RetrogeneDB ID: retro_ocun_1641

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018737:1980796..1981515(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000027720
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MRPS18B
• Ensembl ID: ENSOCUG00000002149
• Aliases: None
• Description: mitochondrial ribosomal protein S18B [Source:HGNC Symbol;Acc:14516]

Sequence

>retro_ocun_1641
ATGGCGGCCTCCGTATTGAACACACTGCGGCGGCGGGTTCCTAGCCTTTCGCTTTTCAGAAGTGCCTACGGAGTTCAGGT
GCCCTTTCAGACTCTTTGCACCAAAGCCCCCCTGAGAAAGATTCTTTGCCCACTGGTCCCATTTCCCCTTATAAGGATGA
ACCCTGGAAATACCTGGACTCAGAAGAATACCAGAACCGCTATGGTTCTCGCCCAGTCTGGGCTGACTACCGCCGCAACC
ACAAAGGTGGGGTACCCCCACAGCGGACTCGAAAGACATGTATTCATAAAGATAAAATTGCCGGGAATCCCTGCCCCATC
TGTCGGGATCACAAGTTGCACGTGGACTTCAGGAACATGAAGCTCTTGGAACAGTTTGTCTGCGCCCACACGGGTATCAT
CTTCCACGCTCCATACACAGGAGTCTGCATGAAGCAGCACAAGAAGTTGACCCAGGCCATCCAGAAAGCCAGAGATCACG
GTCTCCTCAGGTACCACATTCCCCAGGTTGAGCCTCGGGACCTTGACTTCAGTGCCTCTCACGGAGCTGTGAGTGCCACT
CTACCAGCTCCCACCCTGGTTTCCGGCGATCCCTGGTACCCGTGGTACAGCTGGACACAGCCACCAGAGAGAGAACTGTC
CCGCCTTCGGCAGCTCTATCAGGGCCATCTCGGAGAAGAGAGTGGCCCTCCGCCTGCAGCACCAGCGGAAGCCCCCTCC

Alignment

ORF - retro_ocun_1641 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.85 %
• Parental protein coverage: 96. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAASVLNTLLWRVPRLSLFRSAYGVQVPFQTLCTKA-PPEKDSLPTGPISPYKDEPWKYLDSEEYQNRYG
          MAASVLNTL..RVP.LSLFRSAYGVQVPFQTLCTKA.PPEKDSLPTGPISPYKDEPWKYLDSEEYQNRYG
Retrocopy MAASVLNTLRRRVPSLSLFRSAYGVQVPFQTLCTKA<PPEKDSLPTGPISPYKDEPWKYLDSEEYQNRYG

Parental  SRPVWADYRRNHKGGVPPQRTRKTCIRKDKIAGNPCPICRDHKLHVDFRNVKLLEQFVCAHTGIIFHAPY
          SRPVWADYRRNHKGGVPPQRTRKTCI.KDKIAGNPCPICRDHKLHVDFRN.KLLEQFVCAHTGIIFHAPY
Retrocopy SRPVWADYRRNHKGGVPPQRTRKTCIHKDKIAGNPCPICRDHKLHVDFRNMKLLEQFVCAHTGIIFHAPY

Parental  TGVCMKQHKKLTQAIQKARDHGLLRYHIPQVEPRDLDFSTSHGAVSATPPAPTLVSGDPWYPWYSWTQPP
          TGVCMKQHKKLTQAIQKARDHGLLRYHIPQVEPRDLDFS.SHGAVSAT.PAPTLVSGDPWYPWYSWTQPP
Retrocopy TGVCMKQHKKLTQAIQKARDHGLLRYHIPQVEPRDLDFSASHGAVSATLPAPTLVSGDPWYPWYSWTQPP

Parental  ERELSRLRRLYQGHLREESGPPPAAPAEAPS
          ERELSRLR.LYQGHL.EESGPPPAAPAEAPS
Retrocopy ERELSRLRQLYQGHLGEESGPPPAAPAEAPS

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	0.06 RPM	10.76 RPM
SRP017611_kidney	0.00 RPM	28.18 RPM
SRP017611_liver	0.00 RPM	7.25 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1641 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1641 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1641 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005581	1 retrocopy	retro_chof_505,
Macropus eugenii	ENSMEUG00000012457	10 retrocopies	retro_meug_1183, retro_meug_2004, retro_meug_2124, retro_meug_215, retro_meug_610, retro_meug_648, retro_meug_696, retro_meug_712, retro_meug_717, retro_meug_734,
Macaca mulatta	ENSMMUG00000006525	1 retrocopy	retro_mmul_900,
Monodelphis domestica	ENSMODG00000015933	1 retrocopy	retro_mdom_426,
Mus musculus	ENSMUSG00000024436	1 retrocopy	retro_mmus_2036,
Nomascus leucogenys	ENSNLEG00000005224	1 retrocopy	retro_nleu_1811,
Oryctolagus cuniculus	ENSOCUG00000002149	2 retrocopies	retro_ocun_1307, retro_ocun_1641 ,
Pongo abelii	ENSPPYG00000016412	1 retrocopy	retro_pabe_2050,
Pan troglodytes	ENSPTRG00000017932	1 retrocopy	retro_ptro_1648,
Rattus norvegicus	ENSRNOG00000000804	1 retrocopy	retro_rnor_1328,
Ictidomys tridecemlineatus	ENSSTOG00000011853	1 retrocopy	retro_itri_254,
Tarsius syrichta	ENSTSYG00000003333	1 retrocopy	retro_tsyr_1769,