RetrogeneDB ID: retro_eeur_254

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_224979:972..1442(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EAF1
• Ensembl ID: ENSEEUG00000002084
• Aliases: None
• Description: ELL associated factor 1 [Source:HGNC Symbol;Acc:20907]

Sequence

>retro_eeur_254
AAAACAAGAGCTAAGGGGATTAGTAAAATCCATGCTCACATGGAACAGTAGCGCACTCATCCCCTGCAGCCATCACAGCC
ACCTGGGCCTCTAGCACCTATGCCATTCAGAGCTCCAACCAAACCTCCAGGTGGCCCCAAAATTTCTCCCTTGATAGATA
ACCCCTCACCCGAACATCATCTGGATGACATCAAAAGAGAGCTGAGGGCTGAAGTTGACTCACTAAACAGATGAGCAGTA
CTAGTGGAAGAAGCTCCTCAGACTCTGAGAGCTCCTCAGGAAGTGAGGACAGCTCCAGCAGCAGAAGTGAGGACAATGGC
CCAGCGTCACCTCCACAGCCTTCACACTAGCAGCACTACAAGAGATCAGTCGTATCCAATGGAACCAGCTGGCCACAAGG
AAGCAACCAGCTCATAAACAACCCCAGGAATGACTTGCAGTTGAGTGAGTCTGGAAGTGACAGTGACGAC

Alignment

ORF - retro_eeur_254 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.75 %
• Parental protein coverage: 59.33 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KTRAEGSSKIQARMEQQPTRPPQPTQPPPPPPPMPFRAPTKPPAGPKTSPLKDNPSPEPQLDDIKRELRA
          KTRA.G.SKI.A.MEQ..T.P.QP.QPP.P..PMPFRAPTKPP.GPK.SPL.DNPSPE..LDDIKRELRA
Retrocopy KTRAKGISKIHAHMEQ*RTHPLQPSQPPGPLAPMPFRAPTKPPGGPKISPLIDNPSPEHHLDDIKRELRA

Parental  EVD-IIEQMSSTSGSSSSDSESSSGSDDDSSSSGAEDNGPASPPQPSHQQTYNSRPAVANGTSRPQGSNQ
          EVD....QMS......SS....................GPASPPQPSH.Q.Y..R..V.NGTS.PQGSNQ
Retrocopy EVD<LTKQMS-STSGRSSSDSEXXXXXXXXXXXXXXXXGPASPPQPSH*QHYK-RSVVSNGTSWPQGSNQ

Parental  LMNTLRNDLQLSESGSDSDD
          L.N..RNDLQLSESGSDSDD
Retrocopy LINNPRNDLQLSESGSDSDD

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	38.67 RPM
SRP017611_kidney	0