RetrogeneDB ID: retro_ocun_959

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 17:81964205..81965644(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZFYVE20
• Ensembl ID: ENSOCUG00000006988
• Aliases: None
• Description: zinc finger, FYVE domain containing 20 [Source:HGNC Symbol;Acc:20759]

Sequence

>retro_ocun_959
AGGATGACAGCATCATTAAATGCCGGTGAGACAACCTATAGTCTGGAACATGCAAATGACCTTCCAGTGGAGGTCCAGAA
AGTGTATGAGCTAATAGATGCTTTGAGTAGGAGGATCTTAACCTTAGACTTGAACCAGGACCCTCCACCACATCAAACAC
TTTGTGGCTGTAGGATCAACTACTCAGCTACACTTTTTGTGCAGGAAAAGTTGCCTGGCTTAATGTCACTGCCATCCAAG
AACAATCTGAGGAGCTGCAAAAGAAAAGGAAGCAGGAAATGGAGAGGAAGAGGATCATGGGGAGACTGGTTGCTCTTGAG
ACCCAGAGAAGACTTGAGGAAAGGCAGAGTGGCCTGGCCTCTCCCACGGCCAGCAGGGAGCTGGCATCTCTACACAGGGG
CCCTGCCCCTCCGAGAAAGGCTGAGGGCTGGCTCCCGCTGCTGAGATGTCAGGGACAAAGTGAAGATCCCGACCCCTTCC
TCCCGCAGGTCCACAACACCGGTAGTTCATCAGGCAGACCAGCGATGCCGGCCGCGCTGACGGTGCGCGCTGCAGGAGAA
CCTGAGGCAGCTGCAGAATGCCTGAGACCAGCAGCAGACGGAGAAGGCCATCGAGCTGTCCCGGAGGCAGGCCGAGGAGG
AGGACCTGCAGCGGGGACAGCGGCAGATGCTCCGGGAGCGGCAGTCGCCACGAGAACGGGTGCAGTTCAGGGTCGCATCC
CTGCACGCGCACACCCGGTCCCTGGACTTCAGAGAAATTGGGCCTTTTCAGCTGGAGCCCAGCAGGGAGCCCCGCCCCCA
CCTTGCGTGTGCGCTGGATCTGGGCCCTTCCTCAGGGCGGAGCAGCACAGCTCCCAGGACCTCTTCCCCCAGCCCAGCGC
AGGAGCCCGTCCAAGTGTGGTCTGGGCCCTCAGCCCGCGGCCAGGAACGCCCTCCCCAGGGTCCCACGTCACAGCCAAAC
GAGGTGCCCTCCCTCAACCCCTTTGAAGAGGAAGACCTCGCCGGCCCCAGAGAGGAGGAGCCCAGGCACCTTCCCGCTGC
AGAGGCGTCCATCAGCCCCACAGCCCATGTCCCAGCAGAGTATAATCCTTTTGAGGAAGAGGAGGAAGAGGTAGCTGCAG
GGAATCCGGTCACAAGTGCAGACACCTGCGCCCACCCCTTTGAGGAGGAGGATGAGCCTCCCCACCTGGGGCCCTCCAGC
CCGCCTGTCCCTGGCGGCCCCTTTGAGGAGTCGGCTGGTCCCACCCTCTTCGATGTGGACAGTGACAGCGGAGCCGAGGC
CGAGGAGCCCATAGATGAGGAGCTCCTGCCCCAGCAGACCGACAACATCGAGCCTCCATCTCCGACGCCACGCAGTGCGC
CCGCCTGGACGAGGTGGCCGTCCTGACGGAGAACCTGCGGGAGCTGACACGCACCCTGGTCAGGCAGAAAGGGGGCCCG

Alignment

ORF - retro_ocun_959 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.41 %
• Parental protein coverage: 61.94 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  RMAASLNAGETTYSLEHANDLRVEVQKVYELIDALSKKILTLGLNQDPPPHPNTLRLQRMIRYSATLFVQ
          RM.ASLNAGETTYSLEHANDL.VEVQKVYELIDALS..ILTL.LNQDPPPH.........I.YSATLFVQ
Retrocopy RMTASLNAGETTYSLEHANDLPVEVQKVYELIDALSRRILTLDLNQDPPPHQTLCGCR--INYSATLFVQ

Parental  EKLLGLMSLPTK-EQFEDLKKKRKQEMERKRIMERQVALESQRRLEERQSGLASRTANGELASLPRGPAP
          EKL.GLMSLP.K.EQ.E.L.KKRKQEMERKRIM.R.VALE.QRRLEERQSGLAS.TA..ELASL.RGPAP
Retrocopy EKLPGLMSLPSK<EQSEELQKKRKQEMERKRIMGRLVALETQRRLEERQSGLASPTASRELASLHRGPAP

Parental  LRKAEGWLPLSRCQGQSEDPD-PLLQQIHNITSFIGQARAAGRADEVRTLQENLRQLQDAYEQQQVEKAI
          .RKAEGWLPL.RC..Q....D.P........T....QA....R......LQENLRQLQ.A..QQQ.EKAI
Retrocopy PRKAEGWLPLLRC--QGQSED>PTPSSRRSTTPVVHQADQRCRPR*RCALQENLRQLQNA*DQQQTEKAI

Parental  ELSRRQAEEEDLQREQLQRLREREWERELEQFRVASLHTRTRSLDFREIGPFQLEPSREPRPHLAYALDL
          ELSRRQAEEEDLQR.Q.Q.LRER...RE..QFRVASLH..TRSLDFREIGPFQLEPSREPRPHLA.ALDL
Retrocopy ELSRRQAEEEDLQRGQRQMLRERQSPRERVQFRVASLHAHTRSLDFREIGPFQLEPSREPRPHLACALDL

Parental  GPSSGQSSTAPTTSSPSPAQEPNLVWAGPSACGQECPPQGPVSQPNEVPSLNPFEEEDLASPREEDPTHP
          GPSSG.SSTAP.TSSPSPAQEP..VW.GPSA.GQE.PPQGP.SQPNEVPSLNPFEEEDLA.PREE.P.H.
Retrocopy GPSSGRSSTAPRTSSPSPAQEPVQVWSGPSARGQERPPQGPTSQPNEVPSLNPFEEEDLAGPREEEPRHL

Parental  PTAEVSVSPAAPVPKEYNPFEEEEEEVVAGNPFTSPDSPAPNPFEEEEESPHLRPSSPPVPGNPFEEPAG
          P.AE.S.SP.A.VP.EYNPFEEEEEEV.AGNP.TS.D..A..PFEEE.E.PHL.PSSPPVPG.PFEE.AG
Retrocopy PAAEASISPTAHVPAEYNPFEEEEEEVAAGNPVTSADTCA-HPFEEEDEPPHLGPSSPPVPGGPFEESAG

Parental  PNPFEVDSDSGAEAEEPIEEELLLQQIDNI-KAYIFDAKQCGRLDEVEVLAENLRELKRTLARQKGGP
          P..F.VDSDSGAEAEEPI.EELL.QQ.DNI..A.I.DA.QC.RLDEV.VL.ENLREL.RTL.RQKGGP
Retrocopy PTLFDVDSDSGAEAEEPIDEELLPQQTDNI<RASISDATQCARLDEVAVLTENLRELTRTLVRQKGGP

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	55.91 RPM
SRP017611_kidney	0.00 RPM	21.18 RPM
SRP017611_liver	0.00 RPM	15.34 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_959 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_959 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_959 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Oryctolagus cuniculus	ENSOCUG00000006988	1 retrocopy	retro_ocun_959 ,