RetrogeneDB ID: retro_ocun_676

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 13:139438904..139439931(-)
• Located in intron of: ENSOCUG00000002458

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCNE1
• Ensembl ID: ENSOCUG00000009143
• Aliases: None
• Description: cyclin E1 [Source:HGNC Symbol;Acc:1589]

Sequence

>retro_ocun_676
AAACAGAGGTATGCAAAGGAACAGAGCATCATGAATGAAGGCAGCACCAACTTATCGTCGCTGCAGATGAAGAAGGCAAA
TGTGGCCTTTTGTTTGCTTTTGGCAGGATCAAGATGAAGAAACTGCCAAGTTTGACAAGACTGTGAGAGGCCAGAGTAGC
AGTCAGCCTTGGGACAATGATGCAGTACGTGTAAACCCCTGCTCCTTGATCCCCACACCCAACAAGGAAGAGGATGAACT
AGTACATGCATATCCCACATTTGATCCTCAGGGTGTCATACCATCCAGAGCCTCACTGCTGCCTGTACTGAACTGGGCAG
AGAGAGGAAGTCTGGAAAGTCATGTTACACGAGGAAAAGAAGTACTTAGGGGATAAGCACTTTTGCAGCAACATCCTCTT
CTGCAGCCTAAAACGCGAGCGATTCTTCTGGACTGGTTAACGGAGGTACGTGATGTCTATAAACTCCACAGGAAGACATT
TTACTTGACACAGGGTTTCTTTGATCAGTGTGTGGCAACACAAGAAAATATTGTAAAAACACTTGTTCAGCTTACTGGAA
TTTCATCTTTATTCACTGCTGCTAAACATGAGGAAATCTATTCTCCCAAGTTGCATCAGTTTTCTTGTGTTACAGACAGG
GCTTGTCCAGGTGATGGAATAGTTACCATGGAATTAGCAACAATGAAGGCCTGTAAGTGGCAATTAAGTCTCCTGAGCCC
CTGTGTCTTAGCTGAATGTATACAGACAGGATGCCTATCTAAATGATGAGTATGAAGTGCTACTGCCACAGTATCCCCAG
GAAATCTTTATAGCAACTGCAGAACTTTTGATCTCTGTCCCAGACATTGACTACTGAGGATTTTTATATAATATTCTTGC
TGTTTCTGCCTTATGTCATTTCTTTTCATCTGAATTGATACAAAAAGTTTCAGAGTATCAGTGGTGTGACACAGAGAAGT
GCATTAAGTGGATAGTTCCACTTGCCATGGTCATCGAAGAGTTAGGAAGTTCCAACTTAAGCACTTC

Alignment

ORF - retro_ocun_676 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.54 %
• Parental protein coverage: 83.9 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KERDAKERGTMKDDGGSDFSVRSRKRKANVAVFL-QDPDEQIAKIDRTVRGQCGSQPWDSDAVRADPCSS
          K.R.AKE...M........S....K........L.QD.DE..AK.D.TVRGQ..SQPWD.DAVR..PCS.
Retrocopy KQRYAKEQSIMNEGSTNLSSLQMKKANVAFCLLL>QDQDEETAKFDKTVRGQSSSQPWDNDAVRVNPCSL

Parental  IPTPDKEEDEPVYANSTFDPHSLAPARASPLPVLNWANREEVWKIMLNKEKKYLRDQHFLQRHPLLQPKM
          IPTP.KEEDE.V.A..TFDP....P.RAS.LPVLNWA.R...........K..LR....LQ.HPLLQPK.
Retrocopy IPTPNKEEDELVHAYPTFDPQGVIPSRASLLPVLNWAERGSL-ESHVTRGKEVLRG*ALLQQHPLLQPKT

Parental  RAILLDWLMEVCEVYKLHRETFYLAQDFFDRYMATQENIVKTLLQLIGISSLFIAAKLEEIYPPKLHQFA
          RAILLDWL.EV..VYKLHR.TFYL.Q.FFD...ATQENIVKTL.QL.GISSLF.AAK.EEIY.PKLHQF.
Retrocopy RAILLDWLTEVRDVYKLHRKTFYLTQGFFDQCVATQENIVKTLVQLTGISSLFTAAKHEEIYSPKLHQFS

Parental  YVTDGACSGDEILTMELVIMKALKWHLSPLT-IVSWLNVYMQVAYLNDVCEVLLPQYPQQIFTQIAELLD
          .VTD.AC.GD.I.TMEL..MKA.KW.LS.L...VS.LNVY.Q.AYLND..EVLLPQYPQ.IF...AELL.
Retrocopy CVTDRACPGDGIVTMELATMKACKWQLSLLS>PVS*LNVYRQDAYLNDEYEVLLPQYPQEIFIATAELL-

Parental  LCVLDVGCLEFSYGVLAASALYHFSSSELMQKVSGYQWCDIEKCVKWMVPFAMVIRETGSS-KLKHF
          ..V.D.....F.Y..LA.SAL.HF.SSEL.QKVS.YQWCD.EKC.KW.VP.AMVI.E.GSS..LKHF
Retrocopy ISVPDIDY*GFLYNILAVSALCHFFSSELIQKVSEYQWCDTEKCIKWIVPLAMVIEELGSS<QLKHF

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	10.76 RPM
SRP017611_kidney	0.10 RPM	1.93 RPM
SRP017611_liver	0.00 RPM	0.46 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_676 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_676 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_676 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000001857	2 retrocopies	retro_cjac_3786, retro_cjac_3996,
Oryctolagus cuniculus	ENSOCUG00000009143	1 retrocopy	retro_ocun_676 ,
Oryctolagus cuniculus	ENSOCUG00000015589	1 retrocopy	retro_ocun_1277,
Oryctolagus cuniculus	ENSOCUG00000028042	1 retrocopy	retro_ocun_169,
Otolemur garnettii	ENSOGAG00000006217	2 retrocopies	retro_ogar_3309, retro_ogar_930,
Sus scrofa	ENSSSCG00000002855	1 retrocopy	retro_sscr_232,
Vicugna pacos	ENSVPAG00000001390	1 retrocopy	retro_vpac_219,