RetrogeneDB ID: retro_ocun_1883

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: X:35854747..35855319(+)
• Located in intron of: ENSOCUG00000011608

Retrocopy information

• Ensembl ID: ENSOCUG00000004911
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CBR4
• Ensembl ID: ENSOCUG00000006446
• Aliases: None
• Description: carbonyl reductase 4 [Source:HGNC Symbol;Acc:25891]

Sequence

>retro_ocun_1883
CTGGGTGGTTGAGATCATTTGGCACTCAGCTGTGATGTTGCTAAAGAACATGATGTTCAAAATACATTTGAAGAGATGGA
GAAATGTTTAGGTCAAGTAAATTTCCTGGTAAATGCAGCTGATATTATCTGGGATAGTCTTAGAACAAAAACTGAAGATC
TGGTGTCTCAGCTTTATACCAACCTCTTGGTGTCCATGCTGACATGTAGAGCTGCCGTGAGGACTATTATTCAGCAGCAG
GCAGGGTCTGTTGTCAACGTAGGAAGTATTATTGGCTTAAAAGGCAATTCTGGCCAGTCTGTTTACAGTGCCAGTAAAGG
AGGATTAGTTGGATTTTCATATGCTCTTGCCAAAGAGGTAGCAAGAAAGAAAATTTTAGAGTGAATGTAATTGCACCAGG
ATTTATTTGCACAGATACGACAAAAGACTTGAAAGAACATTTAAAGAAAAATATTCCTCTTGGGAAGTTTGGAGAAACTG
TTGAGGTGGCACATGTGATTGTATTTCTTTTAGAGTCACCATATATTACGGGGCATGGTTTAGTAGTGGATGGGGCCTTA
CAAGTCATAGTA

Alignment

ORF - retro_ocun_1883 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.49 %
• Parental protein coverage: 81.01 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LGG-DHLALSCDVAKEHDVQHTFEEMEKHLGQVNFLVNAAGINRDGLLVRTKTEDLVSQLHTNLLGSMLT
          LGG.DHLALSCDVAKEHDVQ.TFEEMEK.LGQVNFLVNAA.I..D.L..RTKTEDLVSQL.TNLL.SMLT
Retrocopy LGG*DHLALSCDVAKEHDVQNTFEEMEKCLGQVNFLVNAADIIWDSL--RTKTEDLVSQLYTNLLVSMLT

Parental  CRAAMRTMIQQQGGSIVNVGSIIGLKGNSGQSVYSASKGGLVG-FSRALAKEVARKKI-RVNVVAPGFVR
          CRAA.RT.IQQQ.GS.VNVGSIIGLKGNSGQSVYSASKGGLVG.F...L.K.....K..RVNV.APGF..
Retrocopy CRAAVRTIIQQQAGSVVNVGSIIGLKGNSGQSVYSASKGGLVG>FHMLLPKR*QERKF>RVNVIAPGFIC

Parental  TDMTKDLKEEHLKKNIPLGRFGETIEVAHAIVFLLESPYITGHVLVVDGGLQLAI
          TD.TKDLKE.HLKKNIPLG.FGET.EVAH.IVFLLESPYITGH.LVVDG.LQ...
Retrocopy TDTTKDLKE-HLKKNIPLGKFGETVEVAHVIVFLLESPYITGHGLVVDGALQVIV

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	1.99 RPM
SRP017611_kidney	0.00 RPM	9.02 RPM
SRP017611_liver	0.00 RPM	2.00 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1883 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1883 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1883 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013400	1 retrocopy	retro_amel_1352,
Canis familiaris	ENSCAFG00000007520	1 retrocopy	retro_cfam_1341,
Felis catus	ENSFCAG00000030280	1 retrocopy	retro_fcat_885,
Oryctolagus cuniculus	ENSOCUG00000006446	1 retrocopy	retro_ocun_1883 ,
Tursiops truncatus	ENSTTRG00000000258	1 retrocopy	retro_ttru_1855,