RetrogeneDB ID: retro_ocun_292

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 1:78452592..78453363(+)
• Located in intron of: ENSOCUG00000012932

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000006235
• Aliases: None
• Description: None

Sequence

>retro_ocun_292
ATTCAGTGGTCCCAATTTAAAGGCTATTTTATTTTCAAACTGGAGAAAGTGATGGATGATTTCAGAACTTCAGCTCCTGA
ACCAAGAGGTCCTCCCAACCCTAATGTCGAGTATATTCCCTTTGATGAAATGAAGGAACGAATACTGAAAATTGTCACTG
GATTTAATGGTATCCCTTTTACTATTCAGCGACTATGTGAATTGCTAACAGATCCAAGAAGAAACTATACAGGAACAGAC
AAATTTCTCAGAGGAGTAGAAAAGAATGTGATGCTTGTTAGCTGTGTTTATCCTTCTTCAGAGAAAACCAGTTCTAATAG
TTTAAATAGAATGAATGGTGTTATGTTTCCTGGAAATTCACCAAGCTATACTGACAGGTCTAATATAAATGGGCCTGGGA
CGCCCAGGCCACTTAATCGACCAAAGGTTTCTTTGTCAGTTCCAATGACAACAAATGGTTTGCCCGAGAGCCCAGACAGT
AAATAGTCAAACTTACAGCAAAATGAAGAGAAAAACCACAGTGACTCGCTGGCAACTGAATCAGAAGTCTCCTCAGTGAG
CCCCATAAAAAATAAACACCCAGATGAAGACGCTGTAGAAGCCGAGGGCCACGAAGTAAAAAGACTCAGGTTTGACAAAG
AAGGGGAAGTGAGAGAGGCGGCCGGGCAGACAGCTTCCAGTGAGAGTCCTTCAGTTCTGGCAGAAGACACAGAAGCCCTG
TCGTCACCTCAGGGTAAAGACAAAGAAAGCCACACTGCCAGGCAGCACTGT

Alignment

ORF - retro_ocun_292 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.05 %
• Parental protein coverage: 68.35 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IQWSQFKGYFIFKLEKVMDDFRTSAPEPRGPPNPNVEYIPFDEMKERILKIVTGFNGIPFTIQRLCELLT
          IQWSQFKGYFIFKLEKVMDDFRTSAPEPRGPPNPNVEYIPFDEMKERILKIVTGFNGIPFTIQRLCELLT
Retrocopy IQWSQFKGYFIFKLEKVMDDFRTSAPEPRGPPNPNVEYIPFDEMKERILKIVTGFNGIPFTIQRLCELLT

Parental  DPRRNYTGTDKFLRGVEKNVMVVSCVYPSSEKTSSNSLNRMNGVMFPGNSPSYTDRSNINGPGTPRPLNR
          DPRRNYTGTDKFLRGVEKNVM.VSCVYPSSEKTSSNSLNRMNGVMFPGNSPSYTDRSNINGPGTPRPLNR
Retrocopy DPRRNYTGTDKFLRGVEKNVMLVSCVYPSSEKTSSNSLNRMNGVMFPGNSPSYTDRSNINGPGTPRPLNR

Parental  PKVSLSVPMTTNGLPESPDSKESNLQQNEEKNHSDSLASESEVSSVSPIKNKHPDEDAVEAEGHEVKRLR
          PKVSLSVPMTTNGLPESPDSK.SNLQQNEEKNHSDSLA.ESEVSSVSPIKNKHPDEDAVEAEGHEVKRLR
Retrocopy PKVSLSVPMTTNGLPESPDSK*SNLQQNEEKNHSDSLATESEVSSVSPIKNKHPDEDAVEAEGHEVKRLR

Parental  FDKEGEVREAAGQTASSESSSVLAEDAEALSSPQGKDKESHTARQHC
          FDKEGEVREAAGQTASSES.SVLAED.EALSSPQGKDKESHTARQHC
Retrocopy FDKEGEVREAAGQTASSESPSVLAEDTEALSSPQGKDKESHTARQHC

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	3.09 RPM	26.77 RPM
SRP017611_kidney	4.56 RPM	24.53 RPM
SRP017611_liver	1.54 RPM	21.66 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_292 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_292 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_292 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007954	3 retrocopies	retro_chof_1347, retro_chof_1914, retro_chof_2285,
Echinops telfairi	ENSETEG00000019946	2 retrocopies	retro_etel_1238, retro_etel_148,
Homo sapiens	ENSG00000163605	6 retrocopies	retro_hsap_2744, retro_hsap_2745, retro_hsap_2746, retro_hsap_2904, retro_hsap_3138, retro_hsap_3283,
Loxodonta africana	ENSLAFG00000000513	1 retrocopy	retro_lafr_603,
Macaca mulatta	ENSMMUG00000016959	1 retrocopy	retro_mmul_1224,
Mus musculus	ENSMUSG00000052144	3 retrocopies	retro_mmus_1068, retro_mmus_1157, retro_mmus_3474,
Oryctolagus cuniculus	ENSOCUG00000006235	1 retrocopy	retro_ocun_292 ,
Pan troglodytes	ENSPTRG00000015108	5 retrocopies	retro_ptro_1855, retro_ptro_1856, retro_ptro_2121, retro_ptro_2220, retro_ptro_2974,