RetrogeneDB ID: retro_ocun_974

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 18:42456502..42457812(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: WBP11
• Ensembl ID: ENSOCUG00000017177
• Aliases: None
• Description: WW domain binding protein 11 [Source:HGNC Symbol;Acc:16461]

Sequence

>retro_ocun_974
ATGGGGCAAAGAGCTGCATCATCCACCAAGAGTGGAAAATTTATGAACCCTGCAGACCAAACCGAAAGGAAGCCCAGAAG
AGAGATTAAAGAACAATAAATAATGCATGATGGTACAAGCTGCAGTTTTGAAGATGAAGGATCCCAAACAAATTATCTGA
GACATGGAAAACTTGGATGAAATGGAGTTTAACCCAGTGCAACAGCCACAGTGAAATGAGAAAGTACTGAAAGACAAGCA
TAAAAATCTATATTAAACTTTTGAACCTATTCTCCAACTTTATGAAAAAGAGAATCCAGATATTTACAAGGAATTGAGAA
AGCTAGAAGTAGCATATGAACAGAAGAGGGCACAACTTAGCCAGTATTTTTATGCTGTCAAGAAGGCTCAGCATGTTGAA
GTGGAGAGTATTGCTTTGCTAGATATGCCGCATGCTCCTTCCAACATCTTGATCCAGGATAGTCCACTTCCTGGTGCCCA
GCCCTCCTCCAACCTTAAGAAAACTTCAGCTGATGGACTTCCAACTCGGGCAGTTTCTATACTTCCTGTTCTTGGACGTG
TTGTTCCATGTTTGCCCCCTGCTAGAAAACCTCCTGGCTCAACCCCTGGCCCACCTCCTCCACAGGTCCTACAGATGTAT
GGCCTTAAAGTGGGCTTTACCCTGGACCTTCCCTCTCGTAGGCAAGACGGAGACATGCTATGTAGTCCTGAACTTGCTCA
GCAGGGTCATGATGATGACGTCTCCAGCACAAGTGAAGACCGTGGTTATCCTGAAGATATGGGTCAGATAAGCATGATGA
CAGCACTGATGACAGTGACACAGACAGATCAGACGGAGAGAGTAGGGGGATGAATCTACATCATGATGATAATGAACGAG
ACGACATTGAAGAAAAAAATCAGGTCTGAGTGTGCAATTTTCTAATATTCTTGGAAAATCAAGGAGGAAAAAGAACATGA
AGGAGCTGGCTCCTCTTCAAGCCATGATGCTCCGAATGGCAGGTCAAGAAATCCCTGCAGAGGGACGAGAAGTAGAGAAA
TTTTCAGAGGACGATGATGAAGATTATTCTGCAGCAGAAGGGCAATCACAAAAACGGCCTAAAGAAGCTCCCATTCTGAT
GGCACGTCTGCATCTAAATCAGCAGCAGGCTCCCCCACAGTCTGTTCCTCCGTCTCAGGTACAAGCACCTCCCATGCCAG
GACCCCCTCCTCTTGGACCACCACCTGCTCCACCTATACGGCCTCCTGGGCCACCTGCAGTTCTTCCTCCTTGACCACCT
CCAGGGGCTCCTTCATTCCTGACCGCTCCA

Alignment

ORF - retro_ocun_974 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.73 %
• Parental protein coverage: 69.38 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MGRRSTSSTKSGKFMNPTDQARKEARKR-ELKKNKKQRMMVRAAVLKMKDPKQIIRDMEKLDEMEFNPVQ
          MG.R..SSTKSGKFMNP.DQ...E...R.E..KN.K..MMV.AAVLKMKDPKQII.DME.LDEMEFNPVQ
Retrocopy MGQRAASSTKSGKFMNPADQT--ERKPR>ERLKNNK*CMMVQAAVLKMKDPKQII*DMENLDEMEFNPVQ

Parental  QPQLNEKVLKDKRKKLRETFERILRLYEKENPDIYKELRKLEVEYEQKRAQLSQYFDAVKNAQHVEVESI
          QPQ.NEKVLKDK.K.L..TFE.IL.LYEKENPDIYKELRKLEV.YEQKRAQLSQYF.AVK.AQHVEVESI
Retrocopy QPQ*NEKVLKDKHKNLY*TFEPILQLYEKENPDIYKELRKLEVAYEQKRAQLSQYFYAVKKAQHVEVESI

Parental  PLPDMPHAPSNILIQDIPLPGAQPPSILKKTSAYGPPTRAVSILPLLGHGVPRLPPGRKPPGPPPGPPPP
          .L.DMPHAPSNILIQD.PLPGAQP.S.LKKTSA.G.PTRAVSILP.LG..VP.LPP.RKPPG..PGPPPP
Retrocopy ALLDMPHAPSNILIQDSPLPGAQPSSNLKKTSADGLPTRAVSILPVLGRVVPCLPPARKPPGSTPGPPPP

