RetrogeneDB ID: retro_ecab_579

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 21:35070581..35070857(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDK2AP2
• Ensembl ID: ENSECAG00000020079
• Aliases: None
• Description: cyclin-dependent kinase 2 associated protein 2 [Source:HGNC Symbol;Acc:30833]

Sequence

>retro_ecab_579
ATGTCCTACAAATCCATTGCCCCCAACCTCAGCAGCAGCCCCAGTCCAGCACCCCTGGGCCCAGCACCCTGCTCTCCATA
GCCTTTAGTGTCCCATCGCCATCAGTGGGACTCGGTGCCCGGAGGCACTGCGTGTTTTGGACCAGTATTTAAGGACTTTG
GTCCACCCTCCTTGGGCTATGTGCAGGTGACGAAGACACCCAGCATCCAGGACTCCCAGGGCACCTACAGGGACCTGCTA
TGGGAGACAGGCAAAGAGCTCTGGCCCGCCTATGCA

Alignment

ORF - retro_ecab_579 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.63 %
• Parental protein coverage: 73.81 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSYKPIAPAPSSTPGSST--PGPGTPVPTGSVPSPSGSVPGAAAPFRPLFNDFGPPSMGYVQAMKPPGAQ
          MSYK.IAP..SS.P......P.P..P.P..S......SVPG..A.F.P.F.DFGPPS.GYVQ..K.P..Q
Retrocopy MSYKSIAPNLSSSPSPAPLGPAPCSP*PLVSHRHQWDSVPGGTACFGPVFKDFGPPSLGYVQVTKTPSIQ

Parental  GSQSTYTDLLSVIEEMGKEIRPTYA
          .SQ.TY.DLL....E.GKE..P.YA
Retrocopy DSQGTYRDLL---WETGKELWPAYA

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	8.32 RPM
SRP021940_cerebellum	0.00 RPM	18.75 RPM
SRP021940_embryo	0.00 RPM	14.63 RPM
SRP021940_placental_villous	0.00 RPM	28.72 RPM
SRP021940_synovial_membrane	0.00 RPM	22.10 RPM
SRP021940_testis	0.00 RPM	12.34 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_579 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_579 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_579 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 31 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000011370	1 retrocopy	retro_cfam_55,
Equus caballus	ENSECAG00000020079	2 retrocopies	retro_ecab_180, retro_ecab_579 ,
Echinops telfairi	ENSETEG00000006428	3 retrocopies	retro_etel_257, retro_etel_334, retro_etel_437,
Homo sapiens	ENSG00000167797	4 retrocopies	retro_hsap_3699, retro_hsap_4172, retro_hsap_4176, retro_hsap_4268,
Gorilla gorilla	ENSGGOG00000010159	3 retrocopies	retro_ggor_2502, retro_ggor_2799, retro_ggor_2800,
Macaca mulatta	ENSMMUG00000011827	5 retrocopies	retro_mmul_1712, retro_mmul_640, retro_mmul_728, retro_mmul_730, retro_mmul_763,
Nomascus leucogenys	ENSNLEG00000006438	1 retrocopy	retro_nleu_176,
Otolemur garnettii	ENSOGAG00000008275	1 retrocopy	retro_ogar_1584,
Pan troglodytes	ENSPTRG00000003966	9 retrocopies	retro_ptro_2508, retro_ptro_2973, retro_ptro_2976, retro_ptro_3002, retro_ptro_3003, retro_ptro_3004, retro_ptro_3005, retro_ptro_3008, retro_ptro_3009,
Tupaia belangeri	ENSTBEG00000005476	2 retrocopies	retro_tbel_439, retro_tbel_612,