RetrogeneDB ID: retro_rnor_2886

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: X:3291763..3292570(-)
• Located in intron of: ENSRNOG00000004150

Retrocopy information

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

Parental gene information

• Parental gene symbol: Rcc1
• Ensembl ID: ENSRNOG00000050106
• Aliases: None
• Description: regulator of chromosome condensation [Source:RefSeq peptide;Acc:NP_001121661]

Sequence

>retro_rnor_2886
TTGCCACCCAAGCACATAGCTAATAGAATGTTGCCCCCAAGAAGATGCCATTCCCAAAAGCAAGAAGGTGAAAGTCTCAC
ACAGGTCCACACAACACAGTACCAGGCTTGGTGCTGACACTGGGCCAGGGCCACATGGGCCAGCTAGGGCTGGGGGAGAG
TGTGCTGGAGAGGAAGAAGGCAGCCTTGGTACTCCTTCTACAGGATGTTGTGCAGGCTGAGGCCCAGAGCATGCATACTG
TGTGTCTGAGCCAAAGTGGCCAGGTCTATTCCTTTGGCTGCAATGACGAGGGTGCCCTGGGAAGGGACACCTCAGTTGAG
GGCTCAGAGATGGTCCCTGGGAAAGTGGAACTGCAAGAGAAAGTCGTGCAAGTGTCAGTGGGGCACACTCACACAGCAGC
CCTCACCGAATACAGCTGAGTCTTACTCTGGGGCTCTTTCTGGGACAACAATGGTGTGATCAGGTTGTTGGAGCTCATGA
AGAAGAGCATGGTGCCTATTCAAGTGCAGCTGTATACTCAGGTGGTAAAGGTAGCCATGGGGAATGACCACTTGGTGATG
CTCACAAGTGATGGAAACCTCAACACCTTGGGTTGTGGGGAGCAAGGTCAGCTGGTCCATGTACCTGAGTTATTTGCCAA
CTGTGGTGGCTTTCAAGGGTCTTGAATGACTCCTGGTCCCCAGATGTGTGCTGCTGAAGTCCCGGGGAACCTGGGGCCAT
GTATGGTTCCAGGATGCCTTCTGTGGGGCCTATTTCACTTTTGCCATCTCCTGTGAGGGCCATGTGTATGGTATGACTTT
GGCCTCT

Alignment

ORF - retro_rnor_2886 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.76 %
• Parental protein coverage: 63.66 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MPPKRIAKRRSPP-EDAIPKSKKVKVSHRS-HNTEPGLVLTLGQGDVGQLGLGESVLERKKPALVPLLQD
          .PPK.IA.R..PP.EDAIPKSKKVKVSHRS.HNT.PGLVLTLGQG..GQLGLGESVLERKK.ALV.LLQD
Retrocopy LPPKHIANRMLPP>EDAIPKSKKVKVSHRS>HNTVPGLVLTLGQGHMGQLGLGESVLERKKAALVLLLQD

Parental  VVQAEAGGMHTVCLSQSGQVYSFGCNDEGALGRDTSVEGSEMVPGKVELQEKVVQVSAGDSHTAALTEDG
          VVQAEA..MHTVCLSQSGQVYSFGCNDEGALGRDTSVEGSEMVPGKVELQEKVVQVS.G..HTAALTE..
Retrocopy VVQAEAQSMHTVCLSQSGQVYSFGCNDEGALGRDTSVEGSEMVPGKVELQEKVVQVSVGHTHTAALTEYS

Parental  RVFLWGSFRDNNGVIGLLEPMKKSMVPVQVQLDTQVVKVASGNDHLVMLTTDGDLYTLGCGEQGQLGRVP
          .V.LWGSF.DNNGVI.LLE.MKKSMVP.QVQL.TQVVKVA.GNDHLVMLT.DG.L.TLGCGEQGQL..VP
Retrocopy *VLLWGSFWDNNGVIRLLELMKKSMVPIQVQLYTQVVKVAMGNDHLVMLTSDGNLNTLGCGEQGQLVHVP

Parental  ELFANRGGRQ-GLERLLVPRCVLLKSRGTRGRVRFQDAFCGAYFTFAISREGHVYGFGLSN
          ELFAN.GG.Q.GLE.LLVPRCVLLKSRGT.G.V.FQDAFCGAYFTFAIS.EGHVYG..L..
Retrocopy ELFANCGGFQ>GLE*LLVPRCVLLKSRGTWGHVWFQDAFCGAYFTFAISCEGHVYGMTLAS

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	6.25 RPM
SRP017611_kidney	0.00 RPM	9.70 RPM
SRP017611_liver	0.00 RPM	4.91 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2886 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2886 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2886 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009686	3 retrocopies	retro_cjac_2440, retro_cjac_3424, retro_cjac_3856,
Erinaceus europaeus	ENSEEUG00000004565	1 retrocopy	retro_eeur_418,
Myotis lucifugus	ENSMLUG00000017075	1 retrocopy	retro_mluc_2278,
Rattus norvegicus	ENSRNOG00000006327	1 retrocopy	retro_rnor_1378,
Rattus norvegicus	ENSRNOG00000050106	1 retrocopy	retro_rnor_2886 ,