RetrogeneDB ID: retro_ocun_1061

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 2:104921517..104922816(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000006338
• Aliases: None
• Description: None

Sequence

>retro_ocun_1061
ACACAGGAGAAAGGGAAATTAAATGTAATGTGTGATGGCTTGGAAGAAGATGAAAAACATCCAGTACTGAATCCTACCTG
TTCTTTGGAATATGCCTTTGAAACTTTTTCTGAAGTGATGAAAAATATTGAAAAGGCAGAATTTATAAAGCCAACGTGAA
TTCCATCACAAGCATGGCCAGTAGTTCTACAAGGGAGAGATGTCATAGGAGTTGCCCAAACAGGAACCAGGAAGACATTG
TCATATTTAATGCTTCGATTTATGCATCTAGATTGCCAACCAGTTGGCAGGGAGGAAAGGAACAGCCCCTGCATGTTAGT
CCTTACACCCACTTGGGAGCTGGCTCTGCAGGTGCAGGCCAAATGTTCTAAGTATTCATACAGAAATCTTAGAAGTGTTT
CTGTATATGGAGGTAGAGACAGATGCACAAATACAGTCTGTTTCAAAAGGTGTTGACATCATAATCACAATTCCTGGAAA
GCTAAATAATCTACAAACAACTAACTTCATCAGACTTAAGACCATAACCTACCTGGTTTTAGCTGAAGCGAATAAAATGT
TGGATATGGAATCTGAACCCCAGATAATGAATTTTTATTATACATGCAACCAGATAGGCAAAACATTGTGACAAGTGCAA
CATGGACCTATGGTGGCCATCGACTTGCACAGTCATACTTGAAAGAAACAATGCTTGTGTATGTTGGAAACTTGGACCTA
GTTTCTTTAAGAACAGTAAAGCAAAATATAATCATTACCACAGAAGAAGAGAAATGGATGCATATACAAAAATTCCTAGA
AAATATGTCACTGAAGGACAAAGTCACAGTATTCATCAGTAGAAAAGCTGTTGTTGATCATTTGTCAAGTGACCTAGACC
TCCGACACATGTCATTAGAGTCATTGCATGGCAACAGAGAATAAAATGATAGGGAGAAAACATTAAAGGACTTTAAAACA
GGTAAAGTGAGGATATTAATTGCTAATGATTTAGCATCAGGTAGATTGAATGTCCATGATATTACACATGTCTATAGTTA
CAACTTTCCAAGGAACATTGAAGAATATGTACACAGAGTAGGACACACTGGAAGAGCGAGGAGAACAGGGTTTCAATCAA
CTCCTCCACTAGAAATGATTTGAGGATTGCTGCTGAACTGATTCATTTCCTGGAAAGAGCAAATCAGAATATCCTAGAAG
TGCTTGTTTCAATGGCTGAGAGATGTAATGCAAGCACGCTTAAAAGAGAAATGGAAAAAAAAAATGGGACAACCTCAAGG
AAAGCCCAAAAAGTTTTAT

Alignment

ORF - retro_ocun_1061 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.8 %
• Parental protein coverage: 67.29 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  TWRKENFNVMCDDLKEGEKRPVPNPTCSFEDAFETFPEVMKNIEKAGFKKPTPIQSQTWPIVLQGIDVIG
          T..K...NVMCD.L.E.EK.PV.NPTCS.E.AFETF.EVMKNIEKA.F.KPT.I.SQ.WP.VLQG.DVIG
Retrocopy TQEKGKLNVMCDGLEEDEKHPVLNPTCSLEYAFETFSEVMKNIEKAEFIKPT*IPSQAWPVVLQGRDVIG

Parental  VAQTGTGKTLSYLMPGFIHLDCQPVGREKRNGPGMLVLTPTRELALQVQAECSKYSYKNLRSVCIYGGG-
          VAQTGT.KTLSYLM..F.HLDCQPVGRE.RN.P.MLVLTPT.ELALQVQA.CSKYSY.NLRSV..Y.GG.
Retrocopy VAQTGTRKTLSYLMLRFMHLDCQPVGREERNSPCMLVLTPTWELALQVQAKCSKYSYRNLRSVSVY-GG>

