RetrogeneDB ID: retro_eeur_21

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_334819:4229..5906(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSEEUG00000004133
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSEEUG00000014393
• Aliases: None
• Description: None

Sequence

>retro_eeur_21
GTGCCAGCCCTATTTGATGAGGTGGCCATATATTTTTCCGATGAAGAGTGGGAAGTTTTGACAGAGCAACAAAAGGCCCT
GTACCGGGAAGTCATGAGGATGAATTATGAGACTGTTCTGTCCCTGGAGTTCCCATTCCCTAAGCCAGATGTGATCACTC
GGCTGGAAAGAGAGAAATCTCAAAACTCTAATGAACGGCAGCTCCAAGGACACACCATTGCAGAAAATGAAGATTTGGAA
ATGAAGGCTCCAGATTGGGCAGGCCCAGTGAACACTTCCTCCCAGCTTTCTCAGCCTCAGCACCTGGATAGTTTTGGCCT
CTGTCTACCTCAGGACATCACAGAGCTGCCTGAGTTGGGTGAAGGATACCCCTTTTACATGGGATTCCCAGGGTATGATC
TTTCTGCGGAAGACCTGGAAGCGAAGTTCCAGTTCAGCCGGGGCATGCGGTGCAGTTATGATGCTGGGTTCAAGCTGATG
GTGGTGGAATATGCTGAAAGTACCAACAACTGTCAAGCAGCGAAGCAGTTTGGCATGCTGGAAAAAAATGTGCGGGACTG
GCGCAAAGTGAAGCCACAGCTACAAAATGCCCATGCCATGCAGCGGGCATTCCGAGGCCCCAAGAATGGACGTTTTGCCC
TGGTGGACCAGCGTGTGGCTGAATATGTGTGCTACATGCAGGCCAAAGGAGACCCTATCACCCAGGAGGCCATGCAGTTG
AAAGCCCTCGAAATTGCCCAGGAAATGAACATTCCAAAGAAAGGGTTCAAGGCCAGCTTGGGTTGGTGTCGAAGAATGAT
GCGACGTTATGACTTATCTCTGAGGCACAAGGTGCATGTACCCCAGCAGCTACTCGAAGACCTGACTGAAAAACTTGTCA
CTTACCAGCGGAGTGTCCTGGCCCTGCGCAGGACACATGACTACCAGGTGGCACAGATGGGCAATGCAGATGAGACTCCA
ATTTTTTTAGAGGTGCCATCTCGGGTGACTGTTGACAACCAGGGTGAGAAGCCTGTCTTGGTCAAGACGCCAGGCAGGGA
GAAACTGAAAATCACTGCCATGCTTGGGGTTCTGGCTGATGGGAGAAAACTGCCCCCATACATCATTCTGAGGGGCACAT
ACATCCCCCCTGGGAAGTTCCCTAGTGGGATGGAAATCCGCTGCCACAGGTATGGATGGATGACGGAGGATTTGATGCAG
GATTGGCTAGAGGTGGTATGGAGGAGGAGGGCAGGTGCCATCCCGAAGCAGCGAGGGATGCTCATTCTCAATGGCTTCCG
GGGCCATGCCACGGATTCCGTGAAGAGTTCCATGGAAAGCATGAACACTGACATGGTCATAATCCCTGGGGGCCTGACAT
CACAGCTCCAGGTTCTGGATGTGGTAGTGTACAAGCCACTGAATGACAGTGTACGGGCCCAGTACTCCAATTGGCTCCTG
TCGGGGAACCTGGCACTGAGTCCTACTGGGAATGCCAAGAAACCACCCCTTGGTCTCTTCCTAGAGTGGGTCATGGTGGC
ATGGAACAGCATCTCTAGTGAATCCATTATCCAAGGCTTTAAGAAGTGCCACATCTCCAGCAACTTAGAGGATGAAGATG
ATGTCTTGTGGGAAATTGAGAACGAGTTGCCAGGAGGAGTGGAACTGCACAGAGAATGTGACCCCGAGAGCCACTGA

