RetrogeneDB ID: retro_ocun_1930

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: X:57438182..57438752(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000016174
• Aliases: None
• Description: None

Sequence

>retro_ocun_1930
GCGGTGACAGCAGCAGCGGGGACTGTGGAGGGGTCGGGGCTCCAGGCTGGCGTGGCGGCACCATCTTGTGCCCTGGACGG
GGCCCCTGGAGGCTTAGGGGGACTAAGGGAACAACCTGGAGTCTGACAAACCGGAACCTGGGGAGCTGTTGCCAGAGCCT
GAGCCCGAAGAGGTGACACCCAGGCCCTGCGCTCCCCCGGGAACTCTGGGTCCTGGGCCTGGCTCAGAGCCCGCCCTCCC
TCCCCCAGCAACCAAGAGGAGGAGGAATCCGGACTGGTCAAGGGTGACCCGGGGGACAGCGCCATTGAGGACCAGGAGTT
GGAAGCGATCAAAGCCAGAGTCAGGGAGATGGAAGAGGAAGCGGAGAAGCTAAAGGAGCTGCAGAACAAAGTGGAGAGGC
ATATGAATAGGAGTCCATCTCCAGGCGGTGCTGGCCCAGTGATCGTGTTTACTGAGGAGAGAATGGAGGCTGACGCCCAT
TCCATCTGTGTTGGCAATGTGAACTACGGTGCATCAGCGGAAGAGCTGGAAGCTCACTTTCATGGTTGTGATTTTGTCAA
CCATGTGACA

Alignment

ORF - retro_ocun_1930 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.21 %
• Parental protein coverage: 63.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AAGAAGGRGSGPGRRRHLVPGAGGEAGEGAPGGAG-DYGNGLESEELEPGELLPEPEPEEEPPRPRAPPG
          A..AA.G...G.G........A...A..GAPGG.G.D.GN.LES...EPGELLPEPEPEE..PRP.APPG
Retrocopy AVTAAAGTVEGSGLQAGVA--APSCALDGAPGGLG>D*GNNLESDKPEPGELLPEPEPEEVTPRPCAPPG

Parental  T----PGPGPG-SGAPGNQEEEEEPGLVEGDPGDSAIEDPELEAIKARVREMEEEAEKLKELQNEVEKQM
          T....PG..P.....P.NQEEEE..GLV.GDPGDSAIED.ELEAIKARVREMEEEAEKLKELQN.VE..M
Retrocopy TLGPGPGSEPA<PPSPSNQEEEES-GLVKGDPGDSAIEDQELEAIKARVREMEEEAEKLKELQNKVERHM

Parental  NMSPPPGNAGPVIMSIEERMEADARSIYVGNVDYGATAEELEAHFHGCGSVNRVT
          N.SP.PG.AGPVI...EERMEADA.SI.VGNV.YGA.AEELEAHFHGC..VN.VT
Retrocopy NRSPSPGGAGPVIVFTEERMEADAHSICVGNVNYGASAEELEAHFHGCDFVNHVT

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	94.37 RPM
SRP017611_kidney	0.00 RPM	57.77 RPM
SRP017611_liver	0.00 RPM	42.70 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1930 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1930 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1930 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000100836	1 retrocopy	retro_hsap_4855,
Mus musculus	ENSMUSG00000022194	1 retrocopy	retro_mmus_403,
Oryctolagus cuniculus	ENSOCUG00000016174	4 retrocopies	retro_ocun_1185, retro_ocun_1741, retro_ocun_1930 , retro_ocun_365,