RetrogeneDB ID: retro_eeur_239

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_219334:1211..1508(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DPY30
• Ensembl ID: ENSEEUG00000012471
• Aliases: None
• Description: dpy-30 homolog (C. elegans) [Source:HGNC Symbol;Acc:24590]

Sequence

>retro_eeur_239
ATGGAGCCAGAGCAGATTCTGGAGGGGCAGACACAGGTCGCCAAGAACCCCTATACCAAGTACGGGCTCACCAACAATGT
GGAAAGGATAGTAGAAAATGAGACGATTAATGCAGAAAAGTCATCAAAACAGAAGGTGGATCTCCACTCTCTGCCAACTC
ATGCCTACCTGGATCAGACAGTTGTGCTTATCTTATTACAGGGGCTCGCTATGCTGGCAAAGGAAAGACCACCAAATCCC
ATTGAGTTTTTAGCATCATATCTTTTAAAATACAAGGCACAGTTTGAAGATCGAAAC

Alignment

ORF - retro_eeur_239 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.87 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEPEPMLEGQTQVAENPHAEYGLTDNVERIVENEKINAEKSSKQKVDLQSLPTRAYLDQTVVPILLQGLA
          MEPE..LEGQTQVA.NP...YGLT.NVERIVENE.INAEKSSKQKVDL.SLPT.AYLDQTVV.ILLQGLA
Retrocopy MEPEQILEGQTQVAKNPYTKYGLTNNVERIVENETINAEKSSKQKVDLHSLPTHAYLDQTVVLILLQGLA

Parental  VLAKERPPNPIEFLASYLLKNKAQFEDRN
          .LAKERPPNPIEFLASYLLK.KAQFEDRN
Retrocopy MLAKERPPNPIEFLASYLLKYKAQFEDRN

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	2.09 RPM	19.02 RPM
SRP017611_kidney	2.63 RPM	55.14 RPM
SRP017611_liver	2.89 RPM	35.05 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_239 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 19 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007768	1 retrocopy	retro_amel_89,
Canis familiaris	ENSCAFG00000005708	1 retrocopy	retro_cfam_1794,
Equus caballus	ENSECAG00000019630	1 retrocopy	retro_ecab_676,
Erinaceus europaeus	ENSEEUG00000012471	1 retrocopy	retro_eeur_239 ,
Echinops telfairi	ENSETEG00000006389	4 retrocopies	retro_etel_1156, retro_etel_1592, retro_etel_1796, retro_etel_682,
Felis catus	ENSFCAG00000026246	1 retrocopy	retro_fcat_1883,
Macropus eugenii	ENSMEUG00000006193	1 retrocopy	retro_meug_335,
Myotis lucifugus	ENSMLUG00000015346	2 retrocopies	retro_mluc_2327, retro_mluc_2367,
Monodelphis domestica	ENSMODG00000015481	1 retrocopy	retro_mdom_1962,
Mustela putorius furo	ENSMPUG00000005211	1 retrocopy	retro_mputfur_1063,
Mus musculus	ENSMUSG00000024067	1 retrocopy	retro_mmus_1867,
Oryctolagus cuniculus	ENSOCUG00000017877	1 retrocopy	retro_ocun_1751,
Otolemur garnettii	ENSOGAG00000034197	2 retrocopies	retro_ogar_3326, retro_ogar_3420,
Ochotona princeps	ENSOPRG00000011833	1 retrocopy	retro_opri_890,
Pteropus vampyrus	ENSPVAG00000005599	1 retrocopy	retro_pvam_1128,
Rattus norvegicus	ENSRNOG00000027126	1 retrocopy	retro_rnor_2141,
Ictidomys tridecemlineatus	ENSSTOG00000013372	2 retrocopies	retro_itri_361, retro_itri_75,
Tupaia belangeri	ENSTBEG00000017486	5 retrocopies	retro_tbel_1154, retro_tbel_1311, retro_tbel_1312, retro_tbel_3073, retro_tbel_4675,
Tarsius syrichta	ENSTSYG00000000146	1 retrocopy	retro_tsyr_1052,