RetrogeneDB ID: retro_ocun_688

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 14:23691898..23692399(+)
• Located in intron of: ENSOCUG00000003819

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000017030
• Aliases: None
• Description: None

Sequence

>retro_ocun_688
GAAAAAGAGGTCCAAGTTCAACAAGATTTTGAATTCATAGAAGAATAAAAGAAACCCATAGGCAAAAATGCAACATGCTC
AGAATTACAAAGTGGAGCTTCTACAGTCCACGCAGTCCCAAGGAGAATTTAAACTGAAGGACCCGAAGAAGCTAGAACCA
ATCCTAAATAATATTCTAACATACAACAAACAATTCCCATGTGATGTTCAGCCTGTTCCATTAAGAATTTTTAGCACCTG
GTAAAGAGAATTTGGAATTTGACCAAGATGAAGAGGGGTACTAGAAAGGGATCCCCTTATTCTTTTTCTGCCAGAATTCC
TGGTAATTCATTACTAAGGTTGCCATCTGAATCAGGAACGATGTTACTCACAATCAGAATGGAGAAAATTGCTAAGAAAG
ATGTTACATAGTGCCTTGATCCCTATATTACAGATAGTGCGAAGGCTCTGAATGGCAGAGATTTAACTCCTGGGCAAGAT
ATTCCTGTGCCTTCAGGAAAA

Alignment

ORF - retro_ocun_688 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.67 %
• Parental protein coverage: 55.88 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  QKEAQAQHNNSEFTEEQKKTIGKIATCLELRSAA-LQSTQSQEEFKLEDLKKLEPILKNILTYNKEFPFD
          .KE.Q.Q....EF.EE.KK.IGK.ATC.EL.S.A.LQSTQSQ.EFKL.D.KKLEPIL.NILTYNK.FP.D
Retrocopy EKEVQVQQD-FEFIEE*KKPIGKNATCSELQSGA>LQSTQSQGEFKLKDPKKLEPILNNILTYNKQFPCD

Parental  VQPVPLRRI-LAPGEEENLEFEEDEEEGG-AGAGSPDSFPARVPGTLLPRLPSEPGMTLLTIRIEKIGLK
          VQPVPL.RI.LAPG.E.NLEF..D..E.G....GSP.SF.AR.PG..L.RLPSE.G..LLTIR.EKI..K
Retrocopy VQPVPL-RI>LAPGKE-NLEF--DQDEEG>TRKGSPYSFSARIPGNSLLRLPSESGTMLLTIRMEKIAKK

Parental  DAGQCIDPYITVSVKDLNGIDLTPVQDTPVASRK
          D...C.DPYIT.S.K.LNG.DLTP.QD.PV.S.K
Retrocopy DVT*CLDPYITDSAKALNGRDLTPGQDIPVPSGK

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	31.07 RPM
SRP017611_kidney	0.00 RPM	26.86 RPM
SRP017611_liver	0.00 RPM	13.64 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_688 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_688 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_688 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 35 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007593	2 retrocopies	retro_btau_1163, retro_btau_573,
Choloepus hoffmanni	ENSCHOG00000010095	2 retrocopies	retro_chof_1919, retro_chof_97,
Dasypus novemcinctus	ENSDNOG00000008380	5 retrocopies	retro_dnov_1765, retro_dnov_1909, retro_dnov_1961, retro_dnov_2172, retro_dnov_2280,
Homo sapiens	ENSG00000186063	4 retrocopies	retro_hsap_1901, retro_hsap_2076, retro_hsap_2998, retro_hsap_410,
Gorilla gorilla	ENSGGOG00000015289	3 retrocopies	retro_ggor_1394, retro_ggor_1627, retro_ggor_2077,
Macaca mulatta	ENSMMUG00000015025	1 retrocopy	retro_mmul_1918,
Monodelphis domestica	ENSMODG00000004774	3 retrocopies	retro_mdom_1417, retro_mdom_1418, retro_mdom_1448,
Mus musculus	ENSMUSG00000042901	3 retrocopies	retro_mmus_1939, retro_mmus_3098, retro_mmus_763,
Nomascus leucogenys	ENSNLEG00000013583	1 retrocopy	retro_nleu_748,
Oryctolagus cuniculus	ENSOCUG00000017030	1 retrocopy	retro_ocun_688 ,
Pongo abelii	ENSPPYG00000000196	2 retrocopies	retro_pabe_2015, retro_pabe_2485,
Pan troglodytes	ENSPTRG00000002010	3 retrocopies	retro_ptro_1254, retro_ptro_1528, retro_ptro_2027,
Pteropus vampyrus	ENSPVAG00000010662	1 retrocopy	retro_pvam_940,
Tarsius syrichta	ENSTSYG00000005745	3 retrocopies	retro_tsyr_101, retro_tsyr_1795, retro_tsyr_514,
Tursiops truncatus	ENSTTRG00000016594	1 retrocopy	retro_ttru_1084,