RetrogeneDB ID: retro_ocun_1729

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018827:414382..415047(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000010667
• Aliases: None
• Description: None

Sequence

>retro_ocun_1729
CCTTCCAAAGCTCATGGCTATCCTATAGAGGGAACGCACTGAGTACAATTCAACATTAACCATACCCAAGAAATGGACAA
AGTTGTGTCTGCAGTGAGAGAAGATGAAGGTGTTCCTGTCACTTCTTTTTCTGCTAGGATTGATGAGGAGAAAAATAAGG
ATCTGCCTGAATTGTACTGAGAAGCCTTTGATGCAGGTGGTGGCTCAGCTCTCTCAAAACAGATAACTTTACCAGAGAAC
TGAAATTCCATCACTGCAGAAGCCTTTGCTCTACATACTGAATGGGTTGATCATGCACCCTGGATGAATCTGTTGCCCTG
GCAACCACGATTGAGCAAATCAAAAGGAGCCTCAAGCTAATTCATATTCAATTAGCTCTTGGGGTAGGAAGGACCTTAGC
ATCGTGAGTCAAAGCTGTGGCCCTGTGTGCTGGTTCTGGGAGCAGCATCCTGCAGGATGTGGAAGCAGACCTGTACCTCA
CGGGTGGGATGTCCCATCATGATGGTCTGGATGCTACTTCCCAAGGAATAAATGCCATCCTCTGTGAACACAGTAACACT
GAATGAGGCTTTCTTTCTGACCTTTGTGATATGCTGGGTGCCCACTTGAAGAATTAGATTAATATTATCTTGTCAGAGAC
AGACAGGGATCTTTTTTGTGTGGTA

Alignment

ORF - retro_ocun_1729 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.99 %
• Parental protein coverage: 59.15 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  PSKAHSYPTEGTHRVEFNVNHTQDLDKVVSAVREIEGVSVTSFSARTDGEEQT-RISLNCTEKALMQVVA
          PSKAH.YP.EGTH.V.FN.NHTQ..DKVVSAVRE.EGV.VTSFSAR.D.EE...RI.LNCTEK.LMQVVA
Retrocopy PSKAHGYPIEGTH*VQFNINHTQEMDKVVSAVREDEGVPVTSFSARID-EEKN>RICLNCTEKPLMQVVA

Parental  QLSQNRQLYQRTEILSLEKPLL-LHTG-MGRLCTLDESVSLATMIERIKRHLKLTHIRLALGVERTLESR
          QLSQNR.LYQRTEI.SL.KPLL.LHT..MG..CTLDESV.LAT.IE.IKR.LKL.HI.LALGV.RTL.S.
Retrocopy QLSQNR*LYQRTEIPSLQKPLL<LHTE<MG*SCTLDESVALATTIEQIKRSLKLIHIQLALGVGRTLAS*

Parental  VEVVALCAGSGSSVLRGVEADLYLTGEMSHHDVLDATSRGISVILCEHSNTERGFLSDLRDMLGVHLENR
          V..VALCAGSGSS.L..VEADLYLTG.MSHHD.LDATS.GI..ILCEHSNTE.GFLSDL.DMLG.HL.N.
Retrocopy VKAVALCAGSGSSILQDVEADLYLTGGMSHHDGLDATSQGINAILCEHSNTE*GFLSDLCDMLGAHLKN*

Parental  IHIVLSETDRDPLCVV
          I.I.LSETDRD..CVV
Retrocopy INIILSETDRDLFCVV

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	9.99 RPM
SRP017611_kidney	0.00 RPM	15.71 RPM
SRP017611_liver	0.00 RPM	5.47 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1729 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1729 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1729 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000023186	1 retrocopy	retro_fcat_589,
Macaca mulatta	ENSMMUG00000006639	1 retrocopy	retro_mmul_444,
Nomascus leucogenys	ENSNLEG00000006935	1 retrocopy	retro_nleu_1504,
Oryctolagus cuniculus	ENSOCUG00000010667	16 retrocopies	retro_ocun_1105, retro_ocun_1534, retro_ocun_1539, retro_ocun_1691, retro_ocun_1692, retro_ocun_1710, retro_ocun_1729 , retro_ocun_1749, retro_ocun_1789, retro_ocun_1828, retro_ocun_1837, retro_ocun_1841, retro_ocun_1846, retro_ocun_1847, retro_ocun_1854, retro_ocun_929,
Pongo abelii	ENSPPYG00000013063	1 retrocopy	retro_pabe_244,
Tupaia belangeri	ENSTBEG00000000704	1 retrocopy	retro_tbel_3512,