RetrogeneDB ID: retro_ecab_576

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 21:27407468..27407855(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRDX4
• Ensembl ID: ENSECAG00000010085
• Aliases: None
• Description: peroxiredoxin 4 [Source:HGNC Symbol;Acc:17169]

Sequence

>retro_ecab_576
CTTGATTTCACATTTTGGGGTCCAACAAAAACCATCAATTTAGGGACAGAATTGAGACTTTCGATTGATAAACACTGAAG
TGAGAGCATGCCCTGTGGATTCACAGTTTGCCTATTTAGCATGGAGTGGTGCCCCTCACACACAAAGGAGACTTAAGCCT
CTGGAGATTTCACTTCTTTCAGATTTGACTCGTTAGATTTCAAAGAATTCTAGTGCTGGAGAGAACCTGGGACACAAACT
TAGAGGTCGCTTTACTACTGATGAAAAAGGAAATCCAAAGGCAGTTTGCGATGGACAACCCTCCTGTTGGCAGAGTACTG
ATGAGGTACTACGCCTGGTCCAAGTATTCCAGCACACTGACAACACGGGAATGTCTGTCCCGGTGGG

Alignment

ORF - retro_ecab_576 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.09 %
• Parental protein coverage: 55.51 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  LDFTFVCPTEIIAFG-DRIE-EFRSINTEVVACSVDSQFTHLAWINTPRRQGGLGPIRIPLLSDLTHQIS
          LDFTF..PT..I..G.DRIE..FR.INTEV.AC.VDSQF..LAW...P..Q..L.P..I.LLSDLT..IS
Retrocopy LDFTFWGPTKTINLG<DRIE<DFRLINTEVRACPVDSQFAYLAWSGAPHTQRRLKPLEISLLSDLTR*IS

Parental  KDYGVYLEDSGHTLRGLFIIDDKG-ILRQITLNDLPVGR-SVDETLRLVQAFQYTD-KHGEVCPAG
          K......E..GH.LRG.F..D.KG.I.RQ......PVGR.S.DE.LRLVQ.FQ.TD..HG.VCP.G
Retrocopy KNSSAG-ENLGHKLRGRFTTDEKG>IQRQFAMDNPPVGR<STDEVLRLVQVFQHTD<QHGNVCPGG

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	65.35 RPM
SRP021940_cerebellum	0.00 RPM	11.94 RPM
SRP021940_embryo	0.03 RPM	26.29 RPM
SRP021940_placental_villous	0.00 RPM	28.87 RPM
SRP021940_synovial_membrane	0.00 RPM	32.45 RPM
SRP021940_testis	0.00 RPM	65.48 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_576 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_576 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_576 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3165
Gorilla gorilla	retro_ggor_1351
Macaca mulatta	retro_mmul_2001

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006165	1 retrocopy	retro_btau_439,
Cavia porcellus	ENSCPOG00000004185	1 retrocopy	retro_cpor_353,
Equus caballus	ENSECAG00000008678	1 retrocopy	retro_ecab_81,
Equus caballus	ENSECAG00000010085	1 retrocopy	retro_ecab_576 ,
Equus caballus	ENSECAG00000017026	1 retrocopy	retro_ecab_408,
Homo sapiens	ENSG00000123131	1 retrocopy	retro_hsap_3165,
Gorilla gorilla	ENSGGOG00000026790	1 retrocopy	retro_ggor_1351,
Myotis lucifugus	ENSMLUG00000004904	2 retrocopies	retro_mluc_2347, retro_mluc_2619,
Macaca mulatta	ENSMMUG00000021366	1 retrocopy	retro_mmul_2001,
Tupaia belangeri	ENSTBEG00000004454	5 retrocopies	retro_tbel_2164, retro_tbel_2467, retro_tbel_2522, retro_tbel_2811, retro_tbel_2978,
Tarsius syrichta	ENSTSYG00000000602	1 retrocopy	retro_tsyr_404,
Tursiops truncatus	ENSTTRG00000012368	1 retrocopy	retro_ttru_547,