RetrogeneDB ID: retro_rnor_2209

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 5:38648680..38649033(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Copz1
• Ensembl ID: ENSRNOG00000036835
• Aliases: None
• Description: coatomer subunit zeta-1 [Source:RefSeq peptide;Acc:NP_001101587]

Sequence

>retro_rnor_2209
GCCACCCTGATTCTGGACAATGATGGAGTCAAACTCTTTGCTAAGTACTATGATGACACCTATCCCAGCATCAAGGAGAA
AAAGCCTTTGAGAAGAACATTTGCAACAAGACCCATTGAATGGATCCTGAAATTGCCCTGTTGGAAGGCATGCCAGTGGC
CTATGAAAGTGTCATCAATCTCTATTTCTATGTAACTATCAGCTCCTGTGAAGGTGAATTGATGCTTATGGCTGTTCTCA
ACTGCCTCTTCAACTCCCTGAGCCAGATGCTGAGGAGAAATGGAGAAAAGCTAGCTCTGCTGGAGAACATGGAGGGGCTC
TTCTTGGCTATGGATGAAACTGTAGATGGAGGG

Alignment

ORF - retro_rnor_2209 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.15 %
• Parental protein coverage: 66.67 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AILILDNDGDRLFAKYYDDTYPSVKE-QKAFEKNIFNKTHRTDSEIALLEGLTVVYKSSIDLYFYVIGSS
          A.LILDNDG..LFAKYYDDTYPS.KE..KAFEKNI.NKTH..D.EIALLEG..V.Y.S.I.LYFYV..SS
Retrocopy ATLILDNDGVKLFAKYYDDTYPSIKE<EKAFEKNICNKTH*MDPEIALLEGMPVAYESVINLYFYVTISS

Parental  YENELMLMAVLNCLFDSLSQMLRKNVEKRALLENMEGLFLAVDEIVDGG
          .E.ELMLMAVLNCLF.SLSQMLR.N.EK.ALLENMEGLFLA.DE.VDGG
Retrocopy CEGELMLMAVLNCLFNSLSQMLRRNGEKLALLENMEGLFLAMDETVDGG

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	79.88 RPM
SRP017611_kidney	0.00 RPM	131.75 RPM
SRP017611_liver	0.00 RPM	110.81 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2209 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2209 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2209 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Mus musculus	retro_mmus_2439

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005384	1 retrocopy	retro_btau_1500,
Canis familiaris	ENSCAFG00000006536	1 retrocopy	retro_cfam_30,
Callithrix jacchus	ENSCJAG00000018887	2 retrocopies	retro_cjac_1771, retro_cjac_3951,
Echinops telfairi	ENSETEG00000013499	1 retrocopy	retro_etel_1782,
Microcebus murinus	ENSMICG00000008401	1 retrocopy	retro_mmur_757,
Mus musculus	ENSMUSG00000060992	1 retrocopy	retro_mmus_2439,
Oryctolagus cuniculus	ENSOCUG00000013364	2 retrocopies	retro_ocun_1511, retro_ocun_797,
Rattus norvegicus	ENSRNOG00000036835	1 retrocopy	retro_rnor_2209 ,
Tupaia belangeri	ENSTBEG00000008730	1 retrocopy	retro_tbel_3749,
Tursiops truncatus	ENSTTRG00000001654	2 retrocopies	retro_ttru_114, retro_ttru_856,