RetrogeneDB ID: retro_ecab_495

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 2:70591473..70591886(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL24
• Ensembl ID: ENSECAG00000011340
• Aliases: None
• Description: mitochondrial ribosomal protein L24 [Source:HGNC Symbol;Acc:14037]

Sequence

>retro_ecab_495
ATTTGGCAGTGAAACTGGGTGGGCCTGGATGGGCTGAACACATGCTTACCACTACATTGGCAAGATCAAGGATTACCGGG
GAACCGTGATCCCTAGCGAAACCCCCCTTGCTCCACTGCCAGGTCAAACTTGTGGCTCCTGTGGAGAGAAAACCTACTGA
AGTGGAGTGGAGATTCACTGAGGCAGGAGATGAGGTATGGGTCATCACAAGATCAGGAAGAATTATCCCCAAACCTGAAT
TTCCCAGAGCTGATGGCATTGTCCCTGAAACATGGATTGATGACACCAAGAACACATCAGTGGAAGATGCTCTAGAACAA
ACCTGTATGCCCCATCTAAAGACACTGGAAGAGGAGGCAGTGGAGGCAATGGGGATCCAGGGGACTTAGAAACACAAGAA
AGTCTGTTGGTAT

Alignment

ORF - retro_ecab_495 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.47 %
• Parental protein coverage: 63.76 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  IRQRNWVVLEGLNT-HYRYIGKTKDYRGTMIPSEAPL-LHHQVKLVDPPLTFGKPTEVEWRFTEAGERVR
          I.Q.NWV.L.GLNT..Y.YIGK.KDYRGT.IPSE.PL.LH.QVKLV.P.....KPTEVEWRFTEAG..V.
Retrocopy IWQ*NWVGLDGLNT>AYHYIGKIKDYRGTVIPSETPL>LHCQVKLVAP--VERKPTEVEWRFTEAGDEVW

Parental  VSTRSGRIIPKPEFPRADGIVPETWTDGPKDTSVEDALERTYVPRLKTLEEEVMEAMGIQETRRHKKVYW
          V.TRSGRIIPKPEFPRADGIVPETW.D..K.TSVEDALE.T..P.LKTLEEE..EAMGIQ.T..HKKV.W
Retrocopy VITRSGRIIPKPEFPRADGIVPETWIDDTKNTSVEDALEQTCMPHLKTLEEEAVEAMGIQGT*KHKKVCW

Parental  Y
          Y
Retrocopy Y

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	11.33 RPM
SRP021940_cerebellum	0.00 RPM	19.68 RPM
SRP021940_embryo	0.00 RPM	11.58 RPM
SRP021940_placental_villous	0.00 RPM	16.50 RPM
SRP021940_synovial_membrane	0.00 RPM	13.07 RPM
SRP021940_testis	0.00 RPM	20.33 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_495 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_495 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_495 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000011340	1 retrocopy	retro_ecab_495 ,
Macaca mulatta	ENSMMUG00000000039	1 retrocopy	retro_mmul_1731,
Otolemur garnettii	ENSOGAG00000016825	1 retrocopy	retro_ogar_1541,