RetrogeneDB ID: retro_ocun_606

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 13:32483228..32483989(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NECAP1
• Ensembl ID: ENSOCUG00000004309
• Aliases: None
• Description: NECAP endocytosis associated 1 [Source:HGNC Symbol;Acc:24539]

Sequence

>retro_ocun_606
AGCGTCTACCAGACTCCACCCTGGGCCTCCAAGCGTGGTTGCAAGGCATCTGACTGGAATTCAAACCAGCCTGATGGACT
GGTGGCTCCCAAATCGCTTTGAGGGGGAAGACTGCCTACATCAAACTCCAAGATAAAGTTTCAGGGGCACTCTTTGCACA
GGCACCAATAGAACAATATCCTGGCACTGCTGTGGAGACAGTGGCAGGTTGCAGCGGCTACTTAGTAATCCTGCTCCAGG
ATGGTCCTGGGGGGAGTGCTTTCATTGGCATGCGCTTCACAGATAGGGGAGACGCCTTTGATTTTAATGTCTCCTCGCAG
GACCACTTCCAGTGGGTGAAACAGGAATCTGAGATTTCCAGAGAATCTCAGGAAATAGATGTTCGTCCCAAATTGGATCT
GGGCTTCAAGGAAGGACAGACCACCAACTTGAGTATCAAGACTATTACAACCACGAAAGGAGGTACTTCCAAGGCCAGGA
CTGTAGGAACTGGAGGGCTAACCCTACTCCCACCTTAACATGGCAGTGAAGTTACTATTCTCCCACATTCCTCAGATACC
AGCAGCAGTCATGCCACCCCACCCCCCATTCAAAAATGTAACCATGGTAGTGATGCAAATATCCTTTTAATTTGGATTCT
CCTGCTTTTGTTACGACACCAGCATTGGCATCAATTTCTGCAAGCAATGACTTGTGGGGAGACTCTAAGCATTGCATCTA
GCTCTGTTCCAAACCAGGCACCACAGCCATCCAACTGGGTC

Alignment

ORF - retro_ocun_606 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.81 %
• Parental protein coverage: 93.07 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SVYRIPPRASNRGYRASDWKLDQPD-WTGRLRITSKGKIAYIKLEDKVSGELFAQAPIEQYPGIAVETVA
          SVY..PP.AS.RG..ASDW...QPD.WTG...I...GK.AYIKL.DKVSG.LFAQAPIEQYPG.AVETVA
Retrocopy SVYQTPPWASKRGCKASDWNSNQPD<WTGGSQIALRGKTAYIKLQDKVSGALFAQAPIEQYPGTAVETVA

Parental  DSSRYFVIRIQDGTGRSAFIGIGFTDRGDAFDFNVSLQDHFKWVKQESEISRESQEMDARPKLDLGFKEG
          ..S.Y.VI..QDG.G.SAFIG..FTDRGDAFDFNVS.QDHF.WVKQESEISRESQE.D.RPKLDLGFKEG
Retrocopy GCSGYLVILLQDGPGGSAFIGMRFTDRGDAFDFNVSSQDHFQWVKQESEISRESQEIDVRPKLDLGFKEG

Parental  QTIKLSIGNITTKKGGTSKPRTAGTGGLSLLPPPPGSKVTLPPPSSVAISNHVTPPPIPKSNHGGSDADI
          QT..LSI..ITT.KGGTSK.RT.GTGGL.LLPP..GS.VT..P.SS...S.H.TPPPI.K.NH.GSDA.I
Retrocopy QTTNLSIKTITTTKGGTSKARTVGTGGLTLLPP*HGSEVTILPHSSDTSSSHATPPPIQKCNH-GSDANI

Parental  LL-DLDSPAPVTTPASAPISASNDLWGD-FSTASSSVPNQAPQPSNWV
          LL..LDSPA.VTTPA.A.ISASNDLWGD..S.ASSSVPNQAPQPSNWV
Retrocopy LL<NLDSPAFVTTPALASISASNDLWGD>LSIASSSVPNQAPQPSNWV

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	271.25 RPM
SRP017611_kidney	0.00 RPM	56.86 RPM
SRP017611_liver	0.00 RPM	28.52 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_606 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_606 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_606 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008087	3 retrocopies	retro_chof_1692, retro_chof_1818, retro_chof_1913,
Dasypus novemcinctus	ENSDNOG00000014778	2 retrocopies	retro_dnov_613, retro_dnov_986,
Loxodonta africana	ENSLAFG00000002979	1 retrocopy	retro_lafr_632,
Oryctolagus cuniculus	ENSOCUG00000004309	1 retrocopy	retro_ocun_606 ,