RetrogeneDB ID: retro_ocun_1806

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018954:93700..94290(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CENPN
• Ensembl ID: ENSOCUG00000000024
• Aliases: None
• Description: centromere protein N [Source:HGNC Symbol;Acc:30873]

Sequence

>retro_ocun_1806
ATGGATGAAACAATTCCTGAGTTTATTAGGAAGACCATCTTGAAAATTTCCATGTCTGAAATGATGACAGTCCTAAAACC
CTGGAATTTTTTGTCTGAAAATCAACTGCAAGTGTTAAACTTCCAGCAGAGAAAGGAATCTTTTGCTCCAAGTGTGGTTC
TTCTGTGTGAGAAGTGTGCTGGTCTCAGCCATGTGGCCCTTTTAGACATCATTTGTACTCAAGTTCTTCAACACCAGAAA
ATCTGAGGTGTTTATCAGATTAGTAAAGGACCAGGTGAAGACCTTGACCTCTATGATATAGAACAGTTCAGAAGTTTGTT
TAAGAAAATTCTTCAGAGAACATTAAACAAATGCAATGGTCAGATTCAGAGATGCTGAGAATGCAGTCTGGATTCGAATA
CCCTGGGGAACGCAGTATACTAACCCAAACTAGTACAAACCTACTTACACGGTGCACTATTCCCACACACCTATGCCTTC
ACTTCTTCCTCCAAGCTCAAGAGCAATATCCCCCTGTAGGTCAGGCACTGACAATCCCTAGGAAACACCAACAGACTGTG
AAAATGGACCTAAGAAGCAGATACATGGAC

Alignment

ORF - retro_ocun_1806 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.73 %
• Parental protein coverage: 58.7 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MDETIAEFIRRTILKIPMSEMMTVLEAWNFLSESQLQTLNLRQRKDSLAQSVVLLCEEKCASLSDAALLD
          MDETI.EFIR.TILKI.MSEMMTVL..WNFLSE.QLQ.LN..QRK.S.A.SVVLLCE.KCA.LS..ALLD
Retrocopy MDETIPEFIRKTILKISMSEMMTVLKPWNFLSENQLQVLNFQQRKESFAPSVVLLCE-KCAGLSHVALLD

Parental  IVCTQVHRHQKIWDVYQMSKGPGEDLDLFDIEQFKSSFKKILQRALR-NVTVSFRDAEENAVWIRIAWGT
          I.CTQV..HQKI..VYQ.SKGPGEDLDL.DIEQF.S.FKKILQR.L..N..V.FRDA.ENAVWIRI.WGT
Retrocopy IICTQVLQHQKI*GVYQISKGPGEDLDLYDIEQFRSLFKKILQRTLN>NAMVRFRDA-ENAVWIRIPWGT

Parental  QYTKPNQYKPTYVVYYSHTP-YAFTSSSRLKSNIPL-LGQALTVASKHHQIVKMDLRSRYLD
          QYT.PN.YKPTY.V.YSHTP.YAFTSSS.LKSNIPL..GQALT...KH.Q.VKMDLRSRY.D
Retrocopy QYTNPN*YKPTYTVHYSHTP<YAFTSSSKLKSNIPL<VGQALTIPRKHQQTVKMDLRSRYMD

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	12.42 RPM
SRP017611_kidney	0.00 RPM	3.24 RPM
SRP017611_liver	0.00 RPM	1.54 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1806 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1806 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1806 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000011635	1 retrocopy	retro_btau_1101,
Felis catus	ENSFCAG00000004978	1 retrocopy	retro_fcat_1852,
Homo sapiens	ENSG00000166451	2 retrocopies	retro_hsap_2146, retro_hsap_2291,
Oryctolagus cuniculus	ENSOCUG00000000024	3 retrocopies	retro_ocun_1676, retro_ocun_1806 , retro_ocun_528,
Sarcophilus harrisii	ENSSHAG00000002111	1 retrocopy	retro_shar_331,
Ictidomys tridecemlineatus	ENSSTOG00000007345	1 retrocopy	retro_itri_1431,
Tupaia belangeri	ENSTBEG00000000039	2 retrocopies	retro_tbel_2049, retro_tbel_3055,