RetrogeneDB ID: retro_ocun_325

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 1:177137284..177137815(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000028011
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TPD52
• Ensembl ID: ENSOCUG00000008247
• Aliases: None
• Description: tumor protein D52 [Source:RefSeq peptide;Acc:NP_001075829]

Sequence

>retro_ocun_325
ATGGATTGTAAAGAGATGGATTTGTATGAGGACTACCAGTCCCCGTTTGATTTTGACACAGGCATGAACAAAAGCTACCT
CTACCTCTCTCCTAGCGGGAATGTTTCTCCACCCGGATCTCTGACCCTTCAGGAATGCGGTCTGTTGAGGACGGACACAG
TGCCTGAGGAAGCAGAAGATGCCGCGGCCACCACCAGTGCCACCGAGACGCTGTCTGAGGAGGAGCAAGAAGAGCTGAGA
AGGGAACTCGCCAAGGTAGAAGAAGAAATCCAGACTCTGTCTCAGGTGTTAGCAGCAAAAGAGAAGCATCTAGCAGAGAT
CAAGCGGAAGCTAGGAATCAACTCACTGCAGGAACTAAAGCAGAACATTGCCAAAGGGTGTCAAGATGTGACGGCAACGT
CTGCGTACAAGAAGACATCTGAAACCTTGTTTCAGGCTGGGCAGAAGGCTTCTGCTGCATTTTCGTCTGTTGGCTCGGTC
ATCACCAAAAAGCTGGAAGACGTAAAAAACTCCTCAACCTTCAAATCCTTT

Alignment

ORF - retro_ocun_325 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.09 %
• Parental protein coverage: 71.54 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDCKEMDLYEDYQSPFDFDTGVNKSYLYLSPGGNVSPPGSPTLQK-GLLRTDTVPEEAEDAAATISATET
          MDCKEMDLYEDYQSPFDFDTG.NKSYLYLSP.GNVSPPGS.TLQ..GLLRTDTVPEEAEDAAAT.SATET
Retrocopy MDCKEMDLYEDYQSPFDFDTGMNKSYLYLSPSGNVSPPGSLTLQECGLLRTDTVPEEAEDAAATTSATET

Parental  LSEEEQEELRRELAKVEEEIQTLSQVLAAKEKHLAEIKRKLGINSLQELKQNIAKGWQDVTATSAYKKTS
          LSEEEQEELRRELAKVEEEIQTLSQVLAAKEKHLAEIKRKLGINSLQELKQNIAKG.QDVTATSAYKKTS
Retrocopy LSEEEQEELRRELAKVEEEIQTLSQVLAAKEKHLAEIKRKLGINSLQELKQNIAKGCQDVTATSAYKKTS

Parental  ETLSQAGQKASAAFSSVGSVITKKLEDVKLQAFSHSF
          ETL.QAGQKASAAFSSVGSVITKKLEDVK......SF
Retrocopy ETLFQAGQKASAAFSSVGSVITKKLEDVKNSSTFKSF

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
SRP017611_brain	0.28 RPM	185.16 RPM
SRP017611_kidney	0.81 RPM	92.23 RPM
SRP017611_liver	0.23 RPM	30.06 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_325 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_325 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_325 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001357	1 retrocopy	retro_chof_1370,
Dasypus novemcinctus	ENSDNOG00000017379	2 retrocopies	retro_dnov_1294, retro_dnov_1451,
Mus musculus	ENSMUSG00000027506	1 retrocopy	retro_mmus_3221,
Oryctolagus cuniculus	ENSOCUG00000008247	1 retrocopy	retro_ocun_325 ,
Otolemur garnettii	ENSOGAG00000016601	2 retrocopies	retro_ogar_1677, retro_ogar_348,
Tursiops truncatus	ENSTTRG00000000088	1 retrocopy	retro_ttru_1888,