RetrogeneDB ID: retro_eeur_102

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: GeneScaffold_630:39155..39583(+)
• Located in intron of: ENSEEUG00000008393

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS23
• Ensembl ID: ENSEEUG00000001849
• Aliases: None
• Description: ribosomal protein S23 [Source:HGNC Symbol;Acc:10410]

Sequence

>retro_eeur_102
GGCAAGTGTCGTGGTCTCTGTACTGCCAGTAAGCTGCGTGGCTACCAGTGGGACCAGAAGTGGTATGATAAGCAGTAAAG
AAAGCCTCTCTGGGCATGGCCCTGAAGGCCAGTCCTTTTTGGAGGTGCTTCCCATGCCAAGGGGATTATGCTGAAAAAAG
TAGGGGTTGAAGCCAAACAGCCAAATCCTGCTGTCAGGAAGTGTGTCTGAATCCAGTTGATCAAGAATGGCAAAAAACAT
CACAGCCTTTGTGCCCAATGATGGTCACTTTGAATTTTATTGAGGAAAATGATGAAGTTCTGGTTGCTGTATTTGGTCGT
AATATTCACGCCGTTGGTGACATTCTTGGAGTTTGTTTTAAGGTTGTTGAAGTGGCCAGTGTCTCTCTGTTGGCTTTATA
CAAAGGCAAAAAGGGAAGGTCAAGATCC

Alignment

ORF - retro_eeur_102 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.77 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  GKCRGLRTARKLRSHRRDQKWHDKQ-YKKAHLGTALKANP-FGGASHAKGIVLEKVGVEAKQPNSAIRKC
          GKCRGL.TA.KLR....DQKW.DKQ..KKA.LG.ALKA.P.FGGASHAKGI.L.KVGVEAKQPN.A.RKC
Retrocopy GKCRGLCTASKLRGYQWDQKWYDKQ<VKKASLGMALKASP>FGGASHAKGIMLKKVGVEAKQPNPAVRKC

Parental  VRVQLIKNGKK-ITAFVPNDG-CLNFIEENDEVLVAGFGRKGHAVGDIPGVRFKVVKVANVSLLALYKGK
          V..QLIKNGKK.ITAFVPNDG..LNFIEENDEVLVA.FGR..HAVGDI.GV.FKVV.VA.VSLLALYKGK
Retrocopy V*IQLIKNGKK>ITAFVPNDG>TLNFIEENDEVLVAVFGRNIHAVGDILGVCFKVVEVASVSLLALYKGK

Parental  KERPRS
          K.R.RS
Retrocopy KGRSRS

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	0.32 RPM	55.92 RPM
SRP017611_kidney	0.00 RPM	157.53 RPM
SRP017611_liver	0.00 RPM	110.94 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_102 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 21 parental genes, and 93 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000011136	1 retrocopy	retro_acar_85,
Ailuropoda melanoleuca	ENSAMEG00000015966	3 retrocopies	retro_amel_1096, retro_amel_341, retro_amel_751,
Bos taurus	ENSBTAG00000013358	3 retrocopies	retro_btau_173, retro_btau_205, retro_btau_80,
Callithrix jacchus	ENSCJAG00000011247	2 retrocopies	retro_cjac_126, retro_cjac_256,
Cavia porcellus	ENSCPOG00000022705	2 retrocopies	retro_cpor_1182, retro_cpor_1377,
Equus caballus	ENSECAG00000020523	2 retrocopies	retro_ecab_275, retro_ecab_500,
Erinaceus europaeus	ENSEEUG00000001849	7 retrocopies	retro_eeur_102 , retro_eeur_262, retro_eeur_326, retro_eeur_462, retro_eeur_515, retro_eeur_53, retro_eeur_662,
Felis catus	ENSFCAG00000008839	7 retrocopies	retro_fcat_1557, retro_fcat_1601, retro_fcat_1876, retro_fcat_2000, retro_fcat_5, retro_fcat_609, retro_fcat_644,
Loxodonta africana	ENSLAFG00000031506	3 retrocopies	retro_lafr_1117, retro_lafr_1216, retro_lafr_606,
Microcebus murinus	ENSMICG00000013964	2 retrocopies	retro_mmur_1354, retro_mmur_872,
Myotis lucifugus	ENSMLUG00000013939	2 retrocopies	retro_mluc_1676, retro_mluc_2183,
Macaca mulatta	ENSMMUG00000003578	4 retrocopies	retro_mmul_1239, retro_mmul_1974, retro_mmul_2305, retro_mmul_852,
Oryctolagus cuniculus	ENSOCUG00000010363	2 retrocopies	retro_ocun_195, retro_ocun_95,
Otolemur garnettii	ENSOGAG00000008163	11 retrocopies	retro_ogar_1177, retro_ogar_1303, retro_ogar_1785, retro_ogar_1849, retro_ogar_238, retro_ogar_2479, retro_ogar_253, retro_ogar_2695, retro_ogar_2823, retro_ogar_3519, retro_ogar_364,
Pan troglodytes	ENSPTRG00000017052	6 retrocopies	retro_ptro_1190, retro_ptro_2056, retro_ptro_2223, retro_ptro_2707, retro_ptro_3075, retro_ptro_3122,
Rattus norvegicus	ENSRNOG00000016580	12 retrocopies	retro_rnor_100, retro_rnor_1394, retro_rnor_149, retro_rnor_1691, retro_rnor_1941, retro_rnor_1959, retro_rnor_1982, retro_rnor_2119, retro_rnor_2182, retro_rnor_2492, retro_rnor_525, retro_rnor_559,
Sorex araneus	ENSSARG00000008904	8 retrocopies	retro_sara_194, retro_sara_346, retro_sara_422, retro_sara_481, retro_sara_540, retro_sara_647, retro_sara_648, retro_sara_714,
Sarcophilus harrisii	ENSSHAG00000008347	2 retrocopies	retro_shar_257, retro_shar_348,
Ictidomys tridecemlineatus	ENSSTOG00000000824	3 retrocopies	retro_itri_1418, retro_itri_204, retro_itri_377,
Tarsius syrichta	ENSTSYG00000011385	5 retrocopies	retro_tsyr_1656, retro_tsyr_1946, retro_tsyr_406, retro_tsyr_462, retro_tsyr_933,
Tursiops truncatus	ENSTTRG00000014491	6 retrocopies	retro_ttru_1253, retro_ttru_1555, retro_ttru_186, retro_ttru_458, retro_ttru_487, retro_ttru_578,