RetrogeneDB ID: retro_ocun_1169

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 3:89170378..89171074(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: POLDIP2
• Ensembl ID: ENSOCUG00000007781
• Aliases: None
• Description: polymerase (DNA-directed), delta interacting protein 2 [Source:HGNC Symbol;Acc:23781]

Sequence

>retro_ocun_1169
TCAGAAGCTGTGACCTCCCTGGCTAACCATGATGACAGCTGGGCCCTGTATGCCATCCCAGGCCTGGACTATGTCAGCCA
TGAGGACAGCCTGCCCTACACTTCCAGTGATTAGGTTTACATCCAGCGGGAGCGCTTTGAAAGTTTTCTTCTATACGACC
AGACTAAGCACCTCCTTCTGTGGCTCGGGAGACACTACGGGCCTAGCAAGAGAAGAATCAGCCCTGGCTGGAGCTTTCCA
GTGTCCACCCGGAAACAACTGAGGACATCCGTGTCGCTGTCATCCCCGTCTACACGGGCGTGAGGGAAGCCCAGAATTCC
CATGTCTACTGGTGGGTGTTACCGCATCCGCTTGGAGAACCTTGACAGTGACCTTGGCAGTGACGTCGCGCAGCTCCGGG
TGTGGCACTGGAGGGTATTTAGCCTCTCTGGCACCTTGGGAACAGTGCGAGGCCAAGGCAGGGAACCAGTGTTATCCAGG
GAGGAGCCTGCATCCCAGAACAGCAGCCACGACTCCCTGCAAACGTCTAGTGGGCACACGTGGGGCACATTCCACTTTGA
GAGTCCTGATGGCTGCCACTTTGATGTCCGGAGCCCACCCTTCTCCCTGGAAAGCAATGAAGATGAGAAGACGCCACCCT
CAGGCCTTCACTGGTAGGCCAGCCGAGGCCCTGAGAGCCCGGCTTGGTTCCGAAGA

Alignment

ORF - retro_ocun_1169 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.11 %
• Parental protein coverage: 53.35 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TEAVTFLANHDDSRALYAIPGLDYVSHEDILPYTSTDQVPIQHELFERFLLYDQTK-APPFVARETLRAW
          .EAVT.LANHDDS.ALYAIPGLDYVSHED.LPYTS.D.V.IQ.E.FE.FLLYDQTK.APP.VARETLRA.
Retrocopy SEAVTSLANHDDSWALYAIPGLDYVSHEDSLPYTSSD*VYIQRERFESFLLYDQTK<APPSVARETLRA*

Parental  QEKNHPWLELSDVHRETTENIRVTVIPFYMGMREAQNSHVYWWR-YCIRLENLD----SDVVQLRERHWR
          QEKN.PWLELS.VH.ETTE.IRV.VIP.Y.G.REAQNSHVYWW..Y.IRLENLD....SDV.QLR..HWR
Retrocopy QEKNQPWLELSSVHPETTEDIRVAVIPVYTGVREAQNSHVYWWV>YRIRLENLDSDLGSDVAQLRVWHWR

Parental  IFSLSGTLETVRGRGVVGREPVLSKEQPAFQYSSHVSLQASSGHMWGTFRFERPDGSHFDVRIPPFSLES
          .FSLSGTL.TVRG....GREPVLS.E.PA.Q.SSH.SLQ.SSGH.WGTF.FE.PDG.HFDVR.PPFSLES
Retrocopy VFSLSGTLGTVRGQ---GREPVLSREEPASQNSSHDSLQTSSGHTWGTFHFESPDGCHFDVRSPPFSLES

Parental  NKDEKTPPSGLHWSLGVSNLGPALARR
          N.DEKTPPSGLHW........PA..RR
Retrocopy NEDEKTPPSGLHW*ASRGPESPAWFRR

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	61.92 RPM
SRP017611_kidney	0.00 RPM	110.38 RPM
SRP017611_liver	0.00 RPM	45.94 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1169 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1169 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1169 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000018665	1 retrocopy	retro_cfam_2069,
Callithrix jacchus	ENSCJAG00000012566	1 retrocopy	retro_cjac_1445,
Oryctolagus cuniculus	ENSOCUG00000007781	1 retrocopy	retro_ocun_1169 ,