RetrogeneDB ID: retro_eeur_16

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: GeneScaffold_7890:11211..11673(-)
• Located in intron of: ENSEEUG00000003960

Retrocopy information

• Ensembl ID: ENSEEUG00000003978
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSEEUG00000015224
• Aliases: None
• Description: None

Sequence

>retro_eeur_16
ATGAATGTGGGGGTGGCACACAGTGAAGTAAACCCCAACACTCGAGTGATGAACAGCCGGGGCATCTGGCTGGCCTATGT
CATCTTGGTGGGACTGCTGCACATGATCCTACTCAGCATCTCCTTCATCAGCATTCCTGTTGTCTGGACCCTGACCAACG
TCATACATAACTTGGCTATGTATGTTTTCCTACATACGGTGAAAGGGACACCCTTTGAGACCCCTGACCAAGGAAAATCT
CGGCTACTGACACACTGGGAACAGATGGACTATGGGATCCAATTTACTTCTTCACGCAAATTCCTCAGCATTTTTCCTAT
TGTGCTCTACATCCTGGCCAGCTTCTACACCAAGTACAATGCTGCTCACTTCTTCATCAACACAGCTTCATTGCTCAGTG
TACTGCTACCTAAGTTGCCCCAATTTCATGGGGTTCGTGTTTTTGGCATCAACAAATACTAA

Alignment

ORF - retro_eeur_16 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.08 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNVGVAHSEV-PNTRVMNSRGIWLAYVILVGLLHVILLSIPFISIPVVWTLTNVIHNLAMYVFLHTVKGT
          MNVGVAHSEV.PNTRVMNSRGIWLAYVILVGLLH.ILLSI.FISIPVVWTLTNVIHNLAMYVFLHTVKGT
Retrocopy MNVGVAHSEVNPNTRVMNSRGIWLAYVILVGLLHMILLSISFISIPVVWTLTNVIHNLAMYVFLHTVKGT

Parental  PFETPDQGKSRLLTHWEQMDYGLQFTSSRKFLSISPIVLYILASFYTKYDAAHFFINTASLLSVLLPKLP
          PFETPDQGKSRLLTHWEQMDYG.QFTSSRKFLSI.PIVLYILASFYTKY.AAHFFINTASLLSVLLPKLP
Retrocopy PFETPDQGKSRLLTHWEQMDYGIQFTSSRKFLSIFPIVLYILASFYTKYNAAHFFINTASLLSVLLPKLP

Parental  QFHGVRVFGINKY
          QFHGVRVFGINKY
Retrocopy QFHGVRVFGINKY

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	1.93 RPM
SRP017611_kidney	0.75 RPM	6.19 RPM
SRP017611_liver	0.32 RPM	5.14 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_16 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 12 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003047	2 retrocopies	retro_amel_140, retro_amel_735,
Canis familiaris	ENSCAFG00000000071	8 retrocopies	retro_cfam_1078, retro_cfam_1248, retro_cfam_1512, retro_cfam_1786, retro_cfam_187, retro_cfam_335, retro_cfam_576, retro_cfam_972,
Choloepus hoffmanni	ENSCHOG00000009601	1 retrocopy	retro_chof_2232,
Erinaceus europaeus	ENSEEUG00000015224	1 retrocopy	retro_eeur_16 ,
Felis catus	ENSFCAG00000013964	1 retrocopy	retro_fcat_895,
Macropus eugenii	ENSMEUG00000014896	1 retrocopy	retro_meug_767,
Microcebus murinus	ENSMICG00000010920	1 retrocopy	retro_mmur_212,
Myotis lucifugus	ENSMLUG00000003575	1 retrocopy	retro_mluc_901,
Macaca mulatta	ENSMMUG00000006292	1 retrocopy	retro_mmul_2358,
Mustela putorius furo	ENSMPUG00000000911	2 retrocopies	retro_mputfur_452, retro_mputfur_738,
Mus musculus	ENSMUSG00000025353	1 retrocopy	retro_mmus_2646,
Otolemur garnettii	ENSOGAG00000001695	2 retrocopies	retro_ogar_3016, retro_ogar_951,