RetrogeneDB ID: retro_ocun_1792

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018899:506296..507254(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000003045
• Aliases: None
• Description: None

Sequence

>retro_ocun_1792
ATGGGGCCCTGGGGAGAGCCAGAGCCCCTGGTGTGGTGCTTAGAGGCTGTGGCTTTGGAGCCCCAGTGCCCGGGGGGCTG
GAGGCCCTGGTGCTGCTGCTGGTGCTCACCCTCCTCTGAAGCCTGGTGCCCCTCTGCATGCTGTGGCAGCCTGGAGCCAG
CCATGAAGCCTCAGGTTCCCTCCAGAAAGCCCTGAGCCTAGTGAGCTGCTTGGGGGGGGTGTTTTTGGCCACCTGTCTCC
TGGACCTGCTGCCTGACTACGTAGCTGTGATAGATGAGGCCCTGGGCAGCCCTGCACATGACACTCCAGTTTCTCCTACA
AGAGTTCATCTTAGCCATGAGATTCTTCCTGGTCCTCGTGATGGAACAGATCACCCTGGCTTACAAGGAGCAGTTGGGGC
TACCACCACGGGAGGAAACAAGGGCTCTGCTTGGGAACAGTGCATGGTGGGCCACAGCATTGGCAAGATGGTCCAGGCAT
CCCACAGGCACATGGAGCCCCGGCAGCCCCTCAGCCCTGCGTGCCTGTGTACTGGTCTTCTCTCTGGCCCTGCGCTCGGT
GTTCGAGGGGCTAGCAGTGGGGCTGCAGCAGGACCAGGCTCGGGCCATGGAGCTCTATCTGGCTTTGCTGCTCCACAAGG
GTATCCTGGCTGTTAGCCTGTCTCTATGGCTGCTGCAGAGCCACCTGCGAGTAAAGGTCGTGGCTGGCTGTGGGATCCTC
TTCTCAAGCATGACACCTCTAGGCACTGGGCTGGGTGTGCAGCTCTGGTAGAGTTGGCAGAACCTTGCACCAGCTGGCCC
AGTCTGTGCTAGAGGGCTTGGCAGTGGGCACCTTCCCCTATATCACCTTACTGGGAATCTTGCCTCAGGAGCTGGCCACT
TCTGAGCAGAGGGTCCTCAAGGTCATTCTGCTCATAGCAGGCTTTGCTCTGCTCACTGACCTGCTCCTCACTCAAATC

Alignment

ORF - retro_ocun_1792 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.46 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MGPWGEPELLVWRPEAVASAP-PVPVGLEVKLGALVLLLVLTLLCSLVPICVLRRPGASHEASASRQKAL
          MGPWGEPE.LVW..EAVA..P.PVP.GLE....ALVLLLVLTLL.SLVP.C.L..PGASHEAS.S.QKAL
Retrocopy MGPWGEPEPLVWCLEAVALEP<PVPGGLE----ALVLLLVLTLL*SLVPLCMLWQPGASHEASGSLQKAL

Parental  SLVSCFAGGVFLATCLLDLLPDYLAAIDEAL-AALHVTLQFPLQEFILAMGFFLVLVMEQITLAYKEQSG
          SLVSC..GGVFLATCLLDLLPDY.A.IDEAL.AALH.TLQF.LQEFILAM.FFLVLVMEQITLAYKEQ.G
Retrocopy SLVSCL-GGVFLATCLLDLLPDYVAVIDEAL>AALHMTLQFLLQEFILAMRFFLVLVMEQITLAYKEQLG

Parental  PPPREETRAL-LGTVNGGPQHWHDGPGVPQAHGAPAA-PSALRACVLVFSLALHSVFEGLAVGLQRDRAR
          .PPREETRAL.LGTV.GGPQHW.DGPG.PQAHGAPAA.PSALRACVLVFSLAL.SVFEGLAVGLQ.D.AR
Retrocopy LPPREETRAL>LGTVHGGPQHWQDGPGIPQAHGAPAA<PSALRACVLVFSLALRSVFEGLAVGLQQDQAR

Parental  AMELCLALLLHKGILAVSLSLRLLQSNLRVQVVAGCGILFSCMTPLGIGLGAAL-AELAGPLHQLAQSVL
          AMEL.LALLLHKGILAVSLSL.LLQS.LRV.VVAGCGILFS.MTPLG.GLG..L.......LHQLAQSVL
Retrocopy AMELYLALLLHKGILAVSLSLWLLQSHLRVKVVAGCGILFSSMTPLGTGLGVQL>GRVGRTLHQLAQSVL

Parental  EGMAAGTFLYITFLEILPQELATSEQRILKVILLLAGFALLTGLLFIQI
          EG.A.GTF.YIT.L.ILPQELATSEQR.LKVILL.AGFALLT.LL..QI
Retrocopy EGLAVGTFPYITLLGILPQELATSEQRVLKVILLIAGFALLTDLLLTQI

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	14.35 RPM
SRP017611_kidney	0.00 RPM	35.68 RPM
SRP017611_liver	0.00 RPM	19.27 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1792 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1792 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1792 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000010006	1 retrocopy	retro_cjac_1476,
Macropus eugenii	ENSMEUG00000006754	1 retrocopy	retro_meug_1551,
Microcebus murinus	ENSMICG00000010310	1 retrocopy	retro_mmur_162,
Myotis lucifugus	ENSMLUG00000013282	1 retrocopy	retro_mluc_2366,
Macaca mulatta	ENSMMUG00000005007	1 retrocopy	retro_mmul_28,
Mus musculus	ENSMUSG00000052310	1 retrocopy	retro_mmus_1899,
Oryctolagus cuniculus	ENSOCUG00000003045	1 retrocopy	retro_ocun_1792 ,