RetrogeneDB ID: retro_rnor_2742

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 9:79604015..79604238(-)
• Located in intron of: ENSRNOG00000016472

Retrocopy information

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

Parental gene information

• Parental gene symbol: Cks2
• Ensembl ID: ENSRNOG00000014130
• Aliases: Cks2, RGD1562047
• Description: cyclin-dependent kinases regulatory subunit 2 [Source:RefSeq peptide;Acc:NP_001119555]

Sequence

>retro_rnor_2742
ATGGCCCACAAGCAGATCTACTACACGAACAAGTACTTGGACAAGCACTACAAGTGCTGCCATGTCACGTTACCCAGAGC
ATTCTCTAAACAAGTCCCTAAGACTCATCCATGCCCGAAGAGGAGTGGAGGAGACTTAGTGTCCAACAGAGCTAGGGCGG
GTTCATGACAGGATTCATGAGCCAGAACCACGTAGTCTTCTCTTTAGATGACCTCTTCCAAAA

Alignment

ORF - retro_rnor_2742 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.73 %
• Parental protein coverage: 94.94 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAHKQIYYSDKYFDEHYEYRHVMLPRELSKQVPKTH-LMSEEEWRRLGVQQS-LGWVHYMIHEPEPHILL
          MAHKQIYY..KY.D.HY...HV.LPR..SKQVPKTH..M.EEEWRRL.VQQS.LG.VH..IHEPEP..LL
Retrocopy MAHKQIYYTNKYLDKHYKCCHVTLPRAFSKQVPKTH<SMPEEEWRRLSVQQS<LGRVHDRIHEPEPRSLL

Parental  FRRPLPK
          FR.PLPK
Retrocopy FR*PLPK

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	1.01 RPM
SRP017611_kidney	0.00 RPM	2.37 RPM
SRP017611_liver	0.00 RPM	2.69 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2742 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2742 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2742 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 61 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000002194	2 retrocopies	retro_cfam_1495, retro_cfam_472,
Callithrix jacchus	ENSCJAG00000007792	1 retrocopy	retro_cjac_261,
Dasypus novemcinctus	ENSDNOG00000009427	8 retrocopies	retro_dnov_1200, retro_dnov_1527, retro_dnov_195, retro_dnov_1984, retro_dnov_2530, retro_dnov_2532, retro_dnov_585, retro_dnov_755,
Erinaceus europaeus	ENSEEUG00000004384	7 retrocopies	retro_eeur_183, retro_eeur_255, retro_eeur_293, retro_eeur_551, retro_eeur_632, retro_eeur_639, retro_eeur_640,
Echinops telfairi	ENSETEG00000001260	10 retrocopies	retro_etel_1194, retro_etel_1752, retro_etel_1839, retro_etel_229, retro_etel_590, retro_etel_704, retro_etel_717, retro_etel_721, retro_etel_838, retro_etel_979,
Felis catus	ENSFCAG00000022286	1 retrocopy	retro_fcat_1875,
Homo sapiens	ENSG00000123975	1 retrocopy	retro_hsap_4183,
Macaca mulatta	ENSMMUG00000012534	1 retrocopy	retro_mmul_269,
Mus musculus	ENSMUSG00000062248	4 retrocopies	retro_mmus_1356, retro_mmus_1470, retro_mmus_2392, retro_mmus_409,
Nomascus leucogenys	ENSNLEG00000008729	1 retrocopy	retro_nleu_1793,
Otolemur garnettii	ENSOGAG00000028843	1 retrocopy	retro_ogar_798,
Ochotona princeps	ENSOPRG00000007583	3 retrocopies	retro_opri_111, retro_opri_1122, retro_opri_912,
Pongo abelii	ENSPPYG00000025843	1 retrocopy	retro_pabe_57,
Pan troglodytes	ENSPTRG00000021093	1 retrocopy	retro_ptro_2837,
Pteropus vampyrus	ENSPVAG00000011011	3 retrocopies	retro_pvam_1297, retro_pvam_1307, retro_pvam_605,
Rattus norvegicus	ENSRNOG00000014130	5 retrocopies	retro_rnor_1209, retro_rnor_1909, retro_rnor_2742 , retro_rnor_279, retro_rnor_402,
Rattus norvegicus	ENSRNOG00000042561	1 retrocopy	retro_rnor_97,
Sorex araneus	ENSSARG00000002443	1 retrocopy	retro_sara_213,
Sus scrofa	ENSSSCG00000021161	2 retrocopies	retro_sscr_458, retro_sscr_675,
Ictidomys tridecemlineatus	ENSSTOG00000000048	7 retrocopies	retro_itri_1058, retro_itri_1306, retro_itri_1429, retro_itri_1632, retro_itri_269, retro_itri_585, retro_itri_774,