RetrogeneDB ID: retro_eeur_17

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_292849:624..1308(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSEEUG00000014950
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSEEUG00000001097
• Aliases: None
• Description: None

Sequence

>retro_eeur_17
GTTGCCTATGATGAAGCTACAAATGAATTTGCTTCTTACTTCAACAGAAAGACTTCTCCCAAGATTCTTATCACAACATC
AGACAGACCTCGCGGGAGAACTGTAAGGCTTTGTAATCAGCTCTCCACAGTCATACCGAACTCACATGTTTATTATCGAA
GAGGACTGGCTCTCAAGAAAATTATTCCACAGTGCATCTCAAGAGATTTCACAGATCTGATTGTTATTAATGAAGATCGT
AAAACACCAAATGGATTAATTTTGAGTCACTTACCAAATGGCCCAACTGCTCATTTTAAGATGAGCAGTGTCTGTCTGAG
TAAAGAGATGAAGAGGAGAGGCGAGGATCCCACAGAACACATACCTGAAATCATTCTGAATAATTTTACAACACGGTTTG
GTCATTCTGTTGGTCATATGTTTGCATCCCTATTTCCCCAGAACCCTCAGTTTATTGGAAGGCAGGTTGCTACGTTCCAC
AATCAGCGTGATTATATCTTCTTCAGATTTCACAGATATATATTCAGGAGCGAGAAGAAAGTGGGAATTCAAGAACTTGG
ACCACGTTTCACCTTAAAATTAAGATCTCTTCAGAAAGGGACCTTTGATTCTAAATACGGAGAATATGAATGGGTCCATA
AGCCTCGAGAAATGGATACAAGTAGAAGGAAATTCCACTTGTGA

Alignment

ORF - retro_eeur_17 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.59 %
• Parental protein coverage: 65.04 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VAYDEATDEFASYFNRETSPKILITTSDRPHGRTVRLCNQLSTVIPNSHVYYRRGLALKKIIPQCISRDF
          VAYDEAT.EFASYFNR.TSPKILITTSDRP.GRTVRLCNQLSTVIPNSHVYYRRGLALKKIIPQCISRDF
Retrocopy VAYDEATNEFASYFNRKTSPKILITTSDRPRGRTVRLCNQLSTVIPNSHVYYRRGLALKKIIPQCISRDF

Parental  TDLIVINEDRKTPNGLILSHLPNGPTAHFKMSSVRLRKEIKRRGKDPTEHIPEIILNNFTTRLGHSVGRM
          TDLIVINEDRKTPNGLILSHLPNGPTAHFKMSSV.L.KE.KRRG.DPTEHIPEIILNNFTTR.GHSVG.M
Retrocopy TDLIVINEDRKTPNGLILSHLPNGPTAHFKMSSVCLSKEMKRRGEDPTEHIPEIILNNFTTRFGHSVGHM

Parental  FASLFPHNPQFIGRQVATFHNQRDYIFFRFHRYIFRSEKKVGIQELGPRFTLKLRSLQKGTFDSKYGEYE
          FASLFP.NPQFIGRQVATFHNQRDYIFFRFHRYIFRSEKKVGIQELGPRFTLKLRSLQKGTFDSKYGEYE
Retrocopy FASLFPQNPQFIGRQVATFHNQRDYIFFRFHRYIFRSEKKVGIQELGPRFTLKLRSLQKGTFDSKYGEYE

Parental  WVHKPREMDTSRRKFHL
          WVHKPREMDTSRRKFHL
Retrocopy WVHKPREMDTSRRKFHL

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	0.81 RPM	6.77 RPM
SRP017611_kidney	1.69 RPM	9.75 RPM
SRP017611_liver	2.73 RPM	13.99 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_17 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 7 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000001097	1 retrocopy	retro_eeur_17 ,
Myotis lucifugus	ENSMLUG00000016028	2 retrocopies	retro_mluc_681, retro_mluc_942,
Mus musculus	ENSMUSG00000028187	1 retrocopy	retro_mmus_3026,
Oryctolagus cuniculus	ENSOCUG00000014803	1 retrocopy	retro_ocun_1133,
Pteropus vampyrus	ENSPVAG00000003729	1 retrocopy	retro_pvam_1489,
Rattus norvegicus	ENSRNOG00000015969	1 retrocopy	retro_rnor_1372,
Tupaia belangeri	ENSTBEG00000013600	4 retrocopies	retro_tbel_1027, retro_tbel_2204, retro_tbel_2279, retro_tbel_63,