RetrogeneDB ID: retro_ocun_588

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 12:140158196..140158891(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCNH
• Ensembl ID: ENSOCUG00000004659
• Aliases: None
• Description: cyclin H [Source:HGNC Symbol;Acc:1594]

Sequence

>retro_ocun_588
ATGTACCACAACAGCAGCCTGGAAAGGCACTGGGCTTTCGCCAGCGAGGCGCAGCTGGGCAGACTGTGGGCTGACGCCAA
CCGCAAATGCAAATACAAAGTGGTGGCGAACGGGAAGGTTCTTCCAAAAGACCCAGTCTTTCTTGAGCCTCACGAAGAAA
TGGCACTCTGCAGATAGTGTGAGAAAAGATTATTGGAATTCAGTTCCGTGTTTAAGCCAGCAATGCCAAGGTCTCTTGTG
GGCACAGCTCATATGCATTTCAAGCCTTTTTATCTTAATAACTCAGTAATGGAATATCACCCCCGGATAATTCCTTATCC
GCTCTTCTGTGTGTTTTTGGCCTGCAAAGTGGGTGAATTCAATGTATCTAGTCCTCAGTCTGTTGGAAACCTTCGGGAGG
GTGGTCTTCGACAGGAAAAGGCACTGGAGCAGATTTTGGAGTATGAGCTACCACTTACACAGCAACTTCATTTCCACCTT
ACTGTGCACAATCCTTGCAGACCACCTGAGGGCTTCCTCAATGATTTGAAGACTCGCTGCCCCGTGTTGGAGAACCCAGA
GATGTTGAGGAAAACAATAGATGACTTCCTTGATAGAATTCAGCTGACAGATGCTTAACTTGTGTACACATCTTCTCAAA
TTGCCCTGACTGCGTTTTATCTAGTGCCTCCCGGGCTGGAATCGCTGTGGGAAGT

Alignment

ORF - retro_ocun_588 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.06 %
• Parental protein coverage: 71.3 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MYHNSSQKRHWTFASEEQLGRLRADANRKFKCKAVANGKKVLPNDPVFLEPHEEMTLCKYYEKRLLEFCS
          MYHNSS..RHW.FASE.QLGRL.ADANRK.K.K.VANGK.VLP.DPVFLEPHEEM.LC...EKRLLEF.S
Retrocopy MYHNSSLERHWAFASEAQLGRLWADANRKCKYKVVANGK-VLPKDPVFLEPHEEMALCR*CEKRLLEFSS

Parental  VFKPTMPRSVVGTACMYFKRFYLNNSVMEYHPRIIM--LTCVFLACKVDEFNVSSPQFVGNLRESPLGQE
          VFKP.MPRS.VGTA.M.FK.FYLNNSVMEYHPRII...L.CVFLACKV.EFNVSSPQ.VGNLRE..L.QE
Retrocopy VFKPAMPRSLVGTAHMHFKPFYLNNSVMEYHPRIIPYPLFCVFLACKVGEFNVSSPQSVGNLREGGLRQE

Parental  KALEQILEYELLLIQQLNFHLIVHNPYRPFEGFLIDLKTRYPMLENPEMLRKTADDFLNRIALTDAYLLY
          KALEQILEYEL.L.QQL.FHL.VHNP.RP.EGFL.DLKTR.P.LENPEMLRKT.DDFL.RI.LTDA.L.Y
Retrocopy KALEQILEYELPLTQQLHFHLTVHNPCRPPEGFLNDLKTRCPVLENPEMLRKTIDDFLDRIQLTDA*LVY

Parental  TPSQIALTA-ILSSASRAGITMES
          T.SQIALTA..LSSASRAGI...S
Retrocopy TSSQIALTA<VLSSASRAGIAVGS

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	0.11 RPM	29.36 RPM
SRP017611_kidney	0.00 RPM	21.69 RPM
SRP017611_liver	0.00 RPM	4.24 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_588 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_588 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_588 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000007765	1 retrocopy	retro_dnov_1618,
Homo sapiens	ENSG00000134480	1 retrocopy	retro_hsap_3128,
Gorilla gorilla	ENSGGOG00000005172	1 retrocopy	retro_ggor_2143,
Macaca mulatta	ENSMMUG00000003248	1 retrocopy	retro_mmul_1991,
Mus musculus	ENSMUSG00000021548	1 retrocopy	retro_mmus_2510,
Nomascus leucogenys	ENSNLEG00000013604	1 retrocopy	retro_nleu_2248,
Oryctolagus cuniculus	ENSOCUG00000004659	1 retrocopy	retro_ocun_588 ,
Pongo abelii	ENSPPYG00000015619	2 retrocopies	retro_pabe_2584, retro_pabe_2590,
Pan troglodytes	ENSPTRG00000017063	1 retrocopy	retro_ptro_2116,
Ictidomys tridecemlineatus	ENSSTOG00000000659	1 retrocopy	retro_itri_856,