RetrogeneDB ID: retro_ecab_1106

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: X:41758959..41759316(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMA5
• Ensembl ID: ENSECAG00000011835
• Aliases: None
• Description: proteasome (prosome, macropain) subunit, alpha type, 5 [Source:HGNC Symbol;Acc:9534]

Sequence

>retro_ecab_1106
AATCTTCTCTCATTGTTTCCAAGATTATTTCATGAGTAATATGTCATTGGGATGATCAAGCTTTGTTCCATAGCGATTGG
GATACAGACTTCAGAGGTGTGTGTGCCTAGCTATAAAGAAGAGAATTACCTCCTATTGCCCTGTAGCAGTGAGAAAGTTG
TAGATATTGATGCTCAAACAAGTTGTGTTGAAAGTAACCTAATGGCTGGAGCTAAGACTATAATTGATAAAGCCAGAGTG
GAGACATCGGACCTCTGCTTCACTTACAAAAAGATAAATGATATTGAAGAATAAAGCTAGTTTGAGTCCAACTTGAATGT
GCAATTTGGAGAAGAAAATACAGATCCAGAAGCCATT

Alignment

ORF - retro_ecab_1106 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.41 %
• Parental protein coverage: 50.21 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NTFSPEGRLFQVEYAIEAIKLGSTAIGIQTSEGVCLAVEKRITSPLMEPSSIEKIVEIDAHIGCAMSGLI
          N..S...RLF...Y.I..IKL.S.AIGIQTSE.VC....K.....L..P.S.EK.V.IDA...C..S.L.
Retrocopy NLLSLFPRLFHE*YVIGMIKLCSIAIGIQTSE-VCVPSYKE-ENYLLLPCSSEKVVDIDAQTSCVESNLM

Parental  ADAKTLIDKARVETQNHWFTYNETMTVESVTQAVSNLALQFGEEDADPGAM
          A.AKT.IDKARVET....FTY......E......SNL..QFGEE..DP.A.
Retrocopy AGAKTIIDKARVETSDLCFTYKKINDIEE*S*FESNLNVQFGEENTDPEAI

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	10.68 RPM
SRP021940_cerebellum	0.00 RPM	20.67 RPM
SRP021940_embryo	0.00 RPM	28.10 RPM
SRP021940_placental_villous	0.00 RPM	28.82 RPM
SRP021940_synovial_membrane	0.00 RPM	18.50 RPM
SRP021940_testis	0.00 RPM	34.02 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_1106 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_1106 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_1106 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000013670	1 retrocopy	retro_cpor_1063,
Equus caballus	ENSECAG00000011835	1 retrocopy	retro_ecab_1106 ,
Echinops telfairi	ENSETEG00000012916	1 retrocopy	retro_etel_1053,
Mus musculus	ENSMUSG00000068749	1 retrocopy	retro_mmus_52,
Ochotona princeps	ENSOPRG00000008863	1 retrocopy	retro_opri_449,
Rattus norvegicus	ENSRNOG00000019868	2 retrocopies	retro_rnor_1230, retro_rnor_658,
Sus scrofa	ENSSSCG00000006830	2 retrocopies	retro_sscr_1156, retro_sscr_1194,