RetrogeneDB ID: retro_ocun_711

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 14:91826001..91826302(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PFDN6
• Ensembl ID: ENSOCUG00000010559
• Aliases: None
• Description: prefoldin subunit 6 [Source:HGNC Symbol;Acc:4926]

Sequence

>retro_ocun_711
ATCCAGGGAGAAGTGGAGAAGCAGCAACAGCCACCCAAGGACTTGAGTAAGTCCACATCAGGGAGGCAGCAGCTTGAGCC
CAACTAACAGAAAGCAAGGTCGTGAGGAGGAGCTGGCTCTGCGCCACGGATCTAACGTGCTCTTTAAACTGCTGCCCCGG
GGCCGGTTAGGCAGGAGCTGGGGGAGGCTGGGCCACAGCGGGGAGGAGGCTGGACAGCATCACAACTGAAATCAAGCGAA
GCGAATCCCAGCTCCGGGACCTGGAACGCAGTCGGAGCAGCGGAGGGAGACCCCTGCTCAG

Alignment

ORF - retro_ocun_711 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.96 %
• Parental protein coverage: 79.07 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  LQGEVEKYQQLQKDLSKSMSGRQKLE-AQLTENNIVK-EELALLDGSNVVFKLL-GPVLVKQELGEAR-A
          .QGEVEK.QQ..KDLSKS.SGRQ.LE.AQLTE...V..EELAL..GSNV.FKLL..P..V.QELGEA..A
Retrocopy IQGEVEKQQQPPKDLSKSTSGRQQLE<AQLTESKVVR<EELALRHGSNVLFKLL<APGPVRQELGEAG<A

Parental  TVGKRLDYITAEIKRYESQLRDLER-QSEQQRETLAQ
          T.G.RLD.IT.EIKR.ESQLRDLER.QSEQ.RET.AQ
Retrocopy TAGRRLDSITTEIKRSESQLRDLER<QSEQRRETPAQ

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	30.52 RPM
SRP017611_kidney	0.00 RPM	21.08 RPM
SRP017611_liver	0.00 RPM	6.01 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_711 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_711 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_711 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001576	2 retrocopies	retro_amel_221, retro_amel_824,
Bos taurus	ENSBTAG00000010723	1 retrocopy	retro_btau_619,
Canis familiaris	ENSCAFG00000000956	2 retrocopies	retro_cfam_1749, retro_cfam_1981,
Cavia porcellus	ENSCPOG00000019520	1 retrocopy	retro_cpor_570,
Dipodomys ordii	ENSDORG00000013828	1 retrocopy	retro_dord_453,
Felis catus	ENSFCAG00000028199	1 retrocopy	retro_fcat_1784,
Macropus eugenii	ENSMEUG00000016778	1 retrocopy	retro_meug_1930,
Microcebus murinus	ENSMICG00000000922	1 retrocopy	retro_mmur_1520,
Mustela putorius furo	ENSMPUG00000002364	1 retrocopy	retro_mputfur_608,
Mus musculus	ENSMUSG00000024309	1 retrocopy	retro_mmus_1930,
Oryctolagus cuniculus	ENSOCUG00000010559	1 retrocopy	retro_ocun_711 ,
Otolemur garnettii	ENSOGAG00000028341	4 retrocopies	retro_ogar_1185, retro_ogar_2023, retro_ogar_3508, retro_ogar_85,
Ochotona princeps	ENSOPRG00000000983	1 retrocopy	retro_opri_12,
Pteropus vampyrus	ENSPVAG00000001910	1 retrocopy	retro_pvam_391,
Rattus norvegicus	ENSRNOG00000000473	2 retrocopies	retro_rnor_2216, retro_rnor_2869,
Sorex araneus	ENSSARG00000006330	2 retrocopies	retro_sara_338, retro_sara_453,
Tupaia belangeri	ENSTBEG00000013280	1 retrocopy	retro_tbel_454,