RetrogeneDB ID: retro_ocun_945

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 17:46091538..46092618(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000000552
• Aliases: None
• Description: None

Sequence

>retro_ocun_945
TCTAAACATAGTCTGAGTGCATGGCTACTGAAAGTAACAGAAGATCCTATGGTGAGCATGCCAGGAGAGCAAGGCAAATG
ACTGGTAGGCTTGGAAGCACAGTATTTGTAGCAAATCTGGATTATAAACTTGACAGGAAGAAACAGAAAGAAATATTTAG
TATGGTTGATATGATGGTCCAAGCAGACATTCTGAAGGAAAAAGCTGCTAAAAGTCAAGCAGGCACTGTGACTTTTGAAT
GGTCCATTGAAGCCGTACAAGCTCTATCTATGTTTAATGCCAATTGCTGTCTGATAGACCAATGCATTCCAAAATTGATG
ACAGAGCTTTACCAAAGGGAGTTTTCTTTTTTCTCTCCTGAGCATCCATGACAACTGTTCCTTAAACTTAGTAGCATCAA
CATAGGGTTAGGACTAGGAGAGCAGTCTACTGCTACCAAACACCTGAATGAAGGCATCGAGATGGGAAACATAGGGCCTG
CAGGAATGGAAATGGAAGGCATAGGATTTGGGATAAATAAAATGGGAGCCATGGAGGGCCCCTTTGGTGGTAGTATGGAA
AACATGGGGCAATTTGGATCTGGGATAAACGTGGACAGGATAAATGAAATCCTAAGTAATGCACTAAAAAGAGGAGAGAG
CACTGCAAAGCAAGGAGGAAGTGGAGGCAAAAGCAGCATTTCAGGCATTGATCAAATCAGGGGTGCTGACATGGAGTGCA
CGGGCCCAGGCCTGAGCCATGGCATGAAAAATTGTGGGCTCTGAGATCCAGTGAATGGGCCTGGCCATGAACTGATTTGG
CTCAGTGGAGCGCATGGACTCTGGCATTGAGCACATGGATCAGACCAAGGAACACATTGGCTCTGGTATGGAGTGTATGG
GTGCTGGCATGGGCTTCTTCCTGGAGTACGTGGACCCTACCATTGATTGCACAGGCCTGAGCTTGGAGCACATGGTGTTG
GCAGGAACAGGGGCCAGACTGGAGCAGATGGGCCCTGTGATGCGTCGCATGGCTGCTGGCCTGGAGTGCATGGACACCAA
CAGTGTGCAGTACATGGGGCCTGCTATGGGCCCAGCCTTG

Alignment

ORF - retro_ocun_945 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.96 %
• Parental protein coverage: 52.86 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NKHSLSGRPLKVKEDPD-GEHARRAMQKAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKD
          .KHSLS...LKV.EDP..GEHARRA.Q..GRLGSTVFVANLDYK...KK.KE.FSM....V.ADIL..K.
Retrocopy SKHSLSAWLLKVTEDPM<GEHARRARQMTGRLGSTVFVANLDYKLDRKKQKEIFSMVDMMVQADILKEKA

Parental  GKSRGIGTVTFEQSIEAVQAISMFNGQL-LFDRPMHVKMDERALPKGDFFPPERPQQLPHGLGGIGMGLG
          .KS...GTVTFE.SIEAVQA.SMFN....L.D......M.E.......FF.PE.P.QL...L..I..GLG
Retrocopy AKSQA-GTVTFEWSIEAVQALSMFNANCCLIDQCIPKLMTELYQREFSFFSPEHP*QLFLKLSSINIGLG

Parental  PGGQPIDANHLNKGIGMGNIGPAGMGMEGIGFGINKMGAMEGPFGGGMENMGRFGSGMNMGRINEILSNA
          .G.Q.....HLN.GI.MGNIGPAGM.MEGIGFGINKMGAMEGPFGG.MENMG.FGSG.N..RINEILSNA
Retrocopy LGEQSTATKHLNEGIEMGNIGPAGMEMEGIGFGINKMGAMEGPFGGSMENMGQFGSGINVDRINEILSNA

Parental  LKRGEIIAKQGGGGGGGSVPGIERMGPGIDRIGGAGMERMGAGLGHGMDR-VGSEIERMGLVMDRMGSVE
          LKRGE..AKQ...GG.G....I.....GID.I.GA.ME..G.GL.HGM...VGSEI..MGL.M...GSVE
Retrocopy LKRGESTAKQ---GGSGGKSSIS----GIDQIRGADMECTGPGLSHGMKN>VGSEIQ*MGLAMN*FGSVE

Parental  RMGSGIERMGPLGLDHMASSIERMGQTMERIGSGVERMGAGMGFGLERMAAPIDRVGQTIERMGSGVERM
          RM.SGIE.M......H..S..E.MG..M......V.......G..LE.M.......G...E.MG....RM
Retrocopy RMDSGIEHMDQT-KEHIGSGMECMGAGMGFFLEYVDPTIDCTGLSLEHMV--LAGTGARLEQMGPVMRRM

Parental  GPAIERMGLSMERMVPAGMGASL
          ....E.M...........MG..L
Retrocopy AAGLECMDTNSVQYMGPAMGPAL

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	59.44 RPM
SRP017611_kidney	0.00 RPM	34.36 RPM
SRP017611_liver	0.00 RPM	22.04 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_945 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_945 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_945 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Oryctolagus cuniculus	ENSOCUG00000000552	1 retrocopy	retro_ocun_945 ,