Alignment

ORF - retro_eeur_21 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.52 %
• Parental protein coverage: 90.07 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LPAL-DEVPIYFDEE--EVLTEQQKALYREVMRMNYETVLSLEFPFPKPDVITRLEREKSQNSNERQLQG
          .PAL.DEV.IYF..E..EVLTEQQKALYREVMRMNYETVLSLEFPFPKPDVITRLEREKSQNSNERQLQG
Retrocopy VPALFDEVAIYFSDEEWEVLTEQQKALYREVMRMNYETVLSLEFPFPKPDVITRLEREKSQNSNERQLQG

Parental  HTIAENEDLEMKAPDWAGPVNTSSQLSQPQHLDSFGLRLTQDITELPEWGEGYPFYMGFPGYDLSAEDLA
          HTIAENEDLEMKAPDWAGPVNTSSQLSQPQHLDSFGL.L.QDITELPE.GEGYPFYMGFPGYDLSAEDL.
Retrocopy HTIAENEDLEMKAPDWAGPVNTSSQLSQPQHLDSFGLCLPQDITELPELGEGYPFYMGFPGYDLSAEDLE

Parental  AKFQFSRGMRRSYDAGFKLMVVEYAESTNNCQAAKQFGVLEKNVRDWRKVKPQLQNAHAMRRAFRGPKNG
          AKFQFSRGMR.SYDAGFKLMVVEYAESTNNCQAAKQFG.LEKNVRDWRKVKPQLQNAHAM.RAFRGPKNG
Retrocopy AKFQFSRGMRCSYDAGFKLMVVEYAESTNNCQAAKQFGMLEKNVRDWRKVKPQLQNAHAMQRAFRGPKNG

Parental  RFALVDQRVAEYVRYMQAKGDPITREAMQLKALEIAQEMNIPEKGFKASLGWCRRMMRRYDLSLRHKVHV
          RFALVDQRVAEYV.YMQAKGDPIT.EAMQLKALEIAQEMNIP.KGFKASLGWCRRMMRRYDLSLRHKVHV
Retrocopy RFALVDQRVAEYVCYMQAKGDPITQEAMQLKALEIAQEMNIPKKGFKASLGWCRRMMRRYDLSLRHKVHV

Parental  PQQLLEDLTEKLVTYQRSVLALRRTHDYQVAQMGNADETPICLEVPSRVTVDNQGEKPVLVKTPGREKLK
          PQQLLEDLTEKLVTYQRSVLALRRTHDYQVAQMGNADETPI.LEVPSRVTVDNQGEKPVLVKTPGREKLK
Retrocopy PQQLLEDLTEKLVTYQRSVLALRRTHDYQVAQMGNADETPIFLEVPSRVTVDNQGEKPVLVKTPGREKLK

Parental  ITAMLGVLADGRKLPPYIILRGTYIPPGKFPSGMEIRCHRYGWMTEDLMQDW
          ITAMLGVLADGRKLPPYIILRGTYIPPGKFPSGMEIRCHRYGWMTEDLMQDW
Retrocopy ITAMLGVLADGRKLPPYIILRGTYIPPGKFPSGMEIRCHRYGWMTEDLMQDW

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	11.28 RPM	13.05 RPM
SRP017611_kidney	7.69 RPM	7.88 RPM
SRP017611_liver	2.25 RPM	1.61 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_21 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 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000033914	1 retrocopy	retro_cjac_2779,
Dipodomys ordii	ENSDORG00000006822	1 retrocopy	retro_dord_612,
Erinaceus europaeus	ENSEEUG00000014393	1 retrocopy	retro_eeur_21 ,
Latimeria chalumnae	ENSLACG00000014539	1 retrocopy	retro_lcha_56,
Mus musculus	ENSMUSG00000040596	1 retrocopy	retro_mmus_2572,
Otolemur garnettii	ENSOGAG00000007615	1 retrocopy	retro_ogar_2784,
Tarsius syrichta	ENSTSYG00000011078	1 retrocopy	retro_tsyr_1983,