<NANEFTTSLERGIIA<QLKYIWPSGNNMTMLVPRE*GPEV

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	5.49 RPM
SRP021940_cerebellum	0.00 RPM	7.17 RPM
SRP021940_embryo	0.00 RPM	4.99 RPM
SRP021940_placental_villous	0.00 RPM	5.34 RPM
SRP021940_synovial_membrane	0.00 RPM	3.51 RPM
SRP021940_testis	0.00 RPM	4.09 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_809 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_809 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_809 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 42 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006700	1 retrocopy	retro_amel_453,
Callithrix jacchus	ENSCJAG00000009185	3 retrocopies	retro_cjac_1883, retro_cjac_2760, retro_cjac_3068,
Cavia porcellus	ENSCPOG00000010421	1 retrocopy	retro_cpor_607,
Equus caballus	ENSECAG00000018445	1 retrocopy	retro_ecab_809 ,
Echinops telfairi	ENSETEG00000018068	8 retrocopies	retro_etel_1305, retro_etel_1502, retro_etel_1907, retro_etel_198, retro_etel_2054, retro_etel_2193, retro_etel_454, retro_etel_964,
Mus musculus	ENSMUSG00000091625	4 retrocopies	retro_mmus_1568, retro_mmus_423, retro_mmus_826, retro_mmus_837,
Nomascus leucogenys	ENSNLEG00000015268	1 retrocopy	retro_nleu_179,
Otolemur garnettii	ENSOGAG00000013892	3 retrocopies	retro_ogar_2727, retro_ogar_3062, retro_ogar_881,
Pongo abelii	ENSPPYG00000017661	1 retrocopy	retro_pabe_3449,
Pan troglodytes	ENSPTRG00000019057	1 retrocopy	retro_ptro_2862,
Pteropus vampyrus	ENSPVAG00000009786	1 retrocopy	retro_pvam_1410,
Rattus norvegicus	ENSRNOG00000042126	3 retrocopies	retro_rnor_1171, retro_rnor_567, retro_rnor_694,
Tupaia belangeri	ENSTBEG00000004876	11 retrocopies	retro_tbel_1043, retro_tbel_1107, retro_tbel_1217, retro_tbel_1323, retro_tbel_1549, retro_tbel_1865, retro_tbel_2203, retro_tbel_2908, retro_tbel_2956, retro_tbel_3330, retro_tbel_4335,
Tursiops truncatus	ENSTTRG00000004237	3 retrocopies	retro_ttru_1521, retro_ttru_1585, retro_ttru_874,