RetrogeneDB ID: retro_eeur_348

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_266809:3999..4346(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSEEUG00000008947
• Aliases: None
• Description: None

Sequence

>retro_eeur_348
TCACAAGTGAGCCAGAACTGCCACCAGGACTCCATCAATCACCAGATTAACCTGGAGCTCTCTGCCTCCTCCATCTACCT
GTTGATGTCTTACTACTTTGACCACCATAATGCGACTCTGAAGAACGTTACCAAATATGTCCTTCACCAATCTTATGAGA
AGAGGATATTCAAGAAACTGATAAAGCAGCAAGAGTAAAAGGATGCCTGAATATTCCTTCATCGTATCAAGAAACCAGAC
TAGGACGACTAGGAGAACAGGCTGGGTGCAGTGAAATGTGCAACACACTTGGAAGAAGTGTGGATCCACCAGTACTGGAA
CTACACAAACAAGCCACTTAGAAAAAC

Alignment

ORF - retro_eeur_348 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.02 %
• Parental protein coverage: 50.85 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SQVRQNYHQDSEAAINRQINLELYASYVYLSMSYYFDRDDVALKNFAKYFLHQSHEEREHAEKLMKLQNQ
          SQV.QN.HQDS...IN.QINLEL.AS..YL.MSYYFD.....LKN..KY.LHQS.E.R....KL.K.Q..
Retrocopy SQVSQNCHQDS---INHQINLELSASSIYLLMSYYFDHHNATLKNVTKYVLHQSYEKRIF-KKLIKQQE*

Parental  RGGRIYLQDIKKPERDDWENGLNAMECALHLE-KTVNQSLLELHKLATEKN
          ....I.L..IKKP..DD.EN.L.A..CA.HLE...V....LELHK.AT.KN
Retrocopy KDA*IFLHRIKKPD*DD*ENRLGAVKCATHLE<RSVDPPVLELHKQAT*KN

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	746.42 RPM
SRP017611_kidney	0.00 RPM	1248.45 RPM
SRP017611_liver	0.00 RPM	1637.98 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_348 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 3 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000008947	8 retrocopies	retro_eeur_236, retro_eeur_268, retro_eeur_313, retro_eeur_348 , retro_eeur_376, retro_eeur_384, retro_eeur_391, retro_eeur_483,
Latimeria chalumnae	ENSLACG00000017426	1 retrocopy	retro_lcha_75,
Tursiops truncatus	ENSTTRG00000010405	18 retrocopies	retro_ttru_1059, retro_ttru_1107, retro_ttru_112, retro_ttru_121, retro_ttru_1395, retro_ttru_1484, retro_ttru_152, retro_ttru_1568, retro_ttru_1680, retro_ttru_1760, retro_ttru_1765, retro_ttru_1829, retro_ttru_1881, retro_ttru_248, retro_ttru_517, retro_ttru_58, retro_ttru_834, retro_ttru_97,