RetrogeneDB ID: retro_ocun_1749

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018844:732743..733870(+)
• 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_1749
ATGTTGTCATGTTGCTTACACCTGGTCCCCATGACAGTCTGGTTTATGTAATCTCTGAACTGCAATTCTTCCTGTTCCTT
CATGGGTCTGAAGACTCTCATTTCCTCCTTGAATGACTTTGCATCCCTGTCTTCTGCTGAGAGTTGGGACAATGTTGGAT
TGCTGGTGGAACCAAGCCCACCACAAACTATAAATACACTCTTCCCTGACCAATGACTTGACTGAGCAGGTGATGGAGGA
GGCTCTGCATAAGAAGGCAGATCTCATCTTTTCCTACCTTCCACCTATCTTCCTACACATAAAATGTATTACCTGGATGT
CCTGAAAGGGGTGCCTGGTGTTCTGGGCTTTGGATAACAGAGTTGGCATCTACTCTCTTCACACAGCCTATGATGCTGCA
GCCCAGGGATTGAAAAACTGGTTTTCCAAAGGGCTTGGAGCCTGCACATCCAGGCATATATATCATTCCAAAACTCATGG
CTATCTTTTGAGGGAACCACTGAGTACAATTCAACATTGAGCATACCCAAGATATGGACAAAGCTGTGTCTGTAGTGAGA
GAAGTTGAAGGTGTTCCTGTCACTTCTTTTTCTGCTAGGATTGATGAAGAGAAAAATAAGGATCAGCCTGAATTGTACTG
AGAAGACTTTGATGCAGGTGGTGGCTCAGCTCTCTCAAAACAGATAACTTTACCAGAGAACTGAAATTCTGTCACTGCAG
AAGCCTTTGCTCTACATACTGGAATGGGTCGATCATGCACCCTGGATGATTCTGTTGCCCTGGCAACCATGATTGAGCGA
ATCAAAAGACACCTCAAACTAACTCATATTTACTTAGCTCTTGGGGTAGGAAGGACCTTAGCATCATGAGTCAAAGCTGT
GGCCCTGTGTACTGGTTCTGGGAGCAGCATCCTGCAGGGTGTGGAAGCAGACCTGTACCTCACAGGTGGAATGTCCCATC
ATGATGGCCTGGATGCTACTTCCCAAGGGGTAAATGCCATCCTCTGTGAACACAGTAACACAGAATGAGGCTTTCCTTCT
GACCTTTGTGATATTCTGGGTGCCCACTTGGAGAATTAGATTAATATTATCCTGTCAGAGATGTACAGGGATCTTCTTTG
TGTGGTA

Alignment

ORF - retro_ocun_1749 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.13 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 7
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MLSSCARLAPSTVRLVHSLDCSSSRSFMDLKALISSLNDFASLSFAESWDNVGLLVEPSPPHTVNTLF-L
          MLS.C..L.P.TV....SL.C.SS.SFM.LK.LISSLNDFASLS.AESWDNVGLLVEPSPP.T.NTLF.L
Retrocopy MLSCCLHLVPMTVWFM*SLNCNSSCSFMGLKTLISSLNDFASLSSAESWDNVGLLVEPSPPQTINTLF>L

Parental  TNDLTEPVMEEALQKKADLILSYHPPIFLPMKRITWKSWKERLVIRALENRVAIYSPHTAYDAAPQGVNN
          TNDLTE.VMEEAL.KKADLI.SY.PPIFL..K.ITW.S.K..LV..AL.NRV.IYS.HTAYDAA.QG..N
Retrocopy TNDLTEQVMEEALHKKADLIFSYLPPIFLHIKCITWMS*KGCLVFWALDNRVGIYSLHTAYDAAAQGLKN

Parental  WLSKGLGACTSRPICPSKAHSY-PTEGT-HRVEFNVNHTQDLDKVVSAVREIEGVSVTSFSARTDGEEQT
          W.SKGLGACTSR.I..SK.H.Y...EGT.H.V.FN..HTQD.DK.VS.VRE.EGV.VTSFSAR.D.EE..
Retrocopy WFSKGLGACTSRHIYHSKTHGY<SFEGT<H*VQFNIEHTQDMDKAVSVVREVEGVPVTSFSARID-EEKN

Parental  R-ISLNCTEKALMQVVAQLSQNRQLYQRTEILSLEKPLL-LHTGMGRLCTLDESVSLATMIERIKRHLKL
          ..ISLNCTEK.LMQVVAQLSQNR.LYQRTEILSL.KPLL.LHTGMGR.CTLD.SV.LATMIERIKRHLKL
Retrocopy K>ISLNCTEKTLMQVVAQLSQNR*LYQRTEILSLQKPLL<LHTGMGRSCTLDDSVALATMIERIKRHLKL

Parental  THIRLALGVERTLESRVEVVALCAGSGSSVLRGVEADLYLTGEMSHHDVLDATSRGISVILCEHSNTERG
          THI.LALGV.RTL.S.V..VALC.GSGSS.L.GVEADLYLTG.MSHHD.LDATS.G...ILCEHSNTE.G
Retrocopy THIYLALGVGRTLAS*VKAVALCTGSGSSILQGVEADLYLTGGMSHHDGLDATSQGVNAILCEHSNTE*G

Parental  FLSDLRDMLGVHLENRIHIVLSETDRDPLCVV
          F.SDL.D.LG.HLEN.I.I.LSE..RD.LCVV
Retrocopy FPSDLCDILGAHLEN*INIILSEMYRDLLCVV

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_1749 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1749 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1749 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,