RetrogeneDB ID: retro_eeur_1

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_318910:381..996(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSEEUG00000000869
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSEEUG00000001325
• Aliases: None
• Description: None

Sequence

>retro_eeur_1
ATGATGACGGAGACCTTCGTGAAGGATATCAAGCACGGGCTCAAAAATCTGAACCTCATCTTTATTGTGCTGGAGACAGG
CCGAGTCACCAAGACAAAGGATGGGCATGAGGTTAGAACTTGTAAAGTGGCAGACAAAACACGCAGCATCAATATCTCTG
TCTGGGATGATGTGGGCAACCTGATCCAACCTGGGGATATTATCCGACTAACCAAAGGCTATGCATCAGTGTTCAAAGGC
TGTCTGACATTGTACACTGGTCGTGGAGGTGACCTTCAAAAGATTGGCGAATTCTGTATGGTTTATTCTGAAGTTCCTAA
CTTCAGTGAGCCAAACCCAGAGTACAACGCTCAGCAGCCACCCAACAAGACGGTGCAGAGTGACAGCAGCCCTACAGCTC
CCCAGCCACCTGCGGGTTCCCCTGCTACTCCTCCAGTTTCTGAGAACCAGAATGGGAATGGACTGAGTGTTCCACCAGGT
GCTGGTGGTGGCTCACACCCTGCTCACACTCCTTCCCACCCTCCCATCACCCGAATTACTAGGAGCCAGCCCAACCACAC
AGCCTCTGGCCCTCCTGGCCCTTCCAGCAACCCTGTCAGTAACTGCAAAGAAACC

Alignment

ORF - retro_eeur_1 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.96 %
• Parental protein coverage: 93.63 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MTTETFVKDIKPGLKNLNLIFIVLETGRVTKTKDGHEVRTCKVADKTGSINISVWDDVGNLIQPGDIIRL
          M.TETFVKDIK.GLKNLNLIFIVLETGRVTKTKDGHEVRTCKVADKT.SINISVWDDVGNLIQPGDIIRL
Retrocopy MMTETFVKDIKHGLKNLNLIFIVLETGRVTKTKDGHEVRTCKVADKTRSINISVWDDVGNLIQPGDIIRL

Parental  TKGYASVFKGCLTLYTGRGGDLQKIGEFCMVYSEVPNFSEPNPEYSAQQPPNKTVQSDSSPTAPQPPAGS
          TKGYASVFKGCLTLYTGRGGDLQKIGEFCMVYSEVPNFSEPNPEY.AQQPPNKTVQSDSSPTAPQPPAGS
Retrocopy TKGYASVFKGCLTLYTGRGGDLQKIGEFCMVYSEVPNFSEPNPEYNAQQPPNKTVQSDSSPTAPQPPAGS

Parental  PATPPASENQNGNGLSAPPGAGGGSHPAHTRVTRSQPNHTATGPPGPSSNP
          PATPP.SENQNGNGLS.PPGAGGGSHPAHT.........T...P....S.P
Retrocopy PATPPVSENQNGNGLSVPPGAGGGSHPAHTPSHPPITRITRSQPNHTASGP

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	5.48 RPM	21.59 RPM
SRP017611_kidney	6.75 RPM	32.26 RPM
SRP017611_liver	0.48 RPM	10.93 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_1 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 8 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002798	1 retrocopy	retro_btau_545,
Callithrix jacchus	ENSCJAG00000011455	1 retrocopy	retro_cjac_1961,
Dasypus novemcinctus	ENSDNOG00000013517	1 retrocopy	retro_dnov_1189,
Erinaceus europaeus	ENSEEUG00000001325	1 retrocopy	retro_eeur_1 ,
Gorilla gorilla	ENSGGOG00000009050	1 retrocopy	retro_ggor_2094,
Macropus eugenii	ENSMEUG00000004485	4 retrocopies	retro_meug_1118, retro_meug_123, retro_meug_1835, retro_meug_540,
Mustela putorius furo	ENSMPUG00000001297	1 retrocopy	retro_mputfur_59,
Sarcophilus harrisii	ENSSHAG00000002240	1 retrocopy	retro_shar_493,