RetrogeneDB ID: retro_ecab_431

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 18:43281154..43281935(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000018747
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NDUFS3
• Ensembl ID: ENSECAG00000013454
• Aliases: None
• Description: NADH dehydrogenase (ubiquinone) Fe-S protein 3, 30kDa (NADH-coenzyme Q reductase) [Source:HGNC Symbol;Acc:7710]

Sequence

>retro_ecab_431
GCGGTGGCAGTGGCTAGGGGCTGGTGGTGGGGGCTCGTGGGGGCCGTGGCACTGGCCAGAGTGGCCAGGCAACCCTTGGT
ACTGTTGCTGCCAGTGAGGATGGAAAGCACTTCAGTGGACACGCGCCCCACTGTCAGACCATGGAATGATGTGGCCCACA
GGCGGCTCTCAGCTTTTGGAGAGTACGTGGCTGATATCCTGCCCAAATATGTCCACCAAGTTCAGGCGTCCTGCTTCAAT
GAGTTAGAGATCTGTATCCATCCTGAGGGATCATCCCAGTGCTGACTTTCCTCAGGGATCACACCAACGCACAATTCAAA
TCCCTGGCTGACCTGATGGCAGTGGACATCCCCACCCAGCAGAACCATTTTGAGATTATTTACAACCTGTTCTCTCTGCG
CTTCAACTCCCGGATCCCTGTGAAGACCTACACAGATGAGCTGACGTCCATCGAGTCCACTGTCTCTGTGCACAAGGCAG
CCAACTGGTATGAGAGGGAAATCTGGGACATGTTTGGAGTCATCTTTGCTAACCACCCTGACCTAAGAAGGATCCTGACA
GACTATGGCTTCCAGGGACATCCTTTCTGGGAAGACTTCCCCTTGTCTGGCTATGTTGAGCTACGCTATGATGATAAGGT
GAAGTGGGTGGTGGCTGAGCTGGTGGAGTTGGCCCAAGAGTTCCCCAAGTTTGACCTGAACAGCCCATGGGAGGCTTTCC
CTGCCTATCTCCAGCCCCCTAGTATCTCAAGCTTGAAGCCGGAGATGAGAAACCTGAAACC

Alignment

ORF - retro_ecab_431 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.65 %
• Parental protein coverage: 98.49 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AAAAARGWWRGLVGTVALARAARRPSVLLLPVRTESAAADTRPTVRPRNDVAHKQLSAFGEYVAEILPKY
          A.A.ARGWW.GLVG.VALAR.AR.P.VLLLPVR.ES...DTRPTVRP.NDVAH..LSAFGEYVA.ILPKY
Retrocopy AVAVARGWWWGLVGAVALARVARQPLVLLLPVRMESTSVDTRPTVRPWNDVAHRRLSAFGEYVADILPKY

Parental  VQQVQVSCFNELEICIHPDG-VIPVLTFLRDHSNAQFKSLADLTAVDIPTRQNRFEIVYNLLSLRFNCRI
          V.QVQ.SCFNELEICIHP.G..IPVLTFLRDH.NAQFKSLADL.AVDIPT.QN.FEI.YNL.SLRFN.RI
Retrocopy VHQVQASCFNELEICIHPEG<IIPVLTFLRDHTNAQFKSLADLMAVDIPTQQNHFEIIYNLFSLRFNSRI

Parental  RVKTYTDELTPIESAVSVHKAANWYEREIWDMFGVFFANHPDLRRILTDYGFEGHPFRKDFPLSGYVELR
          .VKTYTDELT.IES.VSVHKAANWYEREIWDMFGV.FANHPDLRRILTDYGF.GHPF..DFPLSGYVELR
Retrocopy PVKTYTDELTSIESTVSVHKAANWYEREIWDMFGVIFANHPDLRRILTDYGFQGHPFWEDFPLSGYVELR

Parental  YDDEVKRVVAEPVELAQEFRKFDLNSPWEAFPAYRQPPE-SLKLEAGDKKPET
          YDD.VK.VVAE.VELAQEF.KFDLNSPWEAFPAY.QPP...LKLEAGD.KPET
Retrocopy YDDKVKWVVAELVELAQEFPKFDLNSPWEAFPAYLQPPS<YLKLEAGDEKPET

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	18.54 RPM
SRP021940_cerebellum	0.00 RPM	87.92 RPM
SRP021940_embryo	0.00 RPM	60.25 RPM
SRP021940_placental_villous	0.00 RPM	30.69 RPM
SRP021940_synovial_membrane	0.00 RPM	26.27 RPM
SRP021940_testis	0.06 RPM	95.02 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_431 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_431 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_431 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000008411	1 retrocopy	retro_cfam_1052,
Callithrix jacchus	ENSCJAG00000020194	1 retrocopy	retro_cjac_4059,
Equus caballus	ENSECAG00000013454	1 retrocopy	retro_ecab_431 ,
Erinaceus europaeus	ENSEEUG00000007356	1 retrocopy	retro_eeur_52,
Mus musculus	ENSMUSG00000005510	2 retrocopies	retro_mmus_2338, retro_mmus_792,