RetrogeneDB ID: retro_ecab_164

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 1:60841166..60841589(-)
• Located in intron of: ENSECAG00000012496

Retrocopy information

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

Parental gene information

• Parental gene symbol: ENOPH1
• Ensembl ID: ENSECAG00000019612
• Aliases: None
• Description: enolase-phosphatase 1 [Source:HGNC Symbol;Acc:24599]

Sequence

>retro_ecab_164
CTGGACTGAAAGACCATGGTACTGAAACACCTGCAGGGCTACATGTGGAGGGCAGTTTTCACAGGTGGATCCATGAAAGC
AGCATTTTTTGAAGATGTAGTTCTAGCAGTTAGGAAATGGAGAGAGGCTGGAATGAAGGTATATATCTATTCTTCAGGGA
ATGGAGAGGCACAGAAACTGTTATCTGGGCATTCTTCAGAGGAAGATATTCTTGAGCTTGTTCATAGTTACTTTGATACC
AAGATTGGGCACAAAGTGGAGAGTAAGAGTTATTGAAAGATTGCAGGCAGCACTGGGTACTCAGTCAACAGCATCCTGTT
TCTGACAGACGTTTCTCTAAAGGCTAGTGCTGCTGAGGAAGCAGACATTCATGTAGCTGTGGTGGTAACACATGGCAGTG
TGGGATTAACAGATGATGGAAAG

Alignment

ORF - retro_ecab_164 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.89 %
• Parental protein coverage: 54.23 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LDRKTTALKQLQGHMWRAAFTAGRMKAEFFEDVVPAVRKWREAGMKVYIYSSGSVEAQKLLFGHSTEGDI
          LD.KT..LK.LQG.MWRA.FT.G.MKA.FFEDVV.AVRKWREAGMKVYIYSSG..EAQKLL.GHS.E.DI
Retrocopy LD*KTMVLKHLQGYMWRAVFTGGSMKAAFFEDVVLAVRKWREAGMKVYIYSSGNGEAQKLLSGHSSEEDI

Parental  LELFDGHFDTKIGHKVESESYRKIADSIGCSTNNILFLTDVTLEASAAEEADVHVAVVVRPGNAGLTDDE
          LEL....FDTKIGHKVES.SY.KIA.S.G.S.N.ILFLTDV.L.ASAAEEAD.HVAVVV..G..GLTDD.
Retrocopy LELVHSYFDTKIGHKVESKSY*KIAGSTGYSVNSILFLTDVSLKASAAEEADIHVAVVVTHGSVGLTDDG

Parental  K
          K
Retrocopy K

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	14.93 RPM
SRP021940_cerebellum	0.05 RPM	37.34 RPM
SRP021940_embryo	0.41 RPM	41.30 RPM
SRP021940_placental_villous	0.10 RPM	34.54 RPM
SRP021940_synovial_membrane	0.16 RPM	32.64 RPM
SRP021940_testis	0.06 RPM	36.06 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_164 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_164 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_164 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005140	2 retrocopies	retro_amel_1186, retro_amel_930,
Choloepus hoffmanni	ENSCHOG00000003283	4 retrocopies	retro_chof_2150, retro_chof_470, retro_chof_486, retro_chof_596,
Callithrix jacchus	ENSCJAG00000015251	2 retrocopies	retro_cjac_1376, retro_cjac_2375,
Equus caballus	ENSECAG00000019612	1 retrocopy	retro_ecab_164 ,
Erinaceus europaeus	ENSEEUG00000004274	1 retrocopy	retro_eeur_563,
Homo sapiens	ENSG00000145293	1 retrocopy	retro_hsap_2900,
Gorilla gorilla	ENSGGOG00000003719	1 retrocopy	retro_ggor_2010,
Loxodonta africana	ENSLAFG00000008619	1 retrocopy	retro_lafr_1158,
Macropus eugenii	ENSMEUG00000011458	1 retrocopy	retro_meug_1125,
Myotis lucifugus	ENSMLUG00000014460	1 retrocopy	retro_mluc_2504,
Otolemur garnettii	ENSOGAG00000002502	1 retrocopy	retro_ogar_1549,
Pongo abelii	ENSPPYG00000014887	1 retrocopy	retro_pabe_2399,
Pan troglodytes	ENSPTRG00000016218	1 retrocopy	retro_ptro_1960,
Ictidomys tridecemlineatus	ENSSTOG00000013987	2 retrocopies	retro_itri_1067, retro_itri_1587,
Tursiops truncatus	ENSTTRG00000001800	1 retrocopy	retro_ttru_1231,