RetrogeneDB ID: retro_eeur_473

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_318563:3948..4403(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSEEUG00000001898
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPS18
• Ensembl ID: ENSEEUG00000010297
• Aliases: None
• Description: ribosomal protein S18 [Source:HGNC Symbol;Acc:10401]

Sequence

>retro_eeur_473
ATGTCTCTAGTGATTCCTGAGACGTTCCAGCACATTTTGCGAGTCCTCAACACCAACATGGATGGGCATCGGAAAATAGC
CTTTGCCATTACTGCAGTTAAGGGTGTGGGGTGAAGATATGCTCATGTGGTGTTGCGGAAAGCTGACATTGACTTGACCA
AGAGGGCAGGAGAAATCACTGAGGATGAGGTGGAACGTGTGATCACTATTATGCAGAATCCATGCCAATACAAGTTACCT
GACTGGTTTTTGAACAGACAGAAGGATGCGAAGGATGGAAGATACAGTCAGGTACTGGCTAATGGTTTGGACAAAAAGCT
CCATGAAGATCTGGAGCAGCTGAAGAAGATTTGGGTCCTCAGAGGGCTGCAACACTTTTGGGGACTCCGAGTCCGTGGCC
AACAACCAAGACCATAGGATGCCGTGGCCACACCACAGGTGTGTCCAGGAAGAAA

Alignment

ORF - retro_eeur_473 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.31 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSLVIPEKFQHILRVLNTNIDGRRKIAFAITAIKGVGRRYAHVVLRKADIDLTKRAGELTEDEVERVITI
          MSLVIPE.FQHILRVLNTN.DG.RKIAFAITA.KGVG.RYAHVVLRKADIDLTKRAGE.TEDEVERVITI
Retrocopy MSLVIPETFQHILRVLNTNMDGHRKIAFAITAVKGVG*RYAHVVLRKADIDLTKRAGEITEDEVERVITI

Parental  MQNPRQYKIPDWFLNRQKDVKDGKYSQVLANGLDNKLREDLERLKKIRAHRGLRHFWGLRVRGQH-TKTT
          MQNP.QYK.PDWFLNRQKD.KDG.YSQVLANGLD.KL.EDLE.LKKI...RGL.HFWGLRVRGQ..TKT.
Retrocopy MQNPCQYKLPDWFLNRQKDAKDGRYSQVLANGLDKKLHEDLEQLKKIWVLRGLQHFWGLRVRGQQ<TKTI

Parental  GRRGRTVGVSKKK
          G.RG.T.GVS.KK
Retrocopy GCRGHTTGVSRKK

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	142.77 RPM
SRP017611_kidney	0.19 RPM	346.38 RPM
SRP017611_liver	0.00 RPM	299.53 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_473 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 134 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002648	2 retrocopies	retro_btau_1052, retro_btau_614,
Callithrix jacchus	ENSCJAG00000021650	5 retrocopies	retro_cjac_22, retro_cjac_245, retro_cjac_2529, retro_cjac_2893, retro_cjac_2955,
Dasypus novemcinctus	ENSDNOG00000012084	13 retrocopies	retro_dnov_1295, retro_dnov_1398, retro_dnov_1448, retro_dnov_1675, retro_dnov_1770, retro_dnov_2008, retro_dnov_2115, retro_dnov_2223, retro_dnov_2288, retro_dnov_327, retro_dnov_363, retro_dnov_384, retro_dnov_399,
Erinaceus europaeus	ENSEEUG00000010297	8 retrocopies	retro_eeur_201, retro_eeur_261, retro_eeur_380, retro_eeur_460, retro_eeur_473 , retro_eeur_498, retro_eeur_667, retro_eeur_689,
Homo sapiens	ENSG00000231500	2 retrocopies	retro_hsap_1806, retro_hsap_1974,
Gorilla gorilla	ENSGGOG00000006571	5 retrocopies	retro_ggor_1496, retro_ggor_2310, retro_ggor_344, retro_ggor_77, retro_ggor_93,
Loxodonta africana	ENSLAFG00000032173	1 retrocopy	retro_lafr_1171,
Macropus eugenii	ENSMEUG00000016770	11 retrocopies	retro_meug_1296, retro_meug_1737, retro_meug_1807, retro_meug_1946, retro_meug_212, retro_meug_310, retro_meug_344, retro_meug_387, retro_meug_566, retro_meug_625, retro_meug_627,
Myotis lucifugus	ENSMLUG00000007360	2 retrocopies	retro_mluc_181, retro_mluc_932,
Macaca mulatta	ENSMMUG00000003867	1 retrocopy	retro_mmul_2198,
Oryctolagus cuniculus	ENSOCUG00000010546	1 retrocopy	retro_ocun_31,
Otolemur garnettii	ENSOGAG00000006225	7 retrocopies	retro_ogar_1498, retro_ogar_1832, retro_ogar_2372, retro_ogar_472, retro_ogar_608, retro_ogar_709, retro_ogar_905,
Pongo abelii	ENSPPYG00000025953	14 retrocopies	retro_pabe_1138, retro_pabe_128, retro_pabe_1481, retro_pabe_1482, retro_pabe_1813, retro_pabe_1881, retro_pabe_2303, retro_pabe_2407, retro_pabe_2663, retro_pabe_2833, retro_pabe_2967, retro_pabe_3013, retro_pabe_3070, retro_pabe_368,
Pan troglodytes	ENSPTRG00000018039	1 retrocopy	retro_ptro_121,
Pteropus vampyrus	ENSPVAG00000001902	6 retrocopies	retro_pvam_295, retro_pvam_556, retro_pvam_691, retro_pvam_708, retro_pvam_829, retro_pvam_875,
Rattus norvegicus	ENSRNOG00000028505	4 retrocopies	retro_rnor_102, retro_rnor_234, retro_rnor_29, retro_rnor_70,
Sarcophilus harrisii	ENSSHAG00000006857	2 retrocopies	retro_shar_265, retro_shar_563,
Sarcophilus harrisii	ENSSHAG00000008658	1 retrocopy	retro_shar_618,
Sus scrofa	ENSSSCG00000001502	5 retrocopies	retro_sscr_112, retro_sscr_156, retro_sscr_157, retro_sscr_2, retro_sscr_831,
Tupaia belangeri	ENSTBEG00000012708	40 retrocopies	retro_tbel_1070, retro_tbel_1739, retro_tbel_1745, retro_tbel_1806, retro_tbel_1818, retro_tbel_1827, retro_tbel_1855, retro_tbel_205, retro_tbel_2087, retro_tbel_211, retro_tbel_2299, retro_tbel_2309, retro_tbel_2312, retro_tbel_234, retro_tbel_2364, retro_tbel_2424, retro_tbel_2473, retro_tbel_250, retro_tbel_2682, retro_tbel_2768, retro_tbel_295, retro_tbel_3189, retro_tbel_3317, retro_tbel_3383, retro_tbel_3625, retro_tbel_363, retro_tbel_3686, retro_tbel_3731, retro_tbel_3870, retro_tbel_4100, retro_tbel_4215, retro_tbel_4365, retro_tbel_45, retro_tbel_4562, retro_tbel_4578, retro_tbel_462, retro_tbel_57, retro_tbel_578, retro_tbel_856, retro_tbel_941,
Tursiops truncatus	ENSTTRG00000004302	3 retrocopies	retro_ttru_1012, retro_ttru_1553, retro_ttru_837,