Parental  DREAQIQDVSKGVDIVIATPGRLNDLQMNNFIRLKSVTYLVLDEADKMLDMGFEPQIM-KILLDVRPDRQ
          ...AQIQ.VSKGVDI.I..PG.LN.LQ..NFIRLK..TYLVL.EA.KMLDM..EPQIM...LL...PDRQ
Retrocopy ETDAQIQSVSKGVDIIITIPGKLNNLQTTNFIRLKTITYLVLAEANKMLDMESEPQIM<EFLLYMQPDRQ

Parental  TIMTSATWPYGVRRLAQSYLKEPMLVYVGTLDLVAVSTVKQNIIITTEEEKRIHIQKFLENMSPKDKVIV
          .I.TSATW.YG..RLAQSYLKE.MLVYVG.LDLV...TVKQNIIITTEEEK..HIQKFLENMS.KDKV.V
Retrocopy NIVTSATWTYGGHRLAQSYLKETMLVYVGNLDLVSLRTVKQNIIITTEEEKWMHIQKFLENMSLKDKVTV

Parental  FVSRKIVADHLSSDLVLQHLSVESLHGNREQSDREKALKNFKTGKVRILIATDLASRGLDVHDITHVYNY
          F.SRK.V.DHLSSDL.L.H.S.ESLHGNRE..DREK.LK.FKTGKVRILIA.DLAS..L.VHDITHVY.Y
Retrocopy FISRKAVVDHLSSDLDLRHMSLESLHGNRE*NDREKTLKDFKTGKVRILIANDLASGRLNVHDITHVYSY

Parental  DFPRNIEEYVHRVGRTGRAGNTG-VSITLITRNDWRVAAELIHILERANQNIPEELVAMAERYNASKLKR
          .FPRNIEEYVHRVG.TGRA..TG.VSI...TRND.R.AAELIH.LERANQNI.E.LV.MAER.NAS.LKR
Retrocopy NFPRNIEEYVHRVGHTGRARRTG<VSINSSTRNDLRIAAELIHFLERANQNILEVLVSMAERCNASTLKR

Parental  EME-KKMGRPQAKPKKFY
          EME.KKMG.PQ.KPKKFY
Retrocopy EME>KKMGQPQGKPKKFY

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	0.00 RPM
SRP017611_kidney	0.00 RPM	0.51 RPM
SRP017611_liver	0.00 RPM	0.08 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1061 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1061 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1061 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007851	1 retrocopy	retro_amel_31,
Callithrix jacchus	ENSCJAG00000009966	2 retrocopies	retro_cjac_3639, retro_cjac_3640,
Equus caballus	ENSECAG00000017971	1 retrocopy	retro_ecab_7,
Felis catus	ENSFCAG00000031631	1 retrocopy	retro_fcat_583,
Homo sapiens	ENSG00000080007	1 retrocopy	retro_hsap_76,
Gorilla gorilla	ENSGGOG00000016092	1 retrocopy	retro_ggor_2889,
Microcebus murinus	ENSMICG00000017145	1 retrocopy	retro_mmur_1603,
Monodelphis domestica	ENSMODG00000018546	1 retrocopy	retro_mdom_14,
Mustela putorius furo	ENSMPUG00000004342	1 retrocopy	retro_mputfur_47,
Nomascus leucogenys	ENSNLEG00000001209	1 retrocopy	retro_nleu_1094,
Oryctolagus cuniculus	ENSOCUG00000006338	2 retrocopies	retro_ocun_1061 , retro_ocun_227,
Otolemur garnettii	ENSOGAG00000013660	1 retrocopy	retro_ogar_227,
Procavia capensis	ENSPCAG00000005962	1 retrocopy	retro_pcap_151,
Pongo abelii	ENSPPYG00000016774	1 retrocopy	retro_pabe_39,
Pan troglodytes	ENSPTRG00000018344	1 retrocopy	retro_ptro_35,