RetrogeneDB ID: retro_eeur_639

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_372789:38995..39231(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CKS2
• Ensembl ID: ENSEEUG00000004384
• Aliases: None
• Description: CDC28 protein kinase regulatory subunit 2 [Source:HGNC Symbol;Acc:2000]

Sequence

>retro_eeur_639
ATGGCCCACAAGCAGATCTAATACTCGAATAAGTACTTGGAGGAGCACTGCGAATATCAGCATGCTATGTTACCCAGCGA
ACTTTCCAAACAAGTACCCAAAACTCATCTGATGTCTGAAGAGGAGTGGAGAAGACTTCACTTCCAGAGAGTCTAAGCTG
GGTTCATTCCATGATTCGCGAACCAGAACCACACACTGTTCTCTTCAGACGACCTCTTCCCAAAGATCGACAAAAA

Alignment

ORF - retro_eeur_639 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.5 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAHKQIYYSDKYFDEHYEYRHVMLPRELSKQVPKTHLMSEEEWRRLGVQ-QSLGWVHYMIHEPEPHILLF
          MAHKQI.YS.KY..EH.EY.H.MLP.ELSKQVPKTHLMSEEEWRRL..Q..SL.WVH.MI.EPEPH..LF
Retrocopy MAHKQI*YSNKYLEEHCEYQHAMLPSELSKQVPKTHLMSEEEWRRLHFQ<ESLSWVHSMIREPEPHTVLF

Parental  RRPLPKDQQK
          RRPLPKD.QK
Retrocopy RRPLPKDRQK

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	4.83 RPM
SRP017611_kidney	0.00 RPM	3.94 RPM
SRP017611_liver	0.00 RPM	1.93 RPM

ChIP-Seq

Erinaceus europaeus was not studied using ChIP-Seq data.

EST

Erinaceus europaeus was not studied using EST data.

TSS

Erinaceus europaeus was not studied using FANTOM5 data.

Lab

retro_eeur_639 was not experimentally validated.

Homology

Retrocopy orthology:

Erinaceus europaeus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 53 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,
Erinaceus europaeus	ENSEEUG00000015895	1 retrocopy	retro_eeur_302,
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,
Mus musculus	ENSMUSG00000062248	4 retrocopies	retro_mmus_1356, retro_mmus_1470, retro_mmus_2392, retro_mmus_409,
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,
Rattus norvegicus	ENSRNOG00000014130	5 retrocopies	retro_rnor_1209, retro_rnor_1909, retro_rnor_2742, retro_rnor_279, retro_rnor_402,
Sorex araneus	ENSSARG00000002443	1 retrocopy	retro_sara_213,
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,