RetrogeneDB ID: retro_ocun_1676

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018758:1632103..1632701(+)
• Located in intron of: ENSOCUG00000003116

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_1676
GCCTGGGGAACGCTGTACACTGAGCCAAACCAGTACAAACCTACGTACGTGGTGTGCTGCTCCCACACTCCCTATGCATT
CACGTCTCCCTCCAGGCTCAAGAGCAAGGTCCCGCTTTGGATCAGGCACTGACAGTCGCTAGCCAACACCATCAGCTTCT
GAAAATGCACCTGAGAAGCAGCTACCTGGACTCTCCTAAGGCCATGGCTTTCAAGGAGTATCATCAGGACTTCGAAATCC
ACAACCCTACAACACCTCTACAGGAGAGGCGCCTTGGGCGGGTCATAAACACAGATTCATGGATCATTCATGCAAATGCA
GTAGAGAAAGACAAAGTCCAGAGAATAACCCAAGAAACCTTTGGAGACTATCCTCAACCACAACTAGAATTTGCACAATA
TAAGCTCGAAAGGAAGTTCAAAAGTGCATTGGATGGGGGCATCCTGGCCGTCAGGGCAGAGCCACTGGGGTGCCAAATAA
AGTTCTCCAGCCCACATCCTTTGGAAGCACTGAAATCCCTAGTACCAACCAGAACTGCAGATCCATTGCTCGCTTGCATA
CCCAGCGGGGAATGAATTATTTTAAACTCAGAGATAAA

Alignment

ORF - retro_ocun_1676 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.18 %
• Parental protein coverage: 60.18 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AWGTQYTKPNQYKPTYVVYYSHTPYAFTSSSRLKSNIPL-LGQALTVASKHHQIVKMDLRSRYLDSLKAI
          AWGT.YT.PNQYKPTYVV..SHTPYAFTS.SRLKS..PL.L.QALTVAS.HHQ..KM.LRS.YLDS.KA.
Retrocopy AWGTLYTEPNQYKPTYVVCCSHTPYAFTSPSRLKSKVPL<LDQALTVASQHHQLLKMHLRSSYLDSPKAM

Parental  VFKQYNQNFEIHNPTAPLQERSVGLDINTDSRIIHENAVEKDKVQRITQETFGDYPQPRLEFAQYKLETK
          .FK.Y.Q.FEIHNPT.PLQER..G..INTDS.IIH.NAVEKDKVQRITQETFGDYPQP.LEFAQYKLE.K
Retrocopy AFKEYHQDFEIHNPTTPLQERRLGRVINTDSWIIHANAVEKDKVQRITQETFGDYPQPQLEFAQYKLERK

Parental  FKSDLNGGILADREEPLRCLIKFSSPHLLEALKSLAPAGIADAPLSPLLTCIPS-RGMNYFKIRDK
          FKS.L.GGILA.R.EPL.C.IKFSSPH.LEALKSL.P...AD....PLL.CIPS.RGMNYFK.RDK
Retrocopy FKSALDGGILAVRAEPLGCQIKFSSPHPLEALKSLVPTRTAD----PLLACIPS<RGMNYFKLRDK

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_1676 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1676 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1676 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,