RetrogeneDB ID: retro_ecab_691

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 28:42075565..42076042(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPA1
• Ensembl ID: ENSECAG00000018686
• Aliases: None
• Description: pyrophosphatase (inorganic) 1 [Source:HGNC Symbol;Acc:9226]

Sequence

>retro_ecab_691
CTCTCTCCATTTCGTGATATTCCAATTTATGCAGATGAGGATGTGTTCCACACGGTGGTTGAAGCGCCACTCTGGTCTAA
GACAAAGATGGAGATTGCTACAAAGGACCCTTTCAAACCAATTAAACAAGAAATGATGAAAGGAAAACTTCGTTATGTGG
CAAATTTGTTCCCTTGTAAAGGATATATCTGAAACTATGGTGCCATCCCTCAGACTTGGGAAGACCCAGGACATAATGAC
AAACACACTGGCTGTTGTGGTGAACATGACCCAATTGATGTGTGTGAAATTGGAAGCAAGGTGTGCTCAAGAGGTGAAAT
AATCGTGGTGAAATTTCTGGGCATCTTGGCTATGATTGATGAATGGGAAACCACCTGGAAAGTCATTGCCATTAATGTGG
ATGATCCTGATGCAGCCAATTATAATGATGTTAATGATGTCAAGCGGCTGAAACCTGGTTACCTGGAAGCTACTGTG

Alignment

ORF - retro_ecab_691 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.91 %
• Parental protein coverage: 58.89 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ISPFHDIPIYADKDVFHMVVEVPRWSNAKMEIATKDPLNPIKQDVKKGKLRYVANLFPYKGYIWNYGAIP
          .SPF.DIPIYAD.DVFH.VVE.P.WS..KMEIATKDP..PIKQ...KGKLRYVANLFP.KGYI.NYGAIP
Retrocopy LSPFRDIPIYADEDVFHTVVEAPLWSKTKMEIATKDPFKPIKQEMMKGKLRYVANLFPCKGYI*NYGAIP

Parental  QTWEDPGHNDQHTGCCGDNDPIDVCEIGSKVCARGEIIAVKVLGILAMIDEGETDWKVIAINVDDPDAAN
          QTWEDPGHND.HTGCCG..DPIDVCEIGSKVC.RGEII.VK.LGILAMIDE.ET.WKVIAINVDDPDAAN
Retrocopy QTWEDPGHNDKHTGCCGEHDPIDVCEIGSKVCSRGEIIVVKFLGILAMIDEWETTWKVIAINVDDPDAAN

Parental  YNDINDVKRLKPGYLEATV
          YND.NDVKRLKPGYLEATV
Retrocopy YNDVNDVKRLKPGYLEATV

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	3.01 RPM
SRP021940_cerebellum	0.10 RPM	60.29 RPM
SRP021940_embryo	0.03 RPM	19.64 RPM
SRP021940_placental_villous	0.00 RPM	20.54 RPM
SRP021940_synovial_membrane	0.03 RPM	13.07 RPM
SRP021940_testis	0.06 RPM	18.54 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_691 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_691 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_691 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014033	1 retrocopy	retro_cfam_1040,
Dasypus novemcinctus	ENSDNOG00000014861	1 retrocopy	retro_dnov_1310,
Equus caballus	ENSECAG00000018686	1 retrocopy	retro_ecab_691 ,
Loxodonta africana	ENSLAFG00000004048	1 retrocopy	retro_lafr_990,
Nomascus leucogenys	ENSNLEG00000016098	1 retrocopy	retro_nleu_7,
Procavia capensis	ENSPCAG00000006788	1 retrocopy	retro_pcap_247,
Pongo abelii	ENSPPYG00000029405	1 retrocopy	retro_pabe_37,