RetrogeneDB ID: retro_eeur_541

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_341569:5949..6447(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PNP
• Ensembl ID: ENSEEUG00000002411
• Aliases: None
• Description: purine nucleoside phosphorylase [Source:HGNC Symbol;Acc:7892]

Sequence

>retro_eeur_541
GGAGGACTTAACCCTAAGTTTGTGGTTGGAGATACATGCTGATCCGTGACCACACTAACCTCCCTGGTTTCTCTGCTCAA
AACCCTCTCAGATGACCCAATGAAGAAATATTTGGAGCTTTGTCTCTTGTCATGCCTGATGCCTATGACTAGGACATAAA
GCTTTTGGCTCGAACCTAGAAACAAATGGAAGATCAACACTGAGAACTCCAAGAAGTCATCTATGTGACACTGGCAGGTC
CCAATTTTGAGACTATGGTGGAGTGTCACCTCTTGAAGCAGCTGGGAGTGCAGAAGCTATTGGCATGAGTACAGTACCAG
AAGTGATAGTGGCAAGGCACTGTGGACCTCGAGTCTTTGGGTGCTCTCTCATCACTAATAAGGCCATCATGGATTATGAC
TCCCTGGAGAAAGCCATCACAAGGAAGTGCTAGAAGCTGAGAAACAGGCTACACAGATGTTGAAAGACTTTATCTCCATT
TTTATGGCAAACATTCCA

Alignment

ORF - retro_eeur_541 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.35 %
• Parental protein coverage: 57.59 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GGLNPKFEVGDI-MLIRDHINLPGFCGQNPLRGPNEERFGVRFPAMSDAYDRDIRLLAHSTWKQMENQHR
          GGLNPKF.VGD..MLIRDH.NLPGF..QNPLR.PNEE.FG.....M.DAYD.DI.LLA..T.KQME.QH.
Retrocopy GGLNPKFVVGDT<MLIRDHTNLPGFSAQNPLR*PNEEIFGALSLVMPDAYD*DIKLLAR-T*KQMEDQH*

Parental  ELQEGTYVMLAGPNFETVAESRL-LKQLG-ADAVGMSTVPEVIVARHCGLRVFGFSLITNKVIMDYDSIE
          ELQE..YV.LAGPNFET..E..L.L...G.A.A.GMSTVPEVIVARHCG.RVFG.SLITNK.IMDYDS.E
Retrocopy ELQEVIYVTLAGPNFETMVECHL<LEAAGSAEAIGMSTVPEVIVARHCGPRVFGCSLITNKAIMDYDSLE

Parental  KA-NHEEVLEAGKQAAQKLEEFISILMENIP
          KA..H.EVLEA.KQA.Q.L..FISI.M.NIP
Retrocopy KA<HHKEVLEAEKQATQMLKDFISIFMANIP

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	40.45 RPM
SRP017611_kidney	0.00 RPM	125.46 RPM
SRP017611_liver	0.00 RPM	16.24 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_541 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 20 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005373	1 retrocopy	retro_amel_1666,
Bos taurus	ENSBTAG00000012317	1 retrocopy	retro_btau_1463,
Choloepus hoffmanni	ENSCHOG00000009274	5 retrocopies	retro_chof_1328, retro_chof_1595, retro_chof_1827, retro_chof_1933, retro_chof_348,
Callithrix jacchus	ENSCJAG00000009676	2 retrocopies	retro_cjac_1195, retro_cjac_1511,
Dasypus novemcinctus	ENSDNOG00000011630	1 retrocopy	retro_dnov_322,
Erinaceus europaeus	ENSEEUG00000002411	1 retrocopy	retro_eeur_541 ,
Felis catus	ENSFCAG00000006934	1 retrocopy	retro_fcat_1368,
Homo sapiens	ENSG00000198805	1 retrocopy	retro_hsap_2282,
Gorilla gorilla	ENSGGOG00000002126	1 retrocopy	retro_ggor_1695,
Macropus eugenii	ENSMEUG00000014512	3 retrocopies	retro_meug_1282, retro_meug_1560, retro_meug_211,
Macaca mulatta	ENSMMUG00000019126	1 retrocopy	retro_mmul_287,
Mustela putorius furo	ENSMPUG00000018119	2 retrocopies	retro_mputfur_420, retro_mputfur_822,
Nomascus leucogenys	ENSNLEG00000010969	1 retrocopy	retro_nleu_1964,
Otolemur garnettii	ENSOGAG00000013344	4 retrocopies	retro_ogar_1631, retro_ogar_2141, retro_ogar_3083, retro_ogar_594,
Pongo abelii	ENSPPYG00000005567	1 retrocopy	retro_pabe_1938,
Pan troglodytes	ENSPTRG00000006095	1 retrocopy	retro_ptro_1616,
Pteropus vampyrus	ENSPVAG00000010734	1 retrocopy	retro_pvam_1302,
Rattus norvegicus	ENSRNOG00000009982	1 retrocopy	retro_rnor_891,
Tupaia belangeri	ENSTBEG00000016378	1 retrocopy	retro_tbel_4632,
Tarsius syrichta	ENSTSYG00000000748	3 retrocopies	retro_tsyr_2057, retro_tsyr_2127, retro_tsyr_235,