RetrogeneDB ID: retro_ocun_834

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 15:53124248..53124887(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NAP1L1
• Ensembl ID: ENSOCUG00000013857
• Aliases: None
• Description: nucleosome assembly protein 1-like 1 [Source:HGNC Symbol;Acc:7637]

Sequence

>retro_ocun_834
AATGTTGGCTTGCTCAGTGACATGGTGCAGGAACATGGTGAACCTATTCTAAAGCACTTGACAGATATTAAAGTGAAGTT
CTATGATGCAGGGCAGCCTGTGAAACTTGCCTTAGCATTCACTTTGAACCCAATGAATATTTCACAAATGAAGTGTTCAT
AAAGACATATAGGATGAGATCAGAACCAGAGGATTCTGATCTCTTTTCTTTTGACTGATCAGAAATTATGGGTTGTATGA
TGTGGCAGACAGATTTGGAAAAAGAAAAGAACGTTATTTTGAAACTGTTAAGAAGAAGCAGAAACACAAGTGAAGTGGGA
CAGTTTGTACTGTGACTAAAACAGGTTCCAATGACACTGCTAATTTTTTGCCCCTCCTGAAGTTCCTGAGAGTGGAGATT
TGGATGATGCTGCTGAAGCCATCCTTGCCGCAGACTTTGAAATTGGTCACTTTTTACATGAATGTATCATCCCAAGGTCA
GTGTTATACTTTACTGGAGAGGCTATTGAAGATAATGATGATGATTATGATGAAGAAGATGAAGAAGCAGACGAGGAAGG
GGAAGAAGAAGGAGATGAGGAAAATGATCCAGACTATGATCCAAAGAAGGATCAAAACCCAGCAGAGTGCAAGTGGCAA

Alignment

ORF - retro_ocun_834 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.39 %
• Parental protein coverage: 54.99 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  NVDLLSDMVQEHDEPILKHLKDIKVKFSDAGQPMSFVLEF-HFEPNEYFTNEVLTKTYRMRSEPDDSDPF
          NV.LLSDMVQEH.EPILKHL.DIKVKF.DAGQP....L.F.HFEPNEYFTNEV..KTYRMRSEP.DSD.F
Retrocopy NVGLLSDMVQEHGEPILKHLTDIKVKFYDAGQPVKLALAF<HFEPNEYFTNEVFIKTYRMRSEPEDSDLF

Parental  SFDGPEIMGCTGCQIDWKKGKNVTLK-TIKKKQKHKGRGTVRTVTKTVSNDSFFNF-FAPPEVPESGDLD
          SFD..EIMGC...Q.D..K.KNV.LK.T.KKKQKHK..GTV.TVTKT.SND...NF.FAPPEVPESGDLD
Retrocopy SFD*SEIMGCMMWQTDLEKEKNVILK<TVKKKQKHK*SGTVCTVTKTGSNDT-ANF<FAPPEVPESGDLD

Parental  DDAEAILAADFEIGHFLRERIIPRSVLYFTGEAIEDDDDDYDEEGEEADEEGEEEGDEENDPDYDPKKDQ
          D.AEAILAADFEIGHFL.E.IIPRSVLYFTGEAIED.DDD...................NDPDYDPKKDQ
Retrocopy DAAEAILAADFEIGHFLHECIIPRSVLYFTGEAIEDNDDDXXXXXXXXXXXXXXXXXXXNDPDYDPKKDQ

Parental  NPAECKQQ
          NPAECK.Q
Retrocopy NPAECKWQ

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	135.16 RPM
SRP017611_kidney	0.00 RPM	66.08 RPM
SRP017611_liver	0.00 RPM	36.23 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_834 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_834 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_834 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020908	8 retrocopies	retro_btau_1319, retro_btau_1324, retro_btau_1462, retro_btau_1487, retro_btau_474, retro_btau_652, retro_btau_70, retro_btau_935,
Macropus eugenii	ENSMEUG00000013702	2 retrocopies	retro_meug_1031, retro_meug_604,
Macaca mulatta	ENSMMUG00000015583	1 retrocopy	retro_mmul_233,
Monodelphis domestica	ENSMODG00000020456	4 retrocopies	retro_mdom_1476, retro_mdom_1638, retro_mdom_520, retro_mdom_724,
Mustela putorius furo	ENSMPUG00000017474	1 retrocopy	retro_mputfur_505,
Mus musculus	ENSMUSG00000058799	1 retrocopy	retro_mmus_263,
Oryctolagus cuniculus	ENSOCUG00000005624	1 retrocopy	retro_ocun_384,
Oryctolagus cuniculus	ENSOCUG00000013857	1 retrocopy	retro_ocun_834 ,
Rattus norvegicus	ENSRNOG00000003890	1 retrocopy	retro_rnor_150,
Tursiops truncatus	ENSTTRG00000017062	2 retrocopies	retro_ttru_160, retro_ttru_1921,