RetrogeneDB ID: retro_rnor_1727

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 20:25382744..25383076(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Cbx5
• Ensembl ID: ENSRNOG00000036841
• Aliases: None
• Description: chromobox protein homolog 5 [Source:RefSeq peptide;Acc:NP_001100267]

Sequence

>retro_rnor_1727
CCTAGGGAGAAGTCAGAAGGTAACAAGAAAAAATCCAATTTTTAGAACAACGCTGATGTTACTAAATTGAAGAGAGGGCT
GTGGGTAGCGATGATATCGCTCAGGGCTTTGAGAGGAGACTGGAACCAGAAAAGATCACTTGGGTAACAGATTCCCATGG
TGACTTAATGTTTCTAACAAAACAGAATGGCACCTGGGAAGTAGACCTGGTTCTTGTAAAGACGCCAGTGCGAAATGTCC
ACAAACTGTGGGAGTGTTTCTGAAGGGAGACAGTTGTGACACGTGTATCTATCCAAAAAATGAGAAGCAAAGAAAAATAC
AGTGCCAAGAGC

Alignment

ORF - retro_rnor_1727 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.26 %
• Parental protein coverage: 58.12 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  PREKSEGNKRKSSFSNSADDIKSKK-KREQSNDIARGFERGLEPEKIIGATDSCGDLMFLMKWKDTDEAD
          PREKSEGNK.KS.F.N.AD..K.K......S.DIA.GFER.LEPEKI...TDS.GDLMFL.K...T.E.D
Retrocopy PREKSEGNKKKSNF*NNADVTKLKR<RAVGSDDIAQGFERRLEPEKITWVTDSHGDLMFLTKQNGTWEVD

Parental  LVL-AKEANVKCPQIVIAFYE-ERLTWHAYPEDAENKEKESAKS
          LVL..K.A..KCPQ.V..F...E.............KEK.SAKS
Retrocopy LVL<CKDASAKCPQTVGVFLK>ETVVTRVSIQKMRSKEKYSAKS

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	18.84 RPM
SRP017611_kidney	0.00 RPM	15.91 RPM
SRP017611_liver	0.00 RPM	5.65 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1727 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1727 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1727 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Mus musculus	retro_mmus_650

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000001220	1 retrocopy	retro_etel_678,
Mus musculus	ENSMUSG00000009575	1 retrocopy	retro_mmus_650,
Rattus norvegicus	ENSRNOG00000008689	2 retrocopies	retro_rnor_2388, retro_rnor_2841,
Rattus norvegicus	ENSRNOG00000011814	2 retrocopies	retro_rnor_120, retro_rnor_301,
Rattus norvegicus	ENSRNOG00000036841	1 retrocopy	retro_rnor_1727 ,