RetrogeneDB ID: retro_ecab_1001

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 8:79540228..79540437(-)
• Located in intron of: ENSECAG00000020437

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSME1
• Ensembl ID: ENSECAG00000016855
• Aliases: None
• Description: proteasome (prosome, macropain) activator subunit 1 (PA28 alpha) [Source:HGNC Symbol;Acc:9568]

Sequence

>retro_ecab_1001
CCAATGAATGGCAAGAAGATGGTGGTCGTCCTGCAGCGTCTCAAGCCTGGAACTAGGCCTGTCATTGAGCAGTCAGTCTG
GTCACTATCTGGTTGCCGCTGCAGATACCTTGGCTTGAGGATGGGAACAGTTTTGGAATGGCTGTGCAGGAGACGGTGTT
TGAGCTGATGACCACCCTGCACACCAAGCTGATAGGCTTCAATCTCCAA

Alignment

ORF - retro_ecab_1001 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.28 %
• Parental protein coverage: 59.17 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PVNCNEKIVVLLQRLKPEIKDVIEQ-LNPVTTWLQLQIPRIEDGNNFGVAVQEKVFELMTALHTKLEGFH
          P.N...K.VV.LQRLKP....VIEQ....VT.WL.LQIP..EDGN.FG.AVQE.VFELMT.LHTKL.GF.
Retrocopy PMN-GKKMVVVLQRLKPGTRPVIEQ<VSLVTIWLPLQIPWLEDGNSFGMAVQETVFELMTTLHTKLIGFN

Parental  TQ
          .Q
Retrocopy LQ

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	18.42 RPM
SRP021940_cerebellum	0.00 RPM	21.29 RPM
SRP021940_embryo	0.00 RPM	27.72 RPM
SRP021940_placental_villous	0.05 RPM	27.09 RPM
SRP021940_synovial_membrane	0.05 RPM	23.83 RPM
SRP021940_testis	0.06 RPM	19.37 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_1001 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_1001 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_1001 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016433	1 retrocopy	retro_amel_637,
Bos taurus	ENSBTAG00000021395	1 retrocopy	retro_btau_1189,
Canis familiaris	ENSCAFG00000011924	1 retrocopy	retro_cfam_246,
Equus caballus	ENSECAG00000012620	2 retrocopies	retro_ecab_29, retro_ecab_827,
Equus caballus	ENSECAG00000016855	1 retrocopy	retro_ecab_1001 ,
Felis catus	ENSFCAG00000005583	1 retrocopy	retro_fcat_1567,
Macropus eugenii	ENSMEUG00000014712	1 retrocopy	retro_meug_1052,
Mus musculus	ENSMUSG00000022216	1 retrocopy	retro_mmus_466,
Rattus norvegicus	ENSRNOG00000019041	1 retrocopy	retro_rnor_50,
Tursiops truncatus	ENSTTRG00000008620	1 retrocopy	retro_ttru_569,