RetrogeneDB ID: retro_ocun_227

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: X:8819063..8820971(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000004437
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

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

Sequence

>retro_ocun_227
ATGCCGTGGACCCCAGAGCAGAAGAGGGCACAGCCTAATTCAGGAGATCTTGGGGCCCGCCAAAATGGCGGGGTTGGCAG
AGGCCGAGGCAGGGCCAGAGACGGTGGCGGTGGTGGCAGCAGCTGGAGGGGCCCTGCTAGTGATTTGGGGGCCTCAGGCT
CCTACGAACCACCCCTCTGCTTTAAACTGAAAAACAACGTGGTTGGTGCCATAGTTGGTCGCGGTGGATCAAAATTAAAA
GATCTACAACGCGTGACAAACACTAAAATAAAAATTGTAAAGGGGGACTTTGACTCAGAAATAAAAATTTTTGGCAGTAG
TGACATGAAAGAAAAGGCCAAAGCAGATATAGACGCTGTGGTTAGAAGACAAGAAAGGTACATCTCAGAATCCAGTGTTG
GCCCTGCCACATCCCAATCCTCTGTAACAAGCTGCTCAAGTTCAGGCAACACCGCTCGAGAAGCTCGGCCATTGTTAGAT
TGGGACCAAATTCGTATGCAATTTGTAGAGTGGGAGAAACGGAAGTGGGCAGATTTACCACCAATTAAGAAAAACTTTTA
TATAGAATCAGAAGCTACAAGCTCAATGTCTAAAATACAAGTAGATGAATGGCGAAAGGAAAATTTTAACATAACCTGTG
AAGATTTGAGAGATGGTGAAAAGCGCCCAATTCCCAAACCAACTTGTACATTTGAGGATGCGTTCGCGCAGTATCCTGAG
CTTATGAGAAACATAAAGAAGGCAAGTTTTCAAAAGCCAACACCAATTCAGTCACAGGCGTGGCCAGTTATTCTACAAGG
GATAGATCTTATAGGGGTAGCCCAAACTGGAACTGGTAAAACACTCTCCTACTTAATGCCTGGGTTTATTCATCTTGATT
CTCAACCAACATCTAGAGAAGAAAGGAATGGACCTGGCATGCTAGTCCTTACACCCACTAGAGAACTAGCTCTTCAAGTA
GAAAGTGAATGTTCTAAGTACTCATATAAAGGTTTTAAAAGTAGTTGCATATATGGTGGTGGAAATAGAAGGGGACAAAT
AGAAGACATTGCCAAAGGTGTAGATATCATTATTGCAACTCCTGGAAGATTGAATGATCTACAACTGAATAACCATGTCA
ACCTAAGAAGCATAACCTATTTGGTCTTGGATGAGGCAGATAAAATGCTGGATCTGGGCTTTGAACATCAAATAATGAAG
ATTTTACTAGATGTGCGCCCAGACCGGCAGACTGTTATGACAAGTGCAACTTGGCCGGATGCCATCCGCCGACTTGCACA
CTCTTACCTGAAAGACCCTATGATGGTTTACGTTGGTACTCTAGATCTGGTTGCTGTAAGTACAGTGCAGCAGAATGTAA
TTGTGACTACAGAAGAAGAAAAACGTGCTCTTATACAAGAATTCCTAGAGAACATGACACCCAGAGACAAAGTCATCGTG
TTTGTCAGCCGAAAAATCACTGCTGATGACTTAGCAAGTGATTTGGGCATCCAAGGCATACCCATAGAGTCACTGCATGG
TGATAGAGAACAAAGTGATCGAGAGCAAGCTCTAGAAGACTTCAGAACCGGAAAGGTGAAGATACTCATCGCAACTGATT
TAGCGTCTCGGGGTCTTGATGTTAATGACATCACACATGTCTACAACTATGACTTCCCACGAAATATTGAAGAATATGTA
CACAGGATAGGACGTACTGGAAGAGCGGGAAAGGTTGGAACATCGATTACCCTTGTTACTCCAAATGATGCAAAGATCGC
TGATGAACTGATTAAAATTTTGGAACGAGCAAATCAAAATGTCCCTGAAGATCTTGTAAAAATGGCAGAAGGATACAAGT
TCCATAAGAAAAGCAGCACAGAAAAAAACTTCAAAATGTTTCGAGGAAAATATAAGAACTTTTATTAA

