RetrogeneDB ID: retro_ocun_141

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 4:63510919..63511360(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000020945
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000007729
• Aliases: None
• Description: None

Sequence

>retro_ocun_141
ATGGCGACTGCAGAAACCAGCGGCAGCGACGGGAAAGGGCAAGGGGGCGAGACCTCCATCACCTATTACTGGCTGGAGGA
TGTAGTCAAGTGCTACTCCCCGAAGGACCTATGGCTGGTGATCCACGGGCGGGTCTACAATATCACCCGCTTCCTCAACG
AGCACCCTGGTGGGGAAGAAGTTCTGCTGGAACAAGCTGGCTCAGATGCAAGCGAAAGCTTTGAAGATGTCGGCCATTCC
TCTGATGCCAGAGAGATGCTAAAGCAGTACTACATTGGTGATGTCCACCCGAGTGACCTTAAACCTGGGAGTGGCAGACA
GGACCCTTTGGAAAAGAATGCATGCCGACGTTGCTGGACATATTGGATTCTCCCCATCCTAGGCGCTGTTCTCACAGGTT
TCCTGTATCGTCACTACATGTCAGAAAGCAGATCCTCCTGA

Alignment

ORF - retro_ocun_141 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.04 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MATAEASGSDGKGQGGETSVTYYRLEEVAKRNSPKDLWLVIHGRVYDITRFLNEHPGGEEVLLEQAGVDA
          MATAE.SGSDGKGQGGETS.TYY.LE.V.K..SPKDLWLVIHGRVY.ITRFLNEHPGGEEVLLEQAG.DA
Retrocopy MATAETSGSDGKGQGGETSITYYWLEDVVKCYSPKDLWLVIHGRVYNITRFLNEHPGGEEVLLEQAGSDA

Parental  SESFEDVGHSSDAREMLKQYYIGDVHPSDLKPGSGRQNPSGKNACKRCWKYWILPILGAVLIGFLYRHYT
          SESFEDVGHSSDAREMLKQYYIGDVHPSDLKPGSGRQ.P..KNAC.RCW.YWILPILGAVL.GFLYRHY.
Retrocopy SESFEDVGHSSDAREMLKQYYIGDVHPSDLKPGSGRQDPLEKNACRRCWTYWILPILGAVLTGFLYRHYM

Parental  SESRSS
          SESRSS
Retrocopy SESRSS

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	17.38 RPM
SRP017611_kidney	0.10 RPM	48.85 RPM
SRP017611_liver	0.00 RPM	9.02 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_141 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_141 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_141 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Anas platyrhynchos	ENSAPLG00000007518	1 retrocopy	retro_apla_13,
Cavia porcellus	ENSCPOG00000014234	1 retrocopy	retro_cpor_1117,
Dasypus novemcinctus	ENSDNOG00000008313	9 retrocopies	retro_dnov_1424, retro_dnov_2077, retro_dnov_2123, retro_dnov_2310, retro_dnov_2684, retro_dnov_2685, retro_dnov_706, retro_dnov_716, retro_dnov_728,
Felis catus	ENSFCAG00000024541	1 retrocopy	retro_fcat_1816,
Homo sapiens	ENSG00000103018	1 retrocopy	retro_hsap_1493,
Gallus gallus	ENSGALG00000000660	1 retrocopy	retro_ggal_13,
Gorilla gorilla	ENSGGOG00000015031	1 retrocopy	retro_ggor_1146,
Meleagris gallopavo	ENSMGAG00000008619	1 retrocopy	retro_mgal_12,
Myotis lucifugus	ENSMLUG00000006608	1 retrocopy	retro_mluc_1734,
Macaca mulatta	ENSMMUG00000012039	1 retrocopy	retro_mmul_128,
Mus musculus	ENSMUSG00000031924	1 retrocopy	retro_mmus_2289,
Nomascus leucogenys	ENSNLEG00000005515	1 retrocopy	retro_nleu_1715,
Oryctolagus cuniculus	ENSOCUG00000007729	2 retrocopies	retro_ocun_141 , retro_ocun_255,
Pongo abelii	ENSPPYG00000007506	1 retrocopy	retro_pabe_1243,
Pan troglodytes	ENSPTRG00000008282	1 retrocopy	retro_ptro_1012,
Pteropus vampyrus	ENSPVAG00000015984	1 retrocopy	retro_pvam_977,
Sarcophilus harrisii	ENSSHAG00000014200	1 retrocopy	retro_shar_688,
Ictidomys tridecemlineatus	ENSSTOG00000011316	1 retrocopy	retro_itri_1296,
Tarsius syrichta	ENSTSYG00000014292	1 retrocopy	retro_tsyr_2171,
Tursiops truncatus	ENSTTRG00000010016	1 retrocopy	retro_ttru_521,
Drosophila melanogaster	FBgn0029854	1 retrocopy	retro_dmel_39,