RetrogeneDB ID: retro_ocun_172

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 12:39231025..39232084(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000024437
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000012987
• Aliases: None
• Description: None

Sequence

>retro_ocun_172
ATGGCATTACCGTTCCGGAAGGACTTGGAGAAGTACAAGGACCTTGATGAAGATGAGCTCCTTGGGAATCTGTCCGAAGT
GGAACTGAAACAACTGGAAACTGTTCTGGATGATCTTGATCCTGAGAATGCCCTTCTGCCTGCAGGGTTTCGGCAGAAGA
ACCAGACATCAAAGTCTGCCACGGGGCCGTTTGATAGAGAACACCTCCTGTCATATCTAGAGAAGGAAGCACTGGAGCAT
AAGGACAGGGAAGACTATGTCCCCTACACTGGAGAAAAGAAAGGGAAAATATTCATCCCCAAGCAGAAACCTGTACAGAC
TTTTGCAGAAGAAAACATCTCTCTTGATCCAGAACTAGAAGAAGCTTTGACAAGTGCTACTGATACAGAATTGTGTGACC
TCGCAGCTATTCTTGGGATGCACAATTTGATAACAAATGCACAGTTCTGTAATGTTGTAGGAAGTAGTAATGGTGTCGAC
GAGGAACATTTTTCAAATGTGGTAAAAGGTGAAAAGATTCTTCCAGTATTTGATGAGCCACCAAATCCAACCAATGTTGA
AGAGAGTTTAAGGAGAATTAAAGAAAATGATGCTCGTCTTATTGAAGTTAATTTGAATAACATAAAGAATATCCCAATTC
CAACCCTAAAAGATTTTGCAAAGGCTTTGGAAACCAACACACATGTGCAGTGTTTCAGTCTTGCAGCCACACGGAGCAAT
GACCCCGTTGCTGTTGCTTTTGCAGAAATGCTGACGGTGAACAAAACTTTGAAGAGCTTAAATATGGAGTCCAACTTTAT
TACAGGAACTGGCATTCTGGCACTGATTGATGCTTTAAAAGATAATGAAACCCTGTCAGAGCTCAAGATTGACAATCAGA
GGCAGCAGTTGGGGACAGCTGTAGAATTGGAAATGGCCAAGATGCTAGAGGAAAATACAAATATTCTAAAGTTTGGCTAT
CAGTTTACACAGCAGGGACCCCGAACCAGGGCGGCTAATGCTATTACAAAAAACAATGACTTAGTACGCAAGAGACGAGT
TGAAGGAGACCATCAGTGA

Alignment

ORF - retro_ocun_172 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.72 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MALPFRKDLEKYKDLDEDELLGNLSEVELKQLETVLDDLDPENALLPAGFRQKNQTSKSATGPFDREHLL
          MALPFRKDLEKYKDLDEDELLGNLSEVELKQLETVLDDLDPENALLPAGFRQKNQTSKSATGPFDREHLL
Retrocopy MALPFRKDLEKYKDLDEDELLGNLSEVELKQLETVLDDLDPENALLPAGFRQKNQTSKSATGPFDREHLL

Parental  SYLEKEALEHKDREDYVPYTGEKKGKIFIPKQKPVQTFAEENISLDPELEEALTSATDTELCDLAAILGM
          SYLEKEALEHKDREDYVPYTGEKKGKIFIPKQKPVQTFAEENISLDPELEEALTSATDTELCDLAAILGM
Retrocopy SYLEKEALEHKDREDYVPYTGEKKGKIFIPKQKPVQTFAEENISLDPELEEALTSATDTELCDLAAILGM

Parental  HNLITNAQFCNVVGSSNGVDEEHFSNVVKGEKILPVFDEPPNPTNVEESLRRIKENDARLIEVNLNNIKN
          HNLITNAQFCNVVGSSNGVDEEHFSNVVKGEKILPVFDEPPNPTNVEESLRRIKENDARLIEVNLNNIKN
Retrocopy HNLITNAQFCNVVGSSNGVDEEHFSNVVKGEKILPVFDEPPNPTNVEESLRRIKENDARLIEVNLNNIKN

Parental  IPIPTLKDFAKALETNTHVQCFSLAATRSNDPVAVAFAEMLTVNKTLKSLNMESNFITGTGILALIDALK
          IPIPTLKDFAKALETNTHVQCFSLAATRSNDPVAVAFAEMLTVNKTLKSLNMESNFITGTGILALIDALK
Retrocopy IPIPTLKDFAKALETNTHVQCFSLAATRSNDPVAVAFAEMLTVNKTLKSLNMESNFITGTGILALIDALK

Parental  DNETLSELKIDNQQRQQLGTAVELEMAKMLEENTNILKFGYQFTQQGPRTRAANAITKNNDLVRKRRVEG
          DNETLSELKIDNQ.RQQLGTAVELEMAKMLEENTNILKFGYQFTQQGPRTRAANAITKNNDLVRKRRVEG
Retrocopy DNETLSELKIDNQ-RQQLGTAVELEMAKMLEENTNILKFGYQFTQQGPRTRAANAITKNNDLVRKRRVEG

Parental  DHQ
          DHQ
Retrocopy DHQ

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	1.88 RPM	1.27 RPM
SRP017611_kidney	3.04 RPM	2.23 RPM
SRP017611_liver	0.69 RPM	1.39 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_172 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_172 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_172 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002953	1 retrocopy	retro_chof_1905,
Oryctolagus cuniculus	ENSOCUG00000012987	1 retrocopy	retro_ocun_172 ,