RetrogeneDB ID: retro_ocun_735

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 14:6446124..6446413(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000028154
• Aliases: None
• Description: None

Sequence

>retro_ocun_735
GTGCCTGAAATCTTGGATGATGCAGTGAGAATTCTTGTTGTTGAAGACATGAAGCAAGTATTTGGCGAAGATGACGAGCA
CCTTCAGTGCATTGAGGTTCACAGTAAGACCCTCGAGTCAGCTGGATAGGTATTATGTAGCCTCAAGCTACACTTGCATG
GTCATTGCCAGACCTGCTAAGGCACAGTGGTGACTGCTGTACATAAAGGAGTGCCTGAGAATCTCTGATCCTGACCTTCA
CACCAAAGGACTTGAGCCTGTCTACAGTCAACTCCTGACCAAGGACGAC

Alignment

ORF - retro_ocun_735 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.48 %
• Parental protein coverage: 71.94 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VPANFEDPVNLLVEDEEVEQIFGQDDKYLRCIEEHSNTL-IQLDRYYVACSYTRIIITRPVRAQRWLMYM
          VP....D.V..LV..E...Q.FG.DD..L.CIE.HS.TL..QLDRYYVA.SYT...I.RP..AQ..L.Y.
Retrocopy VPEILDDAVRILVV-EDMKQVFGEDDEHLQCIEVHSKTL>SQLDRYYVASSYTCMVIARPAKAQW*LLYI

Parental  MSCLRIDHPDLQAEGLQMLQHVRSEPLTKED
          ..CLRI..PDL...GL.....V.S..LTK.D
Retrocopy KECLRISDPDLHTKGL---EPVYSQLLTKDD

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	0.00 RPM
SRP017611_kidney	0.00 RPM	0.00 RPM
SRP017611_liver	0.00 RPM	0.00 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_735 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_735 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_735 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000009236	4 retrocopies	retro_dord_249, retro_dord_47, retro_dord_607, retro_dord_82,
Microcebus murinus	ENSMICG00000006451	1 retrocopy	retro_mmur_647,
Macaca mulatta	ENSMMUG00000018573	1 retrocopy	retro_mmul_84,
Mus musculus	ENSMUSG00000067750	1 retrocopy	retro_mmus_464,
Oryctolagus cuniculus	ENSOCUG00000028154	1 retrocopy	retro_ocun_735 ,
Otolemur garnettii	ENSOGAG00000006102	1 retrocopy	retro_ogar_2275,