RetrogeneDB ID: retro_ocun_1846

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL019321:47801..48752(-)
• 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_1846
CCACCACAAACTATAAATACACTCTTCCTGACCAATGACTTGACTGAGCAGGTGATGGGGGAGGCTCTGCATAAGAGAGC
AGATCTCATGTTTTCCTACCTTCCACCTATCTTCCTACACATAAATTGTATTACCTGGACATCCTGAAAGGGGCGCCTGG
TGTTCCAGGCTTTGGAGAACAGAGTTGGCATCTACTCTCTTCACACAGCCTATGATGCTGCACCCCAGGGATTGAAAAAG
TGGTTTTCCAAAGGGCTTGGAGCCTGCACATCCAGGCATATATAGCCTTCCAAAGCTCATGGCTATCCTATAGAGGAACC
ACTGAGTACAATTCAACATTAACCATACCCAAGATATGGACAAAGTTGTGTCTGCAGTGAGAGAAGTTGAAGGTGTTCCT
GTCACTTCTTTTTCTGCTAGGATTGATGAGGAGAAAAATAAGGATCCTCCTGAATTGTACTGAGAAGACTTTGATGCAGG
TGGTGGCTCAGCTCTCTCAAAACAGATAACTTTACCAGAGAACTGAAATTCTGTCACTCCAGAGAAGCCTTTGATCTACA
TACTAGAATGGGTCGATCATGCACCCTGGATGAATCTGTTGCCTTGGCAACCATGATTGAGCAAATCAAAAGACACCTCA
AACTAACTCATATTCAATTAGCTCTTGGGGTAGGAGGGACCTTAGCGTCATGAGTCAAAGCTGTGGCCCTGTGTGCTGGT
TCTGGGAGCAGCGTCCTGCAGGGTGTGGAAGCAGACCTGTACCTCATGGGTGGGATGTCCCATCATGATGATCTGGATGC
TACTTCCCAAGGAATAAATGCCATCCTCTGTGAACACAGTAACACTGAATGAGGCTTTCTTTCTGACCTTTGTGATATTC
TGGGTGCCCGCTTGGAGAATTAGATTAATATTATCTTGTCAGAGACAGACAGGGATCTTCTTTGTGTGGTA

Alignment

ORF - retro_ocun_1846 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.4 %
• Parental protein coverage: 84.35 %
• Number of stop codons detected: 8
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  PPHTVNTLFLTNDLTEPVMEEALQKKADLILSYHPPIFLPMKRITWKSWKERLVIRALENRVAIYSPHTA
          PP.T.NTLFLTNDLTE.VM.EAL.K.ADL..SY.PPIFL....ITW.S.K.RLV..ALENRV.IYS.HTA
Retrocopy PPQTINTLFLTNDLTEQVMGEALHKRADLMFSYLPPIFLHINCITWTS*KGRLVFQALENRVGIYSLHTA

Parental  YDAAPQGVNNWLSKGLGACTSRPICPSKAHSYPTE-GT-HRVEFNVNHTQDLDKVVSAVREIEGVSVTSF
          YDAAPQG...W.SKGLGACTSR.I.PSKAH.YP.E.GT.H.V.FN.NHTQD.DKVVSAVRE.EGV.VTSF
Retrocopy YDAAPQGLKKWFSKGLGACTSRHI*PSKAHGYPIE<GT<H*VQFNINHTQDMDKVVSAVREVEGVPVTSF

Parental  SARTDGEEQT-RISLNCTEKALMQVVAQLSQNRQLYQRTEILSLEKPLL-LHTGMGRLCTLDESVSLATM
          SAR.D.EE...RI.LNCTEK.LMQVVAQLSQNR.LYQRTEILSL...L..LHT.MGR.CTLDESV.LATM
Retrocopy SARID-EEKN>RILLNCTEKTLMQVVAQLSQNR*LYQRTEILSLQRSL*>LHTRMGRSCTLDESVALATM

Parental  IERIKRHLKLTHIRLALGVERTLESRVEVVALCAGSGSSVLRGVEADLYLTGEMSHHDVLDATSRGISVI
          IE.IKRHLKLTHI.LALGV..TL.S.V..VALCAGSGSSVL.GVEADLYL.G.MSHHD.LDATS.GI..I
Retrocopy IEQIKRHLKLTHIQLALGVGGTLAS*VKAVALCAGSGSSVLQGVEADLYLMGGMSHHDDLDATSQGINAI

Parental  LCEHSNTERGFLSDLRDMLGVHLENRIHIVLSETDRDPLCVV
          LCEHSNTE.GFLSDL.D.LG..LEN.I.I.LSETDRD.LCVV
Retrocopy LCEHSNTE*GFLSDLCDILGARLEN*INIILSETDRDLLCVV

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_1846 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1846 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1846 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,