RetrogeneDB ID: retro_ecab_86

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 29:31713527..31713836(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000006491
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSECAG00000023559
• Aliases: None
• Description: None

Sequence

>retro_ecab_86
ATGCTGGAGCACCTGAGCTCGCTGCCCACGCAGATGGATTACAAGGGCCAGAAACTAGCTGAACAGATGTTTCAAGGAAT
TATTCTTTTTTCTGCAATAGTTGGATTTATCTATGGGTACGTGGCTGAACAGTTCGGGTGGACTGTCTATATAGTTATGG
CCGGATTTGCTTTTTCATGTTTGCTGACACTTCCTCCATGGCCCATTTATCGCTGGCACCCCCTCAAGTGGTTACCTGTT
CAAGACTCAGGCACAGAAGACAAGAAACCAGGGGAAAGAAAAATTAAGAGGCATGCTAGAAATAATTGA

Alignment

ORF - retro_ecab_86 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.04 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLEHLSSLPTQMDYKGQKLAEQMFQGIILFSAIVGFIYGYVAEQFGWTVYIVMAGFAFSCLLTLPPWPIY
          MLEHLSSLPTQMDYKGQKLAEQMFQGIILFSAIVGFIYGYVAEQFGWTVYIVMAGFAFSCLLTLPPWPIY
Retrocopy MLEHLSSLPTQMDYKGQKLAEQMFQGIILFSAIVGFIYGYVAEQFGWTVYIVMAGFAFSCLLTLPPWPIY

Parental  RRHPLKWLPVQDSGTEDKKPGERKIKRHAKNN
          R.HPLKWLPVQDSGTEDKKPGERKIKRHA.NN
Retrocopy RWHPLKWLPVQDSGTEDKKPGERKIKRHARNN

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	16.17 RPM
SRP021940_cerebellum	0.10 RPM	18.44 RPM
SRP021940_embryo	0.08 RPM	12.84 RPM
SRP021940_placental_villous	0.24 RPM	34.98 RPM
SRP021940_synovial_membrane	0.16 RPM	14.85 RPM
SRP021940_testis	0.26 RPM	84.66 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_86 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_86 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_86 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 20 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008426	1 retrocopy	retro_amel_1899,
Canis familiaris	ENSCAFG00000008927	1 retrocopy	retro_cfam_2079,
Dasypus novemcinctus	ENSDNOG00000012421	3 retrocopies	retro_dnov_2086, retro_dnov_2245, retro_dnov_698,
Dipodomys ordii	ENSDORG00000000678	4 retrocopies	retro_dord_273, retro_dord_274, retro_dord_686, retro_dord_734,
Equus caballus	ENSECAG00000023559	1 retrocopy	retro_ecab_86 ,
Erinaceus europaeus	ENSEEUG00000007914	1 retrocopy	retro_eeur_25,
Echinops telfairi	ENSETEG00000004020	1 retrocopy	retro_etel_1056,
Homo sapiens	ENSG00000114902	1 retrocopy	retro_hsap_294,
Gorilla gorilla	ENSGGOG00000028027	1 retrocopy	retro_ggor_332,
Loxodonta africana	ENSLAFG00000016073	2 retrocopies	retro_lafr_575, retro_lafr_625,
Microcebus murinus	ENSMICG00000014061	1 retrocopy	retro_mmur_292,
Myotis lucifugus	ENSMLUG00000000744	1 retrocopy	retro_mluc_2104,
Macaca mulatta	ENSMMUG00000017370	1 retrocopy	retro_mmul_549,
Mus musculus	ENSMUSG00000021917	2 retrocopies	retro_mmus_2758, retro_mmus_2928,
Otolemur garnettii	ENSOGAG00000004106	3 retrocopies	retro_ogar_2119, retro_ogar_2315, retro_ogar_2788,
Pongo abelii	ENSPPYG00000013798	1 retrocopy	retro_pabe_380,
Pan troglodytes	ENSPTRG00000015011	1 retrocopy	retro_ptro_241,
Tarsius syrichta	ENSTSYG00000006854	2 retrocopies	retro_tsyr_1359, retro_tsyr_599,
Tursiops truncatus	ENSTTRG00000008576	1 retrocopy	retro_ttru_806,
Vicugna pacos	ENSVPAG00000007380	1 retrocopy	retro_vpac_269,