RetrogeneDB ID: retro_eeur_612

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_364726:8235..8898(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPLP0
• Ensembl ID: ENSEEUG00000007553
• Aliases: None
• Description: ribosomal protein, large, P0 [Source:HGNC Symbol;Acc:10371]

Sequence

>retro_eeur_612
TATATGTTCGCCAAGGAGGACCTCAGAGAGATCAAGGGTATGCTGCTGGCCAACAAGGTGCTAGCAGCTGACCATGCTGG
TGCCATTGCCCAGGCAAGGTCACTGTGCCAGTTCAGAAGACTGGTCTGGGGCCCAAGAAGAACTCCTTTTTCCAGGTTTG
AGACATCACCATTGAGATATCCAGGGGGCACCACTGAAATCCTGAGTGATATGCAGTAGATTAAGACCAGAGACAAAGTA
GAAAACAACAAAGCCACTCTGCTGACCATCTCCTCCTGTGGGGTTATTATTCAACAGGTGTTTGACAGTGGCAGCATCTA
AAACCCTGAAGAGCTGGGCATCACAGAGAAAGCTCTGCATTCTTGCTTCTTAGAGGCTGTTTCTAATGTTGACAGTGTGT
ACCTGCAGAATGGTTGTCTGACTGTAGCATCTGTGCTTCATTTTATTATCACAGGGTACAAGCAGGTTCTGGTCTTCACT
GTCTAGACTGAGTTCACCTTTGTACTTGTTGAAAAGTTCAAGGCCTTCAGGGCTGATCTATCTGCATTTGTGAATGCTGC
TCTTATAACTGCAGTCACTATTGCTACTCTATCTACTGCTGCCACCCCAGTCAGGGAAGAGTTGGAGGAGTCAGATAAGG
ATATGAGATTTAGTCTCTTGAAC

Alignment

ORF - retro_eeur_612 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.41 %
• Parental protein coverage: 72.47 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FVFTKEDLTEIRDMLLANKVPAAARAGAIA-PCEVTVPAQNTGLGPEKTSFFQALGITTKISR-GTIEIL
          ..F.KEDL.EI..MLLANKV.AA..AGAIA.P..VTVP.Q.TGLGP.K.SFFQ...IT..ISR.GT.EIL
Retrocopy YMFAKEDLREIKGMLLANKVLAADHAGAIA<PGKVTVPVQKTGLGPKKNSFFQV*DITIEISR>GTTEIL

Parental  SDVQLIKTGDKEGASEATLLNMLNISPFSGLILQRVFDNGSIYNPEVLDITEQALLSRFLEXXXXXXXXX
          SD.Q.IKT.DK.....ATLL....IS.....I.Q.VFD.GSI.NPE.L.ITE.AL.S.FLE.........
Retrocopy SDMQ*IKTRDKVENNKATLL---TISSCGVIIQQ-VFDSGSI*NPEELGITEKALHSCFLEAVSNVDSVY

Parental  XXXXXPTVASVPHSIINGYKRVLALSVETEYTFPLAEKVKAFLADPSAFAAAAPVAAAATTAAPAAAAPA
          ......TVASV.H.II.GYK.VL...V.TE.TF.L.EK.KAF.AD.SAF..AA...A........AA.P.
Retrocopy LQNGCLTVASVLHFIITGYKQVLVFTV*TEFTFVLVEKFKAFRADLSAFVNAALITAVTIATLSTAATP-

Parental  KAEVKEESEESDEDMGFGLFD
          ...V.EE.EESD.DM.F.L..
Retrocopy ---VREELEESDKDMRFSLLN

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	196.60 RPM
SRP017611_kidney	0.00 RPM	623.38 RPM
SRP017611_liver	0.00 RPM	502.26 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_612 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 14 parental genes, and 38 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002745	2 retrocopies	retro_chof_1115, retro_chof_2341,
Callithrix jacchus	ENSCJAG00000008677	3 retrocopies	retro_cjac_1693, retro_cjac_2840, retro_cjac_786,
Cavia porcellus	ENSCPOG00000021812	5 retrocopies	retro_cpor_298, retro_cpor_449, retro_cpor_475, retro_cpor_498, retro_cpor_601,
Erinaceus europaeus	ENSEEUG00000007553	1 retrocopy	retro_eeur_612 ,
Gorilla gorilla	ENSGGOG00000026582	5 retrocopies	retro_ggor_1088, retro_ggor_1771, retro_ggor_472, retro_ggor_649, retro_ggor_650,
Macaca mulatta	ENSMMUG00000009157	2 retrocopies	retro_mmul_2245, retro_mmul_939,
Mus musculus	ENSMUSG00000067274	2 retrocopies	retro_mmus_143, retro_mmus_2249,
Oryctolagus cuniculus	ENSOCUG00000005749	2 retrocopies	retro_ocun_293, retro_ocun_376,
Otolemur garnettii	ENSOGAG00000003843	4 retrocopies	retro_ogar_2184, retro_ogar_2294, retro_ogar_556, retro_ogar_713,
Petromyzon marinus	ENSPMAG00000001339	1 retrocopy	retro_pmar_6,
Pongo abelii	ENSPPYG00000005022	5 retrocopies	retro_pabe_2113, retro_pabe_3035, retro_pabe_568, retro_pabe_66, retro_pabe_749,
Rattus norvegicus	ENSRNOG00000001148	3 retrocopies	retro_rnor_1350, retro_rnor_2092, retro_rnor_2970,
Sarcophilus harrisii	ENSSHAG00000001623	2 retrocopies	retro_shar_286, retro_shar_413,
Tupaia belangeri	ENSTBEG00000005498	1 retrocopy	retro_tbel_3323,