RetrogeneDB ID: retro_eeur_396

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_283139:7300..7760(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CBX1
• Ensembl ID: ENSEEUG00000004874
• Aliases: None
• Description: chromobox homolog 1 [Source:HGNC Symbol;Acc:1551]

Sequence

>retro_eeur_396
GACTGTCAAGTGGTAAAAGGAAAAGTGGAATATCTGCTAAAGTGGAAAGGATTCTCAGATGAGGACAACACGTGGGAGCC
AGAAGAGAACCTGGATTGCCCCAACCTCATTGCTGAGTTGCTGCAGTCACAGAAAACAGCACAAGAGACAGATAAATCAG
AGGGTGGCAAGGGCAAAGCTGACTCTGATTCTGAAGATAAAGGAGAGGAGAACAAACCAAAGAAGAAGAGTCAGAAAAGC
TTTGCTCAGGGTTTGGAGCCAGAACGAATTATTGGAACTACAGACTCTAGTGGAGAACTCATGTTCCTAATGAAATGGAA
GAACTCTGATGAGACTGACCTGGTCCCCACCAAGGAAGCCAATGTCAAGTGCCCACAGGTTGTCATATCCTTCTATGAAG
AAAGGTTGACATGGCATTCCTACCCCTCACAGGATGATGTCAAAAAAAGATGACAATAAT

Alignment

ORF - retro_eeur_396 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.28 %
• Parental protein coverage: 85.41 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DRRVVKGKVEYLLKWKGFSDEDNTWEPEENLDCPDLIAEFLQSQKTAHETDKSEGGKRKADSDSEDKGEE
          D..VVKGKVEYLLKWKGFSDEDNTWEPEENLDCP.LIAE.LQSQKTA.ETDKSEGGK.KADSDSEDKGEE
Retrocopy DCQVVKGKVEYLLKWKGFSDEDNTWEPEENLDCPNLIAELLQSQKTAQETDKSEGGKGKADSDSEDKGEE

Parental  SKPKKKKEESEKPRGFARGLEPERIIGATDSSGELMFLMKWKNSDEADLVPAKEANVKCPQVVISFYEER
          .KP.KKK........FA.GLEPERIIG.TDSSGELMFLMKWKNSDE.DLVP.KEANVKCPQVVISFYEER
Retrocopy NKP-KKKSQ----KSFAQGLEPERIIGTTDSSGELMFLMKWKNSDETDLVPTKEANVKCPQVVISFYEER

Parental  LTWHSYLSEDD-DKKDDKN
          LTWHSY.S.DD..KKDD.N
Retrocopy LTWHSYPSQDD>SKKDDNN

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	0.48 RPM	21.75 RPM
SRP017611_kidney	0.75 RPM	30.94 RPM
SRP017611_liver	0.00 RPM	7.72 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_396 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 17 parental genes, and 51 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004890	2 retrocopies	retro_amel_1228, retro_amel_54,
Bos taurus	ENSBTAG00000002949	9 retrocopies	retro_btau_1121, retro_btau_1394, retro_btau_148, retro_btau_1583, retro_btau_1615, retro_btau_550, retro_btau_558, retro_btau_714, retro_btau_807,
Callithrix jacchus	ENSCJAG00000007532	2 retrocopies	retro_cjac_191, retro_cjac_51,
Dipodomys ordii	ENSDORG00000000716	2 retrocopies	retro_dord_594, retro_dord_709,
Erinaceus europaeus	ENSEEUG00000004874	3 retrocopies	retro_eeur_121, retro_eeur_228, retro_eeur_396 ,
Echinops telfairi	ENSETEG00000000203	7 retrocopies	retro_etel_1083, retro_etel_1572, retro_etel_1577, retro_etel_1611, retro_etel_2165, retro_etel_382, retro_etel_932,
Felis catus	ENSFCAG00000006056	1 retrocopy	retro_fcat_514,
Myotis lucifugus	ENSMLUG00000005030	2 retrocopies	retro_mluc_1000, retro_mluc_1533,
Mus musculus	ENSMUSG00000018666	1 retrocopy	retro_mmus_3108,
Oryctolagus cuniculus	ENSOCUG00000008021	3 retrocopies	retro_ocun_177, retro_ocun_442, retro_ocun_55,
Otolemur garnettii	ENSOGAG00000005658	9 retrocopies	retro_ogar_1087, retro_ogar_1092, retro_ogar_1322, retro_ogar_2056, retro_ogar_2396, retro_ogar_2443, retro_ogar_2840, retro_ogar_2880, retro_ogar_368,
Ochotona princeps	ENSOPRG00000003699	1 retrocopy	retro_opri_552,
Pongo abelii	ENSPPYG00000008891	1 retrocopy	retro_pabe_78,
Rattus norvegicus	ENSRNOG00000008689	2 retrocopies	retro_rnor_2388, retro_rnor_2841,
Sarcophilus harrisii	ENSSHAG00000008192	1 retrocopy	retro_shar_76,
Ictidomys tridecemlineatus	ENSSTOG00000023986	3 retrocopies	retro_itri_1282, retro_itri_1599, retro_itri_1867,
Tarsius syrichta	ENSTSYG00000004769	2 retrocopies	retro_tsyr_1672, retro_tsyr_467,