Parental  QVLQMYGRKVGFALDLPPRRRDEDMLYSPELAQRGHDDDVSSTSEDDGYPEDMDQ-DKHDDSTDDSDTDR
          QVLQMYG.KVGF.LDLP.RR.D.DML.SPELAQ.GHDDDVSSTSED.GYPEDM.Q.DKHDDSTDDSDTDR
Retrocopy QVLQMYGLKVGFTLDLPSRRQDGDMLCSPELAQQGHDDDVSSTSEDRGYPEDMGQ<DKHDDSTDDSDTDR

Parental  SDGESEGDEFVHRDDNERDNNEE-KKSGLSVRFADMPGKSRKKKKNMKELTPLQAMMLRMAGQEIPEEGR
          SDGES.G....H.DDNERD..EE.KKSGLSV.F....GKSR..KKNMKEL.PLQAMMLRMAGQEIP.EGR
Retrocopy SDGESRGMN-LHHDDNERDDIEE<KKSGLSVQFSNILGKSR-RKKNMKELAPLQAMMLRMAGQEIPAEGR

Parental  EVEEFSEDDDEDDSDDSAAEKQSQKQHKE-DSHSDGTSAS-SQQQAPPQSVPPSQIQAPPMPGPPPLGPP
          EVE.FSEDDDED.S...AAE.QSQK..KE..SHSDGTSAS..QQQAPPQSVPPSQ.QAPPMPGPPPLGPP
Retrocopy EVEKFSEDDDEDYS---AAEGQSQKRPKE<SSHSDGTSAS>NQQQAPPQSVPPSQVQAPPMPGPPPLGPP

Parental  PAPPLRPPGPPTGLPPGPPPGAPPFLRPP
          PAPP.RPPGPP..LPP.PPPGAP.FL..P
Retrocopy PAPPIRPPGPPAVLPP*PPPGAPSFLTAP

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	79.91 RPM
SRP017611_kidney	0.00 RPM	76.83 RPM
SRP017611_liver	0.00 RPM	28.36 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_974 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_974 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_974 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 22 parental genes, and 34 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014759	1 retrocopy	retro_btau_20,
Canis familiaris	ENSCAFG00000012926	2 retrocopies	retro_cfam_1369, retro_cfam_1911,
Callithrix jacchus	ENSCJAG00000021611	1 retrocopy	retro_cjac_1737,
Homo sapiens	ENSG00000084463	2 retrocopies	retro_hsap_1878, retro_hsap_4719,
Gorilla gorilla	ENSGGOG00000004448	3 retrocopies	retro_ggor_1375, retro_ggor_1711, retro_ggor_2932,
Macropus eugenii	ENSMEUG00000013971	1 retrocopy	retro_meug_1952,
Myotis lucifugus	ENSMLUG00000015216	1 retrocopy	retro_mluc_1074,
Macaca mulatta	ENSMMUG00000019299	1 retrocopy	retro_mmul_1329,
Monodelphis domestica	ENSMODG00000017949	1 retrocopy	retro_mdom_143,
Mustela putorius furo	ENSMPUG00000011619	1 retrocopy	retro_mputfur_280,
Mus musculus	ENSMUSG00000030216	1 retrocopy	retro_mmus_2740,
Nomascus leucogenys	ENSNLEG00000003926	1 retrocopy	retro_nleu_2651,
Oryctolagus cuniculus	ENSOCUG00000017177	1 retrocopy	retro_ocun_974 ,
Otolemur garnettii	ENSOGAG00000010518	1 retrocopy	retro_ogar_207,
Ochotona princeps	ENSOPRG00000015008	3 retrocopies	retro_opri_107, retro_opri_1159, retro_opri_678,
Pongo abelii	ENSPPYG00000004323	3 retrocopies	retro_pabe_1558, retro_pabe_2099, retro_pabe_3663,
Pan troglodytes	ENSPTRG00000004724	3 retrocopies	retro_ptro_1260, retro_ptro_1637, retro_ptro_3136,
Rattus norvegicus	ENSRNOG00000005505	3 retrocopies	retro_rnor_1287, retro_rnor_2726, retro_rnor_741,
Rattus norvegicus	ENSRNOG00000049593	1 retrocopy	retro_rnor_740,
Sorex araneus	ENSSARG00000007085	1 retrocopy	retro_sara_753,
Sarcophilus harrisii	ENSSHAG00000016649	1 retrocopy	retro_shar_81,
Tupaia belangeri	ENSTBEG00000003394	1 retrocopy	retro_tbel_2213,