RetrogeneDB ID: retro_ecab_792

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 4:78026625..78026973(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C6orf52
• Ensembl ID: ENSECAG00000008229
• Aliases: None
• Description: chromosome 6 open reading frame 52 [Source:HGNC Symbol;Acc:20881]

Sequence

>retro_ecab_792
GTGAAGCCAGAGTTCCAGCCCCACCAAGGTTACTCCTTTGGAAACTAGAATGAGCAACAGCAGAGCTGTTATTCTCTTTC
TGGCTACAGCTGTGGCTGTGCAGTGGGTGGAAATGGACACGACCTTCTTTTTGCACATGAGACATTTTGACACTGACGTG
AAATTTTGGTTACACTTGAGGAAACCACAGTTCTGGCTGAAACCCGAGATAAAGACCCACTAGAAGATCCAAGTCTTCAA
TTGAATATTGAGGAATTAAACAGAGAGTTTATGGTGAAAAGTGAAGAACTCTATGACTCTCTCATGAATTGCCACTGGCA
GTGGCAGTTCACTCTAAAATCCCAGATG

Alignment

ORF - retro_ecab_792 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.93 %
• Parental protein coverage: 76. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VKPEFQPSQGYPFGHWSEHQHSCCSLPDYSSGCAVVGSGHSCLSVCATSGHPAETLVTQEETTSLAENRD
          VKPEFQP.QGY.FG...E.Q.SC.SL..YS.GCAV.G.GH..L....T..H..E.LVT.EETT.LAE.RD
Retrocopy VKPEFQPHQGYSFGN*NEQQQSCYSLSGYSCGCAVGGNGHDLLFAHETF*H*REILVTLEETTVLAETRD

Parental  EDPIADPNLHLNIEE--KEFMMKSEELYDSLMNCHWQPSDTVHSKI
          .DP..DP.L.LNIEE...EFM.KSEELYDSLMNCHWQ...T..S..
Retrocopy KDPLEDPSLQLNIEELNREFMVKSEELYDSLMNCHWQWQFTLKSQM

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	0.89 RPM
SRP021940_cerebellum	0.00 RPM	1.92 RPM
SRP021940_embryo	0.00 RPM	1.53 RPM
SRP021940_placental_villous	0.00 RPM	0.24 RPM
SRP021940_synovial_membrane	0.00 RPM	0.33 RPM
SRP021940_testis	0.00 RPM	0.83 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_792 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_792 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_792 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002583	1 retrocopy	retro_amel_1114,
Canis familiaris	ENSCAFG00000030234	1 retrocopy	retro_cfam_1098,
Choloepus hoffmanni	ENSCHOG00000010768	2 retrocopies	retro_chof_2530, retro_chof_70,
Equus caballus	ENSECAG00000008229	2 retrocopies	retro_ecab_684, retro_ecab_792 ,
Equus caballus	ENSECAG00000012980	1 retrocopy	retro_ecab_452,
Monodelphis domestica	ENSMODG00000028324	12 retrocopies	retro_mdom_1372, retro_mdom_2019, retro_mdom_322, retro_mdom_336, retro_mdom_453, retro_mdom_492, retro_mdom_513, retro_mdom_523, retro_mdom_534, retro_mdom_616, retro_mdom_746, retro_mdom_894,
Tursiops truncatus	ENSTTRG00000003650	1 retrocopy	retro_ttru_927,
Vicugna pacos	ENSVPAG00000003001	2 retrocopies	retro_vpac_198, retro_vpac_609,