RetrogeneDB ID: retro_ecab_616

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 23:23141938..23142129(-)
• Located in intron of: ENSECAG00000023609

Retrocopy information

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

Parental gene information

• Parental gene symbol: YPEL2
• Ensembl ID: ENSECAG00000018575
• Aliases: None
• Description: yippee-like 2 (Drosophila) [Source:HGNC Symbol;Acc:18326]

Sequence

>retro_ecab_616
ATGATAAAAATGACAAACTCAAAAACTTGCCAAGGGTATCTGCCAAATTGTCCTTGAATTTACTGCTGTATCCACTGGAA
AGCCCATTTAGCAAATCCTGCTGTGTTGATCTCCAAGTCCTTTCATGTTAGTCAACATCAAGCCCACCTCTTTAATTCTG
TGTGAAGGTGGCCTGTGGTCCAGGAGAGGAC

Alignment

ORF - retro_ecab_616 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.08 %
• Parental protein coverage: 53.78 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MVKMTRSKTFQAYLPSCHRTYSCIHCRAHLANHDELISKSFQGSQGRAYLFNSV-VNVGCGPAEE
          M.KMT.SKT.Q.YLP.C...Y.CIH..AHLAN...LISKSF..SQ..A.LFNSV.V.V.CGP.E.
Retrocopy MIKMTNSKTCQGYLPNCP*IYCCIHWKAHLANPAVLISKSFHVSQHQAHLFNSV<VKVACGPGED

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	8.03 RPM
SRP021940_cerebellum	0.00 RPM	19.89 RPM
SRP021940_embryo	0.00 RPM	10.56 RPM
SRP021940_placental_villous	0.00 RPM	17.61 RPM
SRP021940_synovial_membrane	0.00 RPM	25.20 RPM
SRP021940_testis	0.00 RPM	10.55 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_616 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_616 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_616 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Callithrix jacchus	retro_cjac_597

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000018575	1 retrocopy	retro_ecab_616 ,
Otolemur garnettii	ENSOGAG00000029581	1 retrocopy	retro_ogar_1226,
Sorex araneus	ENSSARG00000009791	2 retrocopies	retro_sara_318, retro_sara_650,
Ictidomys tridecemlineatus	ENSSTOG00000001013	1 retrocopy	retro_itri_937,
Tupaia belangeri	ENSTBEG00000013138	1 retrocopy	retro_tbel_808,
Tarsius syrichta	ENSTSYG00000005518	1 retrocopy	retro_tsyr_2143,
Vicugna pacos	ENSVPAG00000000381	1 retrocopy	retro_vpac_128,