RetrogeneDB ID: retro_ocun_1842

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL019295:10741..11404(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SPOPL
• Ensembl ID: ENSOCUG00000006944
• Aliases: None
• Description: speckle-type POZ protein-like [Source:HGNC Symbol;Acc:27934]

Sequence

>retro_ocun_1842
TCAGGACATACTAATACAAGCGCTTTGAAGGTGCCTGAATGTCGACTAGCAGAAGATTTAGGCGACTTCTGGGAAAACAT
AAGATTTACAGATAGCAGTTTTTTTTGCGCGTGGACAAGAATTTAAAGCTCATAAATCTGTACTTGCAGCCCAATCCCCA
GTTTTCAATGCAATGTTTGACCATGAAATGGAAGAAAGCAAAAGAATCGAGTAGAAATAAGTGATTTAGACCCTGACCTT
TTTAAAGAAATGATGGTATTCGTTTGCACAGGAAACCACCAAATCTTGATAAAATGGCTGTCAGCTGTTGGCAGCTGCAG
ACGGATCTGCACTGGAGCGACTTTAGGTCATGTGTGAAGAACTTTGTGTATTGACCTTTCAGTAGAAAATGTTGCTGATA
CCCCTCTTCTTGCAGATTTGTACAATGCAGAACGGTTGAAAGCACAAGCCATAGATTTTGTTAACAGGTGCACTGTGCTT
TGCCAGGTTGGGTGTGAAGATGGGAAAATCTGGAACAGCAGTCAAGCAACTGACGTAACAGAAACATCAGGGTGGAAGTC
CATGATTCAGTCACGCCCTCACTTAGTAGCAGAAGCCTTCTGAGCACTTGCCTCTGCACAGTGTTCACAGTTTGGCATTC
CTCGCAAATGGCTAAAACAGTCC

Alignment

ORF - retro_ocun_1842 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.18 %
• Parental protein coverage: 56.63 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  SGHTNTNTLKVPECRLAEDLGDLWENTRFTDCSFF-VRGQEFKAHKSVLAARSPVFNAMFEHEMEESK-K
          SGHTNT..LKVPECRLAEDLGD.WEN.RFTD.SFF..RGQEFKAHKSVLAA.SPVFNAMF.HEMEESK.K
Retrocopy SGHTNTSALKVPECRLAEDLGDFWENIRFTDSSFF>ARGQEFKAHKSVLAAQSPVFNAMFDHEMEESK<K

Parental  NRVEINDLDPEVFKEMMRFVYTG-KAPNLDKMADN-LLAAADKYALERLKVMCEE-ALCSNLSVENVADT
          NRVEI.DLDP..FKEMM.FV.TG.K.PNLDKMA...LLAAAD..ALERL.VMCEE..LC..LSVENVADT
Retrocopy NRVEISDLDPDLFKEMMVFVCTG<KPPNLDKMAVS<LLAAADGSALERL*VMCEE<TLCIDLSVENVADT

Parental  LVLADLHSAEQLKAQAIDFINRCSVLRQLGCKDGKNWNSNQATDIMETSGWKSMIQSHPHLVAEAFRALA
          ..LADL..AE.LKAQAIDF.NRC.VL.Q.GC.DGK.WNS.QATD..ETSGWKSMIQS.PHLVAEAF.ALA
Retrocopy PLLADLYNAERLKAQAIDFVNRCTVLCQVGCEDGKIWNSSQATDVTETSGWKSMIQSRPHLVAEAF*ALA

Parental  SAQCPQFGIPRKRLKQS
          SAQC.QFGIPRK.LKQS
Retrocopy SAQCSQFGIPRKWLKQS

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	34.60 RPM
SRP017611_kidney	0.00 RPM	37.50 RPM
SRP017611_liver	0.00 RPM	13.10 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1842 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1842 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1842 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000014763	1 retrocopy	retro_dnov_546,
Homo sapiens	ENSG00000144228	2 retrocopies	retro_hsap_2943, retro_hsap_3048,
Gorilla gorilla	ENSGGOG00000016285	1 retrocopy	retro_ggor_2040,
Macaca mulatta	ENSMMUG00000002560	2 retrocopies	retro_mmul_1884, retro_mmul_1885,
Nomascus leucogenys	ENSNLEG00000013800	1 retrocopy	retro_nleu_1629,
Oryctolagus cuniculus	ENSOCUG00000006944	1 retrocopy	retro_ocun_1842 ,
Pongo abelii	ENSPPYG00000012825	4 retrocopies	retro_pabe_2438, retro_pabe_2439, retro_pabe_2440, retro_pabe_2599,
Pan troglodytes	ENSPTRG00000012504	2 retrocopies	retro_ptro_1991, retro_ptro_2054,