RetrogeneDB ID: retro_eeur_39

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: GeneScaffold_2406:50412..50804(+)
• Located in intron of: ENSEEUG00000008977

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL32
• Ensembl ID: ENSEEUG00000011609
• Aliases: None
• Description: ribosomal protein L32 [Source:HGNC Symbol;Acc:10336]

Sequence

>retro_eeur_39
CTCAGACCCCTCGTGAAGCCCAAGATAGTCAAGTAGCGGACCAAGAAGTTCATCTGGCATCAGTCGGACCGCTATGTGAA
GATCAAGAGGAACTGGAGGAATCTCAGGGGCATCGACACGCATGCAGCGCCGCTTCAAGGGGCAGATCCTGATGCCCAGT
ATCGGCTACGGCAGCAGCAGGAAGACCAAGCACATGCTGTCCAGCGGCTCCCGCAAGTTCCTCGTGCACAACGTCAAGGA
GCTGGAGGTGCTGCTCATGTTCAACAAGTCCTACTGCTCAGAGATCGCGCACGTCTCCTCCAAGAACCGCAAAGCCATCG
TGGAACGGGCGGGCCAGCCGGGCCATCAGGATCACCAACCCCAACACCAGGCTGCGCAGCGAGGAGAATGAG

Alignment

ORF - retro_eeur_39 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.07 %
• Parental protein coverage: 97.78 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LRPLVKPKIVKKRTKKFIRHQSDRYVKIKRNSRKPRGIDTRV-RRRFKGQILMPNIGYGSSRKTKHMLPS
          LRPLVKPKIVK.RTKKFI.HQSDRYVKIKRN.R..RGIDT...RR.FKGQILMP.IGYGSSRKTKHML.S
Retrocopy LRPLVKPKIVK*RTKKFIWHQSDRYVKIKRNWRNLRGIDTHA>RR-FKGQILMPSIGYGSSRKTKHMLSS

Parental  GFRKFLVHNVKELEVLLMCNKSYCAEIAHNVSSKNRKAIVERAAQ-LAIRVTNPNARLRSEENE
          G.RKFLVHNVKELEVLLM.NKSYC.EIAH.VSSKNRKAIVERA.Q..AIR.TNPN.RLRSEENE
Retrocopy GSRKFLVHNVKELEVLLMFNKSYCSEIAH-VSSKNRKAIVERAGQ>RAIRITNPNTRLRSEENE

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	63.01 RPM
SRP017611_kidney	1.31 RPM	192.42 RPM
SRP017611_liver	1.13 RPM	132.16 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_39 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 13 parental genes, and 103 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000014763	3 retrocopies	retro_acar_104, retro_acar_125, retro_acar_67,
Ailuropoda melanoleuca	ENSAMEG00000004583	26 retrocopies	retro_amel_1004, retro_amel_1041, retro_amel_1059, retro_amel_112, retro_amel_1274, retro_amel_1284, retro_amel_13, retro_amel_1394, retro_amel_1450, retro_amel_150, retro_amel_1651, retro_amel_168, retro_amel_1766, retro_amel_1827, retro_amel_1897, retro_amel_274, retro_amel_275, retro_amel_44, retro_amel_573, retro_amel_658, retro_amel_71, retro_amel_776, retro_amel_781, retro_amel_871, retro_amel_892, retro_amel_923,
Cavia porcellus	ENSCPOG00000019967	2 retrocopies	retro_cpor_1241, retro_cpor_608,
Dipodomys ordii	ENSDORG00000008426	6 retrocopies	retro_dord_175, retro_dord_251, retro_dord_371, retro_dord_458, retro_dord_522, retro_dord_664,
Equus caballus	ENSECAG00000007201	4 retrocopies	retro_ecab_1115, retro_ecab_26, retro_ecab_369, retro_ecab_698,
Erinaceus europaeus	ENSEEUG00000011609	5 retrocopies	retro_eeur_161, retro_eeur_247, retro_eeur_300, retro_eeur_39 , retro_eeur_576,
Homo sapiens	ENSG00000144713	20 retrocopies	retro_hsap_1013, retro_hsap_1115, retro_hsap_1547, retro_hsap_1789, retro_hsap_1956, retro_hsap_2618, retro_hsap_2821, retro_hsap_2891, retro_hsap_3024, retro_hsap_3450, retro_hsap_3536, retro_hsap_3582, retro_hsap_3726, retro_hsap_3805, retro_hsap_3936, retro_hsap_3982, retro_hsap_4008, retro_hsap_4155, retro_hsap_4677, retro_hsap_814,
Loxodonta africana	ENSLAFG00000032737	1 retrocopy	retro_lafr_14,
Myotis lucifugus	ENSMLUG00000022528	6 retrocopies	retro_mluc_100, retro_mluc_1283, retro_mluc_173, retro_mluc_2224, retro_mluc_2256, retro_mluc_48,
Mus musculus	ENSMUSG00000057841	16 retrocopies	retro_mmus_1132, retro_mmus_1142, retro_mmus_1746, retro_mmus_2010, retro_mmus_2263, retro_mmus_2316, retro_mmus_2341, retro_mmus_2699, retro_mmus_3099, retro_mmus_3378, retro_mmus_3605, retro_mmus_385, retro_mmus_442, retro_mmus_496, retro_mmus_533, retro_mmus_985,
Rattus norvegicus	ENSRNOG00000010746	4 retrocopies	retro_rnor_179, retro_rnor_27, retro_rnor_278, retro_rnor_327,
Sarcophilus harrisii	ENSSHAG00000012782	1 retrocopy	retro_shar_580,
Ictidomys tridecemlineatus	ENSSTOG00000026505	9 retrocopies	retro_itri_1294, retro_itri_1322, retro_itri_1465, retro_itri_1639, retro_itri_1715, retro_itri_1748, retro_itri_370, retro_itri_885, retro_itri_948,