RetrogeneDB ID: retro_rnor_2062

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 4:135409455..135409782(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Cdc42
• Ensembl ID: ENSRNOG00000013536
• Aliases: None
• Description: Cell division control protein 42 homolog [Source:UniProtKB/Swiss-Prot;Acc:Q8CFN2]

Sequence

>retro_rnor_2062
ATTTTTCTAGTATGTTTCTCAGTGGTCTCTCCATCCTCATTCAAAAATGTGAAAGAAAAGTGGGTACCTGAGACAACTCA
CCACTGCTCAAGGACTCCTTTCTTACTTGCTGCAACTCAAATGGGTCTCAGAGATGACCTTTGTACTATTGAGAAACTTG
CCAAGAACAAAGTGAAATCTATTACCCTGAAAACTGCTGACAAGCTGGAGTGGGATCTGAAGGCTGTCAAGAATGAGGAT
TGCTGTAACCTCACACAGAAATGGCTAAAGAATGTGTTTCTTGAAGCAACATTGGCTGCCCTGGAACCTTTAGAAGCAAG
GAAAAGC

Alignment

ORF - retro_rnor_2062 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.39 %
• Parental protein coverage: 57.07 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VFLVCFSVVSPSSFENVKEKWVPEITHHCPKTPFLLVGTQIDLRDDPSTIEKLAKNKQKPITPETAEKLA
          .FLVCFSVVSPSSF.NVKEKWVPE.THHC..TPFLL..TQ..LRDD..TIEKLAKNK.K.IT..TA.KL.
Retrocopy IFLVCFSVVSPSSFKNVKEKWVPETTHHCSRTPFLLAATQMGLRDDLCTIEKLAKNKVKSITLKTADKLE

Parental  RDLKAVKYVECSALTQKGLKNVFDEAILAALEPPEPKKS
          .DLKAVK...C..LTQK.LKNVF.EA.LAALEP.E..KS
Retrocopy WDLKAVKNEDCCNLTQKWLKNVFLEATLAALEPLEARKS

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	120.21 RPM
SRP017611_kidney	0.00 RPM	146.40 RPM
SRP017611_liver	0.00 RPM	54.33 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2062 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2062 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2062 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 70 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014707	5 retrocopies	retro_cfam_1587, retro_cfam_1970, retro_cfam_2189, retro_cfam_88, retro_cfam_89,
Choloepus hoffmanni	ENSCHOG00000005306	10 retrocopies	retro_chof_103, retro_chof_1044, retro_chof_1195, retro_chof_1853, retro_chof_2055, retro_chof_2105, retro_chof_2331, retro_chof_2407, retro_chof_50, retro_chof_800,
Callithrix jacchus	ENSCJAG00000005912	6 retrocopies	retro_cjac_1275, retro_cjac_1808, retro_cjac_1826, retro_cjac_2251, retro_cjac_751, retro_cjac_911,
Cavia porcellus	ENSCPOG00000006543	4 retrocopies	retro_cpor_1168, retro_cpor_286, retro_cpor_33, retro_cpor_887,
Equus caballus	ENSECAG00000019180	1 retrocopy	retro_ecab_11,
Echinops telfairi	ENSETEG00000004443	1 retrocopy	retro_etel_2010,
Felis catus	ENSFCAG00000004853	4 retrocopies	retro_fcat_129, retro_fcat_1421, retro_fcat_1579, retro_fcat_896,
Gorilla gorilla	ENSGGOG00000024439	5 retrocopies	retro_ggor_1932, retro_ggor_2057, retro_ggor_2303, retro_ggor_2593, retro_ggor_2695,
Macaca mulatta	ENSMMUG00000022009	8 retrocopies	retro_mmul_1449, retro_mmul_1612, retro_mmul_1685, retro_mmul_1900, retro_mmul_1932, retro_mmul_24, retro_mmul_349, retro_mmul_598,
Monodelphis domestica	ENSMODG00000016078	3 retrocopies	retro_mdom_18, retro_mdom_181, retro_mdom_537,
Mustela putorius furo	ENSMPUG00000015999	2 retrocopies	retro_mputfur_308, retro_mputfur_957,
Mus musculus	ENSMUSG00000006699	3 retrocopies	retro_mmus_2816, retro_mmus_2995, retro_mmus_3170,
Oryctolagus cuniculus	ENSOCUG00000009986	1 retrocopy	retro_ocun_60,
Otolemur garnettii	ENSOGAG00000014261	1 retrocopy	retro_ogar_131,
Pongo abelii	ENSPPYG00000001755	6 retrocopies	retro_pabe_2240, retro_pabe_2461, retro_pabe_2801, retro_pabe_3215, retro_pabe_3239, retro_pabe_3295,
Rattus norvegicus	ENSRNOG00000001068	1 retrocopy	retro_rnor_230,
Rattus norvegicus	ENSRNOG00000013536	1 retrocopy	retro_rnor_2062 ,
Rattus norvegicus	ENSRNOG00000015415	1 retrocopy	retro_rnor_473,
Sorex araneus	ENSSARG00000005184	3 retrocopies	retro_sara_10, retro_sara_220, retro_sara_3,
Ictidomys tridecemlineatus	ENSSTOG00000000805	4 retrocopies	retro_itri_1158, retro_itri_1602, retro_itri_1615, retro_itri_431,