RetrogeneDB ID: retro_ocun_492

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 12:2663717..2664078(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZBTB8OS
• Ensembl ID: ENSOCUG00000000940
• Aliases: None
• Description: zinc finger and BTB domain containing 8 opposite strand [Source:HGNC Symbol;Acc:24094]

Sequence

>retro_ocun_492
GTGGCACAGGGTCAGTAAGATGTTAGAGATTAGTTTAAGGAGCAGGTGGTAATCAAGGCCAGGTAATTCTCGAGTCAACC
CAAGGTAGGAGTAATTGGAGTATACTGCAGCTGTCCAGTTACATGCACAGGCAAGTACTCTGGGGGAAATATTTGAGCAA
AGTGCAGTGGCCATGTCTGGTTACACAGCAGATATTGAGACTGTGGAGCCACTCCAAACAACAGAAGTAGTAACCCAAGG
TGATGACTTGCAGGCTCTTCTCATCCATGTTTTTGATCAGTGGCTTTATAAATTCAGTGCTAACGAATTCTCCATGCTCT
AGGAAGTCAAAGTGCTTAATAATGAGCTAAGAAATTTCAAA

Alignment

ORF - retro_ocun_492 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.35 %
• Parental protein coverage: 73.05 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAQGEEDVRDYNLTEEQKAIKAK-YPPVNRKYEYLDHTADVQLHAWGDTLEEAFEQCAMAMFGYMTDTGT
          .AQG..DVR......EQ..IKA.....VN...E.L..TA.VQLHA...TL.E.FEQ.A.AM.GY..D..T
Retrocopy VAQGQ*DVR--D*FKEQVVIKAR>NSRVNPR*E*LEYTAAVQLHAQASTLGEIFEQSAVAMSGYTADIET

Parental  VEPLQTVEVETQGDDLQSLLFHFLDEWLYKFSADEFFIPREVKVLNIDQRNFK
          VEPLQT.EV.TQGDDLQ.LL.H..D.WLYKFSA.EF....EVKVLN...RNFK
Retrocopy VEPLQTTEVVTQGDDLQALLIHVFDQWLYKFSANEFSML*EVKVLNNELRNFK

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	5.35 RPM
SRP017611_kidney	0.00 RPM	8.31 RPM
SRP017611_liver	0.00 RPM	2.54 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_492 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_492 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_492 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000010550	1 retrocopy	retro_cfam_2152,
Choloepus hoffmanni	ENSCHOG00000004061	2 retrocopies	retro_chof_1005, retro_chof_1158,
Cavia porcellus	ENSCPOG00000015349	2 retrocopies	retro_cpor_356, retro_cpor_903,
Dasypus novemcinctus	ENSDNOG00000001861	2 retrocopies	retro_dnov_1056, retro_dnov_2193,
Equus caballus	ENSECAG00000020982	1 retrocopy	retro_ecab_610,
Felis catus	ENSFCAG00000000700	1 retrocopy	retro_fcat_703,
Homo sapiens	ENSG00000176261	2 retrocopies	retro_hsap_2396, retro_hsap_2992,
Gorilla gorilla	ENSGGOG00000007519	2 retrocopies	retro_ggor_2072, retro_ggor_231,
Myotis lucifugus	ENSMLUG00000000745	5 retrocopies	retro_mluc_1961, retro_mluc_2533, retro_mluc_2570, retro_mluc_2617, retro_mluc_2622,
Macaca mulatta	ENSMMUG00000009939	1 retrocopy	retro_mmul_1915,
Monodelphis domestica	ENSMODG00000017419	2 retrocopies	retro_mdom_400, retro_mdom_901,
Mus musculus	ENSMUSG00000057572	1 retrocopy	retro_mmus_2631,
Oryctolagus cuniculus	ENSOCUG00000000940	1 retrocopy	retro_ocun_492 ,
Otolemur garnettii	ENSOGAG00000011630	1 retrocopy	retro_ogar_3231,
Pongo abelii	ENSPPYG00000001589	2 retrocopies	retro_pabe_13, retro_pabe_2478,
Tursiops truncatus	ENSTTRG00000014968	1 retrocopy	retro_ttru_1200,