RetrogeneDB ID: retro_ocun_1764

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018862:324070..324906(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000005824
• Aliases: None
• Description: None

Sequence

>retro_ocun_1764
GACATCCTTGCCAGGGGAGCGAATGTGAACATGTACATGTTTATAGGTGGGACCCATTTTGCCTATTGGAACAGGGCCAA
CATGCCCTATGCATCACAGCTCACCAGCTAGACTATGACGCCCCCTGAGTGAGGCAGGGGACCTCACCAAGAAGTATTTT
GCTCTGCAGAAGGTTATCGGGAAGTTTGCAGCATTACCAGAAGGTCCCATTCCTCCATCCACACCAAAGTTTGCATATGG
AACAGTCCCGCTGAAAAAGTGAAGGGCAGTGGATGCAGCTCTGGATGTCCTGTGTCCCTCCAGGCCCATCAACAGTGTTT
ATCCCCTGATGTGTACCCAGGTGAAACAGTACTTTGGCTTTGTGCTGTACCGGACAACACTGCCTCGGGACTGCAGCAAC
CCTACACCCCTCCCTTCATCCCTCAATGGAGTCCACGACCGGGCCTGAGTCGCTGTGGATGGGATTCTGCAGGGAGTGCT
GGGGCGAAACCACGTGCTCACGGTGAGCATACAAGGGAAGGCTGGAGCCAGGCTGGACCTCCTGGTGGAGAACATGGGGC
ACGTGCACTACCGCAAAGCCATCAACGACTTTAAGGGCTTGATTTCCAACTTGACCCTGGGTTCCTGCATCCTCACAAAC
TGGACCATCTTCCCCCTGGACACCGAGAGGGCAGTGAGCAGCCTCCTGGGTACTGGGGTGGCCGCCAGAAGGACGCCAGT
GCCTGCAGCTCCCAGAACTACACACTGCCAGCCTTTTACACTGGGAACTTCTCCATCCCCAGTGGCGTCCCGTCCCTGCC
CCAGGACACCTTTATCAAGTTCCCGGGTGGACCAAG

Alignment

ORF - retro_ocun_1764 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.56 %
• Parental protein coverage: 51. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  DILAHGANVNMYMFIGGTNFAYWNGANTPYAPQPTS-YDYDAP-LSEAGDLTEKYFAVRKVIGKFVALPE
          DILA.GANVNMYMFIGGT.FAYWN.AN.PYA.Q.TS..DYDAP.LSEAGDLT.KYFA..KVIGKF.ALPE
Retrocopy DILARGANVNMYMFIGGTHFAYWNRANMPYASQLTS<LDYDAP<LSEAGDLTKKYFALQKVIGKFAALPE

Parental  GPIPPSTPKFAYGTVPLKKLRTVEAALDVLCPSGPISSVYPLTFTQVKQYFGFVLYRTTLPRDCSNPTPL
          GPIPPSTPKFAYGTVPLKK.R.V.AALDVLCPS.PI.SVYPL..TQVKQYFGFVLYRTTLPRDCSNPTPL
Retrocopy GPIPPSTPKFAYGTVPLKK*RAVDAALDVLCPSRPINSVYPLMCTQVKQYFGFVLYRTTLPRDCSNPTPL

Parental  SSPRNGVHDRAYVAVDGIPQGVLERNRVLTVSIQGKAGARLDLLVENMGRVNYGTAINDFKGLISNLTLG
          .S..NGVHDRA.VAVDGI.QGVL.RN.VLTVSIQGKAGARLDLLVENMG.V.Y..AINDFKGLISNLTLG
Retrocopy PSSLNGVHDRA*VAVDGILQGVLGRNHVLTVSIQGKAGARLDLLVENMGHVHYRKAINDFKGLISNLTLG

Parental  SYILTNWTIFPLDTERAVSSLQGD-WGGCQKDARACSPGNYTLPAFYTGNFSIPSGVPSLPQDTFITF-P
          S.ILTNWTIFPLDTERAVSSL.G..WGG.QKDA.ACS..NYTLPAFYTGNFSIPSGVPSLPQDTFI.F.P
Retrocopy SCILTNWTIFPLDTERAVSSLLGT<WGGRQKDASACSSQNYTLPAFYTGNFSIPSGVPSLPQDTFIKF<P

Parental  GWTK
          GWTK
Retrocopy GWTK

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	0.00 RPM	29.03 RPM
SRP017611_kidney	0.10 RPM	53.21 RPM
SRP017611_liver	0.00 RPM	15.57 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1764 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1764 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1764 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Oryctolagus cuniculus	ENSOCUG00000005824	1 retrocopy	retro_ocun_1764 ,