RetrogeneDB ID: retro_ocun_528

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 12:114666556..114667366(+)
• Located in intron of: ENSOCUG00000011863

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_528
GCCGAGTTGATCAGGAGCATCGTCTTGAAAAGCCCCATGTCTGCAATGATGACAGTCCTGAAAGCCTGGAATTTTTCTGT
CTGAAAATCAACTGTAGATGTTAAACTTCTGGCAGAGGAAGGAATCTCTTGCTCAAAGTGTGGTTCTGCTGTGTAAGGAG
AAGTGTGCCAGTCTCAGCGATGCAGCCCTTTCAGACGTCGTTTGCACTCAGGTTCATCGGCACTAGAAAATCCGGGATGT
GTATCAGATGAGTAAAGGACCAGGTGCAGAACTTGACCTTTTTGATTTAGAACAGTTCAAAAGTTCATTTACAAACATTC
TTCGGAAGGCATTAAAAAAATGTGATGGTCAGCTTCAGCGATGCCAAGGAGAATACAGTCTGTATTCAAATCCCTTGGGG
AGCACAGTATACTAAGCCAAAGCAGTACAAACCTACTTCCATGGTGTACTATTCCCACACGCCCTATGCCTTCACTTCTT
CCTCCAGGCTCAGGAGCAATATCCCCCTTCTGGGTCAGGTACTGACAATCACTAGCAAACACCATCAGATCGTACAAATA
GACCTGACAAGCAGATCCCTGGACTCTCTTAAGGCTATTGCTTTCATGTAGTCTAGTCAGAACTTTGAAATCCACAGCAC
TACAACACCTCAACAGAAAAGGAGCCTTTGGCTGGACATAAACACAGATTCAAGGATCATTCACGAAAATTCAGTAGAAA
AAGACAAAGTCCAGAGAATAACCCAAGAAACTTTTGGAGACTATCCTCACACCACGACTAGAATTTGCATAATGGAAGCT
TGAAACAAAG

Alignment

ORF - retro_ocun_528 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.47 %
• Parental protein coverage: 79.35 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  AEFIRRTILKIPMSEMMTVLEAWNF-LSESQLQTLNLRQRKDSLAQSVVLLCEEKCASLSDAALLDIVCT
          AE.IR...LK.PMS.MMTVL.AWNF.LSE.QL..LN..QRK.SLAQSVVLLC.EKCASLSDAAL.D.VCT
Retrocopy AELIRSIVLKSPMSAMMTVLKAWNF>LSENQL*MLNFWQRKESLAQSVVLLCKEKCASLSDAALSDVVCT

Parental  QVHRHQKIWDVYQMSKGPGEDLDLFDIEQFKSSFKKILQRALR-NVTVSFRDAEENAVWIRIAWGTQYTK
          QVHRH.KI.DVYQMSKGPG..LDLFD.EQFKSSF..IL..AL..NV.VSF.DA.EN.V.I.I.WG.QYTK
Retrocopy QVHRH*KIRDVYQMSKGPGAELDLFDLEQFKSSFTNILRKALK>NVMVSFSDAKENTVCIQIPWGAQYTK

Parental  PNQYKPTYVVYYSHTPYAFTSSSRLKSNIPLLGQALTVASKHHQIVKMDLRSRYLDSLKAIVFKQYNQNF
          P.QYKPT..VYYSHTPYAFTSSSRL.SNIPLLGQ.LT..SKHHQIV..DL.SR.LDSLKAI.F....QNF
Retrocopy PKQYKPTSMVYYSHTPYAFTSSSRLRSNIPLLGQVLTITSKHHQIVQIDLTSRSLDSLKAIAFM*SSQNF

Parental  EIHNPTAPLQERSVGLDINTDSRIIHENAVEKDKVQRITQETFGDYPQ-PRLEFAQYKLETK
          EIH..T.P.Q.RS..LDINTDSRIIHEN.VEKDKVQRITQETFGDYP..PRLEFA..KLETK
Retrocopy EIHSTTTPQQKRSLWLDINTDSRIIHENSVEKDKVQRITQETFGDYPH>PRLEFA*WKLETK

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	0.22 RPM	12.42 RPM
SRP017611_kidney	0.41 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_528 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_528 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_528 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,