RetrogeneDB ID: retro_ocun_309

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 1:134454704..134455084(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000010727
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000001353
• Aliases: None
• Description: None

Sequence

>retro_ocun_309
ATGCAGCTCAAGCCAATGGAGATTAACCGCGAGATGCTGAACAAAGTGCTGAGCCGGCTGGGCGTCGCCGGCCAGTATCG
TTTCGCTGACGTGCTGGGGCTGGAGGAGACCCTGGGCTCTGTGCCAGCGCCCGCCTGCGCGCTGCTGCTGCTGTTCCCCC
TCCTGCCCAGCATGGGAACTTCAGGAAAAAGCAGATTGAAGAGCTGAAGGGACAAAAGGTTAGTCCCAAGGTGTACTTCA
TGAAGCAGACCATCGGGAACTCCTGTGGCACCGTCGGGCTGATCCACGCTGTGGCCAATAACCAAGACAAACTGCATTTT
GAGGACGGATCAGTCCTGAAACAGTTTCTGTCTGAAACGGAGAAGATGTCCCCTGAAGAC

Alignment

ORF - retro_ocun_309 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.8 %
• Parental protein coverage: 57.4 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MQLKPMEINPEMLNKVLSRLGVAGQYRFADVLGLEEETLGTVPAPACALLLLFPLT-AQHENFRKKQIEE
          MQLKPMEIN.EMLNKVLSRLGVAGQYRFADVLGLEE.TLG.VPAPACALLLLFPL..AQH.NFRKKQIEE
Retrocopy MQLKPMEINREMLNKVLSRLGVAGQYRFADVLGLEE-TLGSVPAPACALLLLFPLL<AQHGNFRKKQIEE

Parental  LKGQEVSPKVYFMKQTIGNSCGTVGLIHAVANNQDKLQFEDGSVLKQFLSETEKMSPED
          LKGQ.VSPKVYFMKQTIGNSCGTVGLIHAVANNQDKL.FEDGSVLKQFLSETEKMSPED
Retrocopy LKGQKVSPKVYFMKQTIGNSCGTVGLIHAVANNQDKLHFEDGSVLKQFLSETEKMSPED

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	0.39 RPM	472.96 RPM
SRP017611_kidney	0.00 RPM	9.02 RPM
SRP017611_liver	0.00 RPM	0.69 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_309 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_309 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_309 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003295	1 retrocopy	retro_chof_1737,
Callithrix jacchus	ENSCJAG00000019346	1 retrocopy	retro_cjac_365,
Erinaceus europaeus	ENSEEUG00000002185	3 retrocopies	retro_eeur_150, retro_eeur_573, retro_eeur_598,
Echinops telfairi	ENSETEG00000012347	1 retrocopy	retro_etel_44,
Felis catus	ENSFCAG00000025457	1 retrocopy	retro_fcat_1321,
Homo sapiens	ENSG00000154277	2 retrocopies	retro_hsap_781, retro_hsap_782,
Gorilla gorilla	ENSGGOG00000008809	1 retrocopy	retro_ggor_648,
Macropus eugenii	ENSMEUG00000013774	1 retrocopy	retro_meug_8,
Myotis lucifugus	ENSMLUG00000010138	2 retrocopies	retro_mluc_1216, retro_mluc_2113,
Nomascus leucogenys	ENSNLEG00000017176	2 retrocopies	retro_nleu_2582, retro_nleu_2583,
Oryctolagus cuniculus	ENSOCUG00000001353	1 retrocopy	retro_ocun_309 ,
Oryctolagus cuniculus	ENSOCUG00000006789	1 retrocopy	retro_ocun_382,
Pan troglodytes	ENSPTRG00000016009	2 retrocopies	retro_ptro_3028, retro_ptro_3029,
Ictidomys tridecemlineatus	ENSSTOG00000015507	1 retrocopy	retro_itri_288,
Tupaia belangeri	ENSTBEG00000011438	1 retrocopy	retro_tbel_306,
Tarsius syrichta	ENSTSYG00000008305	1 retrocopy	retro_tsyr_1191,
Tursiops truncatus	ENSTTRG00000012095	1 retrocopy	retro_ttru_1370,