RetrogeneDB ID: retro_eeur_47

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: GeneScaffold_2612:179810..180381(+)
• Located in intron of: ENSEEUG00000009989

Retrocopy information

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

Parental gene information

• Parental gene symbol: AP2M1
• Ensembl ID: ENSEEUG00000006073
• Aliases: None
• Description: adaptor-related protein complex 2, mu 1 subunit [Source:HGNC Symbol;Acc:564]

Sequence

>retro_eeur_47
ATGAAGAGCTACCTGAGCGGCATGCCTGAGTGCAAGTTTGGGATGAATGACAAGATCGTCATCGAGAAGCAGGGCAAAGG
CACCGCCGACGAAACAAGCAAGAGTGGGAAGCAGTCTATCGCCATCGACGACTGCACCTTCCACCAGTGCGTGCGGCTCA
GCAAGTTCGACTCGGAGCGCAGCATCAGCTTCATCCCACCAGATGGCGAGTTTGAGCTCATGAGGTACCGCACCACCAAG
GACATCATCCTGCCTTTTTCGCGTGATCCCGCTGGTGCGTGAGGTGGGCCGGACCAAGCTGGAGGTCAAGGTGGTCATCA
AGTCCAACTTTAAGCCCTCACTGCTGGCTCAGAAGATCGAGGTGAGGATCCCCACCCCACTCAACACTAGCGGGGTACAG
GTGATCTGCATGAAGGGGAAGGCCAAGTACAAGGCCAGTGAGAACGCCATCGTGTGGAAGATCAAGCGCATGGCTGGCAT
GAAGGAATCACAGATCAGCGCGGAGATTGAGCTGCTGCCCACCAACGACAAGAAGAAATGGGCTCGGCCCCCCATTTCCA
TGAACTTTGAG

Alignment

ORF - retro_eeur_47 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.81 %
• Parental protein coverage: 68.48 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IKSYLSG-PESKFGMNDKILIEKLGKATADETSKIGKQSIAIDDCTFHQCVRLSKFDSERSISFIPPDGE
          .KSYLSG.PE.KFGMNDKI.IEK.GK.TADETSK.GKQSIAIDDCTFHQCVRLSKFDSERSISFIPPDGE
Retrocopy MKSYLSGMPECKFGMNDKIVIEKQGKGTADETSKSGKQSIAIDDCTFHQCVRLSKFDSERSISFIPPDGE

Parental  FELMRYRTTKDIILP-FRVIPLVREVGRTKLEVKVVIKSNFKPSLLAQKIEVRIPTPLNTSGVQVICMKG
          FELMRYRTTKDIILP.FRVIPLVREVGRTKLEVKVVIKSNFKPSLLAQKIEVRIPTPLNTSGVQVICMKG
Retrocopy FELMRYRTTKDIILP>FRVIPLVREVGRTKLEVKVVIKSNFKPSLLAQKIEVRIPTPLNTSGVQVICMKG

Parental  KAKYKASENAIVWKIKRMAGMKESQISAEIELLPTNDKKKWARPPISMNFE
          KAKYKASENAIVWKIKRMAGMKESQISAEIELLPTNDKKKWARPPISMNFE
Retrocopy KAKYKASENAIVWKIKRMAGMKESQISAEIELLPTNDKKKWARPPISMNFE

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	120.54 RPM	94.59 RPM
SRP017611_kidney	91.71 RPM	76.14 RPM
SRP017611_liver	31.51 RPM	27.17 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_47 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012998	1 retrocopy	retro_cjac_3340,
Erinaceus europaeus	ENSEEUG00000006073	1 retrocopy	retro_eeur_47 ,
Echinops telfairi	ENSETEG00000004759	1 retrocopy	retro_etel_2124,
Macropus eugenii	ENSMEUG00000002558	1 retrocopy	retro_meug_43,
Oryctolagus cuniculus	ENSOCUG00000004556	1 retrocopy	retro_ocun_98,
Tarsius syrichta	ENSTSYG00000006101	1 retrocopy	retro_tsyr_1873,