RetrogeneDB ID: retro_ocun_384

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 1:111963362..111963931(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NAP1L4
• Ensembl ID: ENSOCUG00000005624
• Aliases: None
• Description: nucleosome assembly protein 1-like 4 [Source:HGNC Symbol;Acc:7640]

Sequence

>retro_ocun_384
AGAGAATTCGTCACTGGTGATGTTAAGCCAACAGATGTTGAGCTGGAATGACATAGTGACAATGAAGAGGAGGATAAGTT
GGTTGGAAAACATGAAAAACAAGTTAGTCATAGAAGAGAAGGAAGAAGCAGCAGCAGAGAGTGAAACCCCAGAAGGATCC
TGGAGTTCTGGTTCACCATCTTCAGAAATGTGAACATGCTGAGGGGGCTCATCTGGGGCTATGATAAACCAAACTTGAAA
CACCTGCAGGACATTAAAGTGAAGTTCTCAGACCCAAGACAGCCTCTGTCTTCTGTTTTGGAGTTCTACTTTGAACCCAA
CAACTACTTTACCAACTTAGTCTTGACAAAAATCTACAAGATGAAGTCAGAGCCAGATAAGGCTGATCCCTTTTCCTTTG
AAGTTCTTGAAATTGTTGACTGTGTTGAGTGTACAGTTGACTGGAAGAAAGGAATAATTGGGACGGTCAAAACTATCAAG
AAAACGCGGAAGCACTAGGACTGGGAACTGTCAGAACAACCACTAAGAAAGTGCCCAACAAGTTGTTTTTCAATTTCTTC
AAGCATCTG

Alignment

ORF - retro_ocun_384 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.5 %
• Parental protein coverage: 52.2 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  REFITGDVEPTDAESEWHSDDEEEEKLAG-DMKSKLVTDEKEEAAAEEPTPRG-IPEFWFTIFRNVDMLS
          REF.TGDV.PTD.E.E.HSD.EEE.KL.G..MK.KLV..EKEEAAAE..TP.G.I.EFWFTIFRNV.ML.
Retrocopy REFVTGDVKPTDVELE*HSDNEEEDKLVG>NMKNKLVIEEKEEAAAESETPEG<ILEFWFTIFRNVNMLR

Parental  ELVREYDEPILKHLQDIKVKFSDPGQPMSFVLEFHFEPNDYFTNSVLTKTYKMKSEPDKADPFSFEGPEI
          .L...YD.P.LKHLQDIKVKFSDP.QP.S.VLEF.FEPN.YFTN.VLTK.YKMKSEPDKADPFSFE..EI
Retrocopy GLIWGYDKPNLKHLQDIKVKFSDPRQPLSSVLEFYFEPNNYFTNLVLTKIYKMKSEPDKADPFSFEVLEI

Parental  VDCDGCTIDWKKGKNVTVKTVRKKQKH-RGRGTVRTITKQVPSESFFNFFSPL
          VDC..CT.DWKKG...TVKT..K..KH..G.GTVRT.TK.VP...FFNFF..L
Retrocopy VDCVECTVDWKKGIIGTVKTIKKTRKH<LGLGTVRTTTKKVPNKLFFNFFKHL

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	86.54 RPM
SRP017611_kidney	0.00 RPM	65.48 RPM
SRP017611_liver	0.00 RPM	20.81 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_384 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_384 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_384 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000205531	1 retrocopy	retro_hsap_438,
Gorilla gorilla	ENSGGOG00000013223	1 retrocopy	retro_ggor_423,
Nomascus leucogenys	ENSNLEG00000010841	1 retrocopy	retro_nleu_1876,
Oryctolagus cuniculus	ENSOCUG00000005624	1 retrocopy	retro_ocun_384 ,
Oryctolagus cuniculus	ENSOCUG00000013857	1 retrocopy	retro_ocun_834,
Pongo abelii	ENSPPYG00000002938	1 retrocopy	retro_pabe_288,
Pan troglodytes	ENSPTRG00000028747	1 retrocopy	retro_ptro_192,