RetrogeneDB ID: retro_eeur_270

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_232119:7768..8353(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EXOSC1
• Ensembl ID: ENSEEUG00000005647
• Aliases: None
• Description: exosome component 1 [Source:HGNC Symbol;Acc:17286]

Sequence

>retro_eeur_270
ATGGCGCCACCCATGAGGTACTACATCCCCGGAGAACATCTGTGTAACTTGGAGGAAGGGAGCCCGGGCAGCGGCACCTA
CACCCGGCATGGTTACATCTTTTCCTCACTTGCTGGTTGCCTGACCAAAAGCAGCGAGAATGGCGCGCTTCCCATTGTGT
CTGTCACAAGAGAAACAGAGTCCCAATTACTGCCAGATGTGGGGGCTATAGTAACCTGTAAGGTCTCTAGCATCAATTCA
CGATTTGCCAAAGTACACATCCTCTATGTGGGGTCCACACCACTTAAGAACTCTTTTCGAGGAACTATCCGCAAGGAAGA
TGTTCGAGCCACTGAAAAAGACAAGGTTGAAATTTATAAGAGTTTCCGCCCAGGTGACATTGTCTTGGCCAAAGTGATTT
CCCTAGGTGATGCACAGTCCAATTACCTCCTGACCACTGCCGAAAATGAGCTGGGGGTAGTGGTGGCCCACAGTGAGTCA
GGTGTCCAGATGGTTCCCATCAGCTGGTGTGAGATGCAGTGCCCTAAAACCCACACTAAAGAATTTCGGAAAGTTGCCCT
GGTGTAGCCTGAGTTCTTGCAGACC

Alignment

ORF - retro_eeur_270 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.92 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAPPVRYCIPGERLCNLEEGSPGSGTYTRHGYIFSSLAGCLTKSSENGALPIVSVTRETESQLLPDVGAI
          MAPP.RY.IPGE.LCNLEEGSPGSGTYTRHGYIFSSLAGCLTKSSENGALPIVSVTRETESQLLPDVGAI
Retrocopy MAPPMRYYIPGEHLCNLEEGSPGSGTYTRHGYIFSSLAGCLTKSSENGALPIVSVTRETESQLLPDVGAI

Parental  VTCKVSSINSRFAKVHILYVGSTPLKNSFRGTIRKEDVRATEKDKVEIYKSFRPGDIVLAKVISLGDAQS
          VTCKVSSINSRFAKVHILYVGSTPLKNSFRGTIRKEDVRATEKDKVEIYKSFRPGDIVLAKVISLGDAQS
Retrocopy VTCKVSSINSRFAKVHILYVGSTPLKNSFRGTIRKEDVRATEKDKVEIYKSFRPGDIVLAKVISLGDAQS

Parental  NYLLTTAENELGVVVAHSESGVQMDPISWCEMQCPKTHTKEFRKVARVQPEFLQT
          NYLLTTAENELGVVVAHSESGVQM.PISWCEMQCPKTHTKEFRKVA.V.PEFLQT
Retrocopy NYLLTTAENELGVVVAHSESGVQMVPISWCEMQCPKTHTKEFRKVALV*PEFLQT

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	1.77 RPM	4.03 RPM
SRP017611_kidney	2.44 RPM	9.94 RPM
SRP017611_liver	1.45 RPM	5.95 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_270 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 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006477	1 retrocopy	retro_chof_2075,
Dasypus novemcinctus	ENSDNOG00000007983	1 retrocopy	retro_dnov_104,
Erinaceus europaeus	ENSEEUG00000005647	3 retrocopies	retro_eeur_270 , retro_eeur_438, retro_eeur_464,
Macropus eugenii	ENSMEUG00000002246	2 retrocopies	retro_meug_1799, retro_meug_951,
Myotis lucifugus	ENSMLUG00000009228	1 retrocopy	retro_mluc_1563,
Mus musculus	ENSMUSG00000034321	1 retrocopy	retro_mmus_691,
Oryctolagus cuniculus	ENSOCUG00000011898	1 retrocopy	retro_ocun_173,
Otolemur garnettii	ENSOGAG00000016259	1 retrocopy	retro_ogar_2496,
Pteropus vampyrus	ENSPVAG00000003372	1 retrocopy	retro_pvam_686,
Rattus norvegicus	ENSRNOG00000048708	1 retrocopy	retro_rnor_899,
Ictidomys tridecemlineatus	ENSSTOG00000006615	1 retrocopy	retro_itri_1253,