Alignment

ORF - retro_ocun_227 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.14 %
• Parental protein coverage: 98.14 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  WVVAARRGSAAPRAAGQRPSEQPGR-RGQGGNRGGRGGSWSEPSGRDIVVGSRRESPLCFDLKSELVGAV
          W.....R........G.R.....GR.RG.....GG.G.SW..P...D.......E.PLCF.LK...VGA.
Retrocopy WTPEQKRAQPNSGDLGARQNGGVGRGRGRARDGGGGGSSWRGPAS-DLGASGSYEPPLCFKLKNNVVGAI

Parental  IGRGGSKIKEIQSRTNTKIQIIKGTPNSEVKIFGSKTMQTKAKAVIDDFVKKQENYNLSRKSDIEAFQPS
          .GRGGSK.K..Q..TNTKI.I.KG...SE.KIFGS..M..KAKA.ID..V..QE.Y...........Q.S
Retrocopy VGRGGSKLKDLQRVTNTKIKIVKGDFDSEIKIFGSSDMKEKAKADIDAVVRRQERYISESSVGPATSQSS

Parental  GREVSTDANGVKD-RPLIDWDQIREEAVRWEKKKWEDLLPIKKNFYVESEKTRSMTQEEIDTWRKENFNV
          ....S...N.....RPL.DWDQIR...V.WEK.KW.DL.PIKKNFY.ESE.T.SM.....D.WRKENFN.
Retrocopy VTSCSSSGNTAREARPLLDWDQIRMQFVEWEKRKWADLPPIKKNFYIESEATSSMSKIQVDEWRKENFNI

Parental  MCDDLKEGEKRPVPNPTCSFEDAFETFPEVMKNIEKAGFKKPTPIQSQTWPIVLQGIDVIGVAQTGTGKT
          .C.DL..GEKRP.P.PTC.FEDAF...PE.M.NI.KA.F.KPTPIQSQ.WP..LQGID.IGVAQTGTGKT
Retrocopy TCEDLRDGEKRPIPKPTCTFEDAFAQYPELMRNIKKASFQKPTPIQSQAWPVILQGIDLIGVAQTGTGKT

Parental  LSYLMPGFIHLDCQPVGREKRNGPGMLVLTPTRELALQVQAECSKYSYKNLRSVCIYGGGDREAQIQDVS
          LSYLMPGFIHLD.QP..RE.RNGPGMLVLTPTRELALQV..ECSKYSYK...S.CIYGGG.R..QI.D..
Retrocopy LSYLMPGFIHLDSQPTSREERNGPGMLVLTPTRELALQVESECSKYSYKGFKSSCIYGGGNRRGQIEDIA

Parental  KGVDIVIATPGRLNDLQMNNFIRLKSVTYLVLDEADKMLDMGFEPQIMKILLDVRPDRQTIMTSATWPYG
          KGVDI.IATPGRLNDLQ.NN...L.S.TYLVLDEADKMLD.GFE.QIMKILLDVRPDRQT.MTSATWP..
Retrocopy KGVDIIIATPGRLNDLQLNNHVNLRSITYLVLDEADKMLDLGFEHQIMKILLDVRPDRQTVMTSATWPDA

Parental  VRRLAQSYLKEPMLVYVGTLDLVAVSTVKQNIIITTEEEKRIHIQKFLENMSPKDKVIVFVSRKIVADHL
          .RRLA.SYLK.PM.VYVGTLDLVAVSTV.QN.I.TTEEEKR..IQ.FLENM.P.DKVIVFVSRKI.AD.L
Retrocopy IRRLAHSYLKDPMMVYVGTLDLVAVSTVQQNVIVTTEEEKRALIQEFLENMTPRDKVIVFVSRKITADDL

Parental  SSDLVLQHLSVESLHGNREQSDREKALKNFKTGKVRILIATDLASRGLDVHDITHVYNYDFPRNIEEYVH
          .SDL..Q....ESLHG.REQSDRE.AL..F.TGKV.ILIATDLASRGLDV.DITHVYNYDFPRNIEEYVH
Retrocopy ASDLGIQGIPIESLHGDREQSDREQALEDFRTGKVKILIATDLASRGLDVNDITHVYNYDFPRNIEEYVH

Parental  RVGRTGRAGNTGVSITLITRNDWRVAAELIHILERANQNIPEELVAMAERYNASKLKREMEKKMGRPQAK
          R.GRTGRAG..G.SITL.T.ND...A.ELI.ILERANQN.PE.LV.MAE.Y...K.K...EK.......K
Retrocopy RIGRTGRAGKVGTSITLVTPNDAKIADELIKILERANQNVPEDLVKMAEGYKFHK-KSSTEKNFKMFRGK

Parental  PKKFY
          .K.FY
Retrocopy YKNFY

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_227 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_227 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_227 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,