RetrogeneDB ID: retro_ocun_1924

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: X:42526846..42527476(-)
• Located in intron of: ENSOCUG00000011267

Retrocopy information

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

Parental gene information

• Parental gene symbol: UCK2
• Ensembl ID: ENSOCUG00000008446
• Aliases: None
• Description: uridine-cytidine kinase 2 [Source:HGNC Symbol;Acc:12562]

Sequence

>retro_ocun_1924
AGCGGCAAGTCTTCCGTCTGTGCCAAGATTGTGCAGCTCCTGGGCCAGAACGAAGTGGATTATCGCCAGAAGCAGGTGGT
CGTTCTGAGTCAGGACAGTTTCTATCGAGTTCTCACATCAGAGCAGAAAGCCAAGGCCCTTAAGGGCCAGTTCAACTTCG
ATCACCCGGATGCTTTTGACAGTGAGCTCGTCTTCAGGACACTCAAAGAAATCGCTGAAGGGAAAACGGTTCAGATCCCG
GTGTACGACTTTGTCTCCCATTCCCGGAAGGAGGAGACAGTTACTATCTACCCGGCTGACGTGGTGCTCTTTGAAGGGAT
CCTGGCCTTCTACTCCCAGGAGATCCGCGACCTATTCCGAATGAAGCTTTTTGTGGACACAGACGCCGACACCCGTCTCT
CCCGCAGAGTATTAAGAGACATCAGCGAAAGAGGAAGGGATCTTGAGCAGATTCTGTCTCAGTATGTTGCCTTCGTCAAG
CCCACCTTTGAGGAATTCTGCTTGCCGACGAAAAAATACGCTGATGTGATAATTCCTAGAGGTGCAGATAATCTCGTGGC
CATCAACCTCATCGTGAAACACATCCAGGATATCCTCAACGGTGGGCATGCCAAACGGCAGACCAATGGC

Alignment

ORF - retro_ocun_1924 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.38 %
• Parental protein coverage: 90.91 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  STQSSVCAKIVQLLGQNEVDYRQKQVVILSQDSFYRVLTSEQKAKALKGQFNFDHPDAFDNELIFKTLKE
          S..SSVCAKIVQLLGQNEVDYRQKQVV.LSQDSFYRVLTSEQKAKALKGQFNFDHPDAFD.EL.F.TLKE
Retrocopy SGKSSVCAKIVQLLGQNEVDYRQKQVVVLSQDSFYRVLTSEQKAKALKGQFNFDHPDAFDSELVFRTLKE

Parental  ITEGKTVQIPVYDFVSHSRKEETVTVYPADVVLFEGILAFYSQEVRDLFQMKLFVDTDADTRLSRRVLRD
          I.EGKTVQIPVYDFVSHSRKEETVT.YPADVVLFEGILAFYSQE.RDLF.MKLFVDTDADTRLSRRVLRD
Retrocopy IAEGKTVQIPVYDFVSHSRKEETVTIYPADVVLFEGILAFYSQEIRDLFRMKLFVDTDADTRLSRRVLRD

Parental  ISERGRDLEQILSQYITFVKPAFEEFCLPTKKYADVIIPRGADNLVAINLIVQHIQDILNGGLSKRQTNG
          ISERGRDLEQILSQY..FVKP.FEEFCLPTKKYADVIIPRGADNLVAINLIV.HIQDILNGG..KRQTNG
Retrocopy ISERGRDLEQILSQYVAFVKPTFEEFCLPTKKYADVIIPRGADNLVAINLIVKHIQDILNGGHAKRQTNG

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	6.68 RPM
SRP017611_kidney	0.00 RPM	1.82 RPM
SRP017611_liver	0.00 RPM	1.39 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1924 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1924 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1924 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000013484	1 retrocopy	retro_eeur_199,
Myotis lucifugus	ENSMLUG00000016012	1 retrocopy	retro_mluc_589,
Oryctolagus cuniculus	ENSOCUG00000008446	1 retrocopy	retro_ocun_1924 ,
Pteropus vampyrus	ENSPVAG00000007694	1 retrocopy	retro_pvam_793,