RetrogeneDB ID: retro_rnor_2226

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 5:80202844..80203806(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Cct6a
• Ensembl ID: ENSRNOG00000000923
• Aliases: None
• Description: T-complex protein 1 subunit zeta [Source:RefSeq peptide;Acc:NP_001028856]

Sequence

>retro_rnor_2226
ATGGCAGCAGAGAAGACCTAAATCCTAAAGCCGAGGTGGCCCCAGGCTCAGGCAGCACTAGTGGTGAACATCAGTGTGGC
ACAGGGCCTGTAGGATGTTTTGAGGACCAACTTGGGGCCTAAGGGCACCATGAAGATGCTAGTATCTGGTTCTGGAGACA
TCGAACTTACTAAAGATGGCAATGTGCTGCTTCATGAAATGCAAATTCAACACCCAACAGCCTCTTTGATAGCAAAAATG
GCTACAGCCCAGGGTGACATAACTGGCGATGGCACTACATCCAATGTCCTCATCATTGGGAGCTGCTCAAACAAGTGGAC
CTCTACATTTCTGAAGGTCCTCGTCCCAGAATAATAACCGAAGGTTTTGAAGCTGCAAAGGAAAAGCACTCCAGTTTTTG
GAACAAGTCAAAGTAAGCAAAGAGATGGACAGAGAAGCACTCATCGATGTGGCCAGGACATCTCTGTGGACTAAAGTTCA
TGCTGAACTTGCAGATGTCTTTACAGAGGCTATGGTGGACTCCATTTTGGCCATTGGGAAAAAGAAGAGCCCACTGAACT
TTTCATGGTTGAGACCATGGAGATGAAGCATAAATATGAAACTGATACAAGCTTAATCAGAGGGCTTGTTTTGGATCATG
GGGCGTGGCATCCTGATATGAAGAAAAGAGTAGAAAATGCCTACATCCTCACAGGCAACGTGTCCTTGGAGTATGAGAAG
ACAGAAGGGAATTCTGGGTCTTTTACAAGAGTGCAGAAGAGAGAGAGAAACTAGTAAAGGCTGAAAGAAAACTCATTGAA
AATAGAGTTAAAAAAATCATAGAACTGAAGAAGAAAGTCTGTGGTGATTTGGATAAAGGATTTCTCATTATTAATCAAAA
GGGCATTGACCCCTTTTCTTTAGATGCCCTTGCAAAAGAAGGTATCGTAGCTCTGTGCAGAGCCAAGAGGAGAAAGGCTG
AC

Alignment

ORF - retro_rnor_2226 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.89 %
• Parental protein coverage: 60.64 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  MAAVKT-LNPKAEVA-RAQAALAVNISAARGLQDVLRTNLGPKGTMKMLVSGAGDIKLTKDGNVLLHEMQ
          MAA.KT.LNPKAEVA..AQAAL.VNIS.A.GL.DVLRTNLGPKGTMKMLVSG.GDI.LTKDGNVLLHEMQ
Retrocopy MAAEKT<LNPKAEVA>QAQAALVVNISVAQGL*DVLRTNLGPKGTMKMLVSGSGDIELTKDGNVLLHEMQ

Parental  IQHPTASLIAKVATAQDDITGDGTTSNVLIIG-ELLKQADLYISEGLHPRIITEGFEAAKE-KALQFLEQ
          IQHPTASLIAK.ATAQ.DITGDGTTSNVLIIG.ELLKQ.DLYISEG..PRIITEGFEAAKE.KALQFLEQ
Retrocopy IQHPTASLIAKMATAQGDITGDGTTSNVLIIG<ELLKQVDLYISEGPRPRIITEGFEAAKE<KALQFLEQ

Parental  VKVSKEMDRETLIDVARTSLRTKVHAELADVLTEAVVDSILAIRK-KDEPIDLFMVEIMEMKHKSETDTS
          VKVSKEMDRE.LIDVARTSL.TKVHAELADV.TEA.VDSILAI.K.K.EP..LFMVE.MEMKHK.ETDTS
Retrocopy VKVSKEMDREALIDVARTSLWTKVHAELADVFTEAMVDSILAIGK<KEEPTELFMVETMEMKHKYETDTS

Parental  LIRGLVLDHGARHPDMKKRVENAYILTCNVSLEYEKTEVNSG-FFYKSAEEREKLVKAERKFIEDRVKKI
          LIRGLVLDHGA.HPDMKKRVENAYILT.NVSLEYEKTE.NSG..FYKSAEEREKLVKAERK.IE.RVKKI
Retrocopy LIRGLVLDHGAWHPDMKKRVENAYILTGNVSLEYEKTEGNSG<VFYKSAEEREKLVKAERKLIENRVKKI

Parental  VELKKKVCGDSDKGFVVINQKGIDPFSLDALAKEGIVALRRAKRRNME
          .ELKKKVCGD.DKGF..INQKGIDPFSLDALAKEGIVAL.RAKRR...
Retrocopy IELKKKVCGDLDKGFLIINQKGIDPFSLDALAKEGIVALCRAKRRKAD

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	105.62 RPM
SRP017611_kidney	0.00 RPM	135.17 RPM
SRP017611_liver	0.00 RPM	55.54 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2226 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2226 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2226 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,