RetrogeneDB ID: retro_ocun_521

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 12:97173484..97173842(+)
• Located in intron of: ENSOCUG00000006035

Retrocopy information

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

Parental gene information

• Parental gene symbol: N6AMT1
• Ensembl ID: ENSOCUG00000001084
• Aliases: None
• Description: N-6 adenine-specific DNA methyltransferase 1 (putative) [Source:HGNC Symbol;Acc:16021]

Sequence

>retro_ocun_521
AAAGTCCACATCAACCAGTGGCTATAGACTTGGTCAAAGGCTTGTCACCAAGCTTGAAGGAAAAGTGGATCTTCCGGTGT
TTCACCCCCCCCCCCCCCATCACCTGCCCCCTGGGTGATTCCGTCACGGAATAGAGGTGGTTTGGGCTGGTGGCAGAAGT
GATCATGAAGTCACAGATTTTCCCCCTAGCGACAGATCTACTTTCCCCAGGAGGAGTCTTCTGTTTAGTTACTGTGAAAC
AAGAGACGGGAAGCAGGTTTTGAAAGCGGTGAGGACAGAAGGTCTGTGAGGGACCACGGCATTGACATTTTCCAGGCACG
CAGGCTGAGCAAGCCTTTCAGTGCTCAAGTTCGCCCAG

Alignment

ORF - retro_ocun_521 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.97 %
• Parental protein coverage: 56.07 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  QVHI-QPVITDLVKGLLPRLK-GKVDLLVFNPPYVVTPPEEVGSHGIQAAWAGGRNGREVMDRVFP-LVT
          .VHI.QPV..DLVKGL.P.LK.GKVDL.VF.PP.....P.....HGI...WAGGR...EV.D..FP.L.T
Retrocopy KVHI<QPVAIDLVKGLSPSLK<GKVDLPVFHPPPPHHLPPG*FRHGIEVVWAGGRSDHEVTD--FP>LAT

Parental  ELLSPRGLFYLVTIKE-NNPEEILETMRIKGLHGTTAL--SRQTGQEILSVLKFSK
          .LLSP.G.F.LVT.K........L...R..GL.GTTAL..SR..G...LSVLKF..
Retrocopy DLLSPGGVFCLVTVKQ<RDGKQVLKAVRTEGL*GTTALTFSRHAG*ASLSVLKFAQ

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	1.27 RPM
SRP017611_kidney	0.00 RPM	1.62 RPM
SRP017611_liver	0.00 RPM	1.39 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_521 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_521 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_521 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005227	1 retrocopy	retro_chof_1139,
Homo sapiens	ENSG00000156239	1 retrocopy	retro_hsap_916,
Gorilla gorilla	ENSGGOG00000022382	1 retrocopy	retro_ggor_739,
Nomascus leucogenys	ENSNLEG00000002845	1 retrocopy	retro_nleu_282,
Oryctolagus cuniculus	ENSOCUG00000001084	1 retrocopy	retro_ocun_521 ,
Ochotona princeps	ENSOPRG00000001551	3 retrocopies	retro_opri_200, retro_opri_867, retro_opri_925,
Pongo abelii	ENSPPYG00000011314	1 retrocopy	retro_pabe_790,
Pan troglodytes	ENSPTRG00000013817	1 retrocopy	retro_ptro_635,
Pteropus vampyrus	ENSPVAG00000012777	2 retrocopies	retro_pvam_1166, retro_pvam_1200,
Sus scrofa	ENSSSCG00000026046	1 retrocopy	retro_sscr_130,
Ictidomys tridecemlineatus	ENSSTOG00000021743	1 retrocopy	retro_itri_497,
Tupaia belangeri	ENSTBEG00000001269	1 retrocopy	retro_tbel_777,