RetrogeneDB ID: retro_ocun_468

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 11:42119238..42120162(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000024067
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CCT6
• Ensembl ID: ENSOCUG00000017674
• Aliases: None
• Description: chaperonin containing TCP1, subunit 6A (zeta 1) (CCT6A), mRNA [Source:RefSeq mRNA;Acc:NM_001082039]

Sequence

>retro_ocun_468
AGAGTAGAAGATGCGTACATCCTCACATGCAATGTGTCATTGGAATATGAAAAAACGGAAGTGAATTCTGGCTTTTTTTA
CAAGAGTGCGGAAGAGAGAGAAAAACTAGTAAAAGCTGAAAGAAAATTCATTGAAGATAGAGTTAAAAAAATAGTAGAAC
TGAAAAAGAAAGTCTGTGGTGATTCAGATAAAGGATTTGTTGTTATTAATCAAAAGGGAATTGACCCCTTTTCCTTAGAT
GCTCTTGCAAAAGAAGGCATAGTAGCTCTGCGCAGGGCTAAAAGGAGAAATATGGAGAGGCTGACTCTTGCTTGTGGTGG
AGTACCTCTGAATTCTCTAGATGACCTAAATCCTGATTGTTTGGGACATGCAGGACTTGTGTATGAATATACATTGGGAG
AAGAGAAGTTCACCTTTATTGAGAAATGTAACAATCCTCGCTCTGTCACATTATTGGTCAAAGGACCAAATAAGCACACA
CTTACTCAAATCAAAGATGCGATAAGAGATGGCTTGAGGGCTGTCAAAAATGCTATTGATGATGGCTGTGTGGTTCCAGG
TGCTGGTGCAGTAGAAGTGGCAATGGCAGAAGCCCTGATAAAATACAAATCCAGTGTAAAGGGCAGGGCCCAACTTGGAG
TTCAAGCATTTGCTGATGCATTGCTCATTATTCCCAAGGTTCTTGCTCAGAACTCTGGCTTTGACCTTCAGGAAACATTA
GTTAAAATTCGAACAGAACATTCTGAATCAGGTCAACTTGTGGGTGTGGACTTGAACACAGGGGAGCCAATGGTGGCAGC
AGAAGTAGGCATTTGGGATAACTATTGTGTGAAGAAACAGCTTCTTCACTCCTGCACTGTGATTGCAACCAACATTCTCT
TGGTTGATGAGATCATGCGAGCTGGAATGTCTTCTCTCAAAGGT

Alignment

ORF - retro_ocun_468 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100.0 %
• Parental protein coverage: 58.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RVEDAYILTCNVSLEYEKTEVNSGFFYKSAEEREKLVKAERKFIEDRVKKIVELKKKVCGDSDKGFVVIN
          RVEDAYILTCNVSLEYEKTEVNSGFFYKSAEEREKLVKAERKFIEDRVKKIVELKKKVCGDSDKGFVVIN
Retrocopy RVEDAYILTCNVSLEYEKTEVNSGFFYKSAEEREKLVKAERKFIEDRVKKIVELKKKVCGDSDKGFVVIN

Parental  QKGIDPFSLDALAKEGIVALRRAKRRNMERLTLACGGVPLNSLDDLNPDCLGHAGLVYEYTLGEEKFTFI
          QKGIDPFSLDALAKEGIVALRRAKRRNMERLTLACGGVPLNSLDDLNPDCLGHAGLVYEYTLGEEKFTFI
Retrocopy QKGIDPFSLDALAKEGIVALRRAKRRNMERLTLACGGVPLNSLDDLNPDCLGHAGLVYEYTLGEEKFTFI

Parental  EKCNNPRSVTLLVKGPNKHTLTQIKDAIRDGLRAVKNAIDDGCVVPGAGAVEVAMAEALIKYKSSVKGRA
          EKCNNPRSVTLLVKGPNKHTLTQIKDAIRDGLRAVKNAIDDGCVVPGAGAVEVAMAEALIKYKSSVKGRA
Retrocopy EKCNNPRSVTLLVKGPNKHTLTQIKDAIRDGLRAVKNAIDDGCVVPGAGAVEVAMAEALIKYKSSVKGRA

Parental  QLGVQAFADALLIIPKVLAQNSGFDLQETLVKIRTEHSESGQLVGVDLNTGEPMVAAEVGIWDNYCVKKQ
          QLGVQAFADALLIIPKVLAQNSGFDLQETLVKIRTEHSESGQLVGVDLNTGEPMVAAEVGIWDNYCVKKQ
Retrocopy QLGVQAFADALLIIPKVLAQNSGFDLQETLVKIRTEHSESGQLVGVDLNTGEPMVAAEVGIWDNYCVKKQ

Parental  LLHSCTVIATNILLVDEIMRAGMSSLKG
          LLHSCTVIATNILLVDEIMRAGMSSLKG
Retrocopy LLHSCTVIATNILLVDEIMRAGMSSLKG

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	0.55 RPM	73.12 RPM
SRP017611_kidney	0.51 RPM	72.17 RPM
SRP017611_liver	0.31 RPM	28.59 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_468 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_468 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_468 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016077	1 retrocopy	retro_amel_855,
Canis familiaris	ENSCAFG00000010149	1 retrocopy	retro_cfam_431,
Choloepus hoffmanni	ENSCHOG00000000654	3 retrocopies	retro_chof_1183, retro_chof_1193, retro_chof_150,
Callithrix jacchus	ENSCJAG00000021279	2 retrocopies	retro_cjac_1320, retro_cjac_580,
Dipodomys ordii	ENSDORG00000001249	1 retrocopy	retro_dord_617,
Felis catus	ENSFCAG00000027654	2 retrocopies	retro_fcat_1102, retro_fcat_320,
Homo sapiens	ENSG00000146731	2 retrocopies	retro_hsap_2741, retro_hsap_3290,
Gorilla gorilla	ENSGGOG00000011439	1 retrocopy	retro_ggor_133,
Loxodonta africana	ENSLAFG00000012791	1 retrocopy	retro_lafr_808,
Macaca mulatta	ENSMMUG00000015272	1 retrocopy	retro_mmul_2582,
Monodelphis domestica	ENSMODG00000006565	1 retrocopy	retro_mdom_1330,
Nomascus leucogenys	ENSNLEG00000015664	1 retrocopy	retro_nleu_1355,
Oryctolagus cuniculus	ENSOCUG00000017674	1 retrocopy	retro_ocun_468 ,
Procavia capensis	ENSPCAG00000015532	1 retrocopy	retro_pcap_263,
Pongo abelii	ENSPPYG00000025820	1 retrocopy	retro_pabe_2719,
Pan troglodytes	ENSPTRG00000019206	2 retrocopies	retro_ptro_1854, retro_ptro_2225,
Pteropus vampyrus	ENSPVAG00000001421	1 retrocopy	retro_pvam_663,
Rattus norvegicus	ENSRNOG00000000923	1 retrocopy	retro_rnor_2226,
Tursiops truncatus	ENSTTRG00000015158	1 retrocopy	retro_ttru_1552,