RetrogeneDB ID: retro_ocun_1106

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 2:78729351..78729777(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDV3
• Ensembl ID: ENSOCUG00000012748
• Aliases: None
• Description: CDV3 homolog (mouse) [Source:HGNC Symbol;Acc:26928]

Sequence

>retro_ocun_1106
AAAGAAGATCCAGGTGATAACTGGGAAGAAGGTGGAGGTGGTGATAGTAGTATAGAAAAATCTTCAGCTCCATGGAGTAA
AACCACTACAGCACAAGCACCCCCTGCTCCAGTAATTGCTACATAAACTCCAGAACCAGCGATGACAGTGGTGTGTGTAT
AGGCCACCTGGAGCCAGGCTAACCACAATCAGGAAGATGCCACAAGGGCCTCCGGAGATACACAGGGATACACCGTTCCT
GTCCCTGCAGTCCACTGCCAAGCATGTAGAAAGCAAGAAGGATAAAGAAATGGAGAAGATTTTGAAGTAATAAGACACAA
ACATAGAGGTAGAGGTAAGGCTTCAAAACATCAGGCCCTCAAACTTCACCTAGGGAACCAGTGTGCTGGGCTTGAAACTC
AGAGAAGAAGCCACACACAGGGCAAT

Alignment

ORF - retro_ocun_1106 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.75 %
• Parental protein coverage: 95.83 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EEDDNEKREDPGG----TEKSSGPWNKAAPAQAPPAPGVVTETPEPATTSG-VYRPPGARLTTTRKTPQG
          .ED.....E..GG.....EKSS.PW.K...AQAPPAP...T.TPEPA.T...VYRPPGARLTT.RK.PQG
Retrocopy KEDPGDNWEEGGGGDSSIEKSSAPWSKTTTAQAPPAPVIAT*TPEPAMTVV>VYRPPGARLTTIRKMPQG

Parental  PPEIYSDTQFPSLQSTAKHVESRKDKEMEK-SFEVVRHKHRGRDEASKHQALKLELGNPYAVLEAQRSSH
          PPEI..DT.F.SLQSTAKHVES.KDKEMEK..FEV.RHKHRGR..ASKHQALKL.LGN..A.LE.QR.SH
Retrocopy PPEIHRDTPFLSLQSTAKHVESKKDKEMEK<DFEVIRHKHRGRGKASKHQALKLHLGNQCAGLETQRRSH

Parental  TQCN
          TQ.N
Retrocopy TQGN

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	102.76 RPM
SRP017611_kidney	0.00 RPM	212.95 RPM
SRP017611_liver	0.00 RPM	116.23 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1106 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1106 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1106 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000035556	1 retrocopy	retro_btau_253,
Choloepus hoffmanni	ENSCHOG00000008963	5 retrocopies	retro_chof_1355, retro_chof_1701, retro_chof_1763, retro_chof_2308, retro_chof_818,
Dasypus novemcinctus	ENSDNOG00000010208	5 retrocopies	retro_dnov_2359, retro_dnov_2616, retro_dnov_460, retro_dnov_496, retro_dnov_656,
Equus caballus	ENSECAG00000015689	2 retrocopies	retro_ecab_444, retro_ecab_636,
Myotis lucifugus	ENSMLUG00000009864	1 retrocopy	retro_mluc_1296,
Nomascus leucogenys	ENSNLEG00000003470	1 retrocopy	retro_nleu_1181,
Oryctolagus cuniculus	ENSOCUG00000012748	1 retrocopy	retro_ocun_1106 ,
Sus scrofa	ENSSSCG00000011637	1 retrocopy	retro_sscr_701,
Tupaia belangeri	ENSTBEG00000014910	5 retrocopies	retro_tbel_2284, retro_tbel_2443, retro_tbel_4022, retro_tbel_4157, retro_tbel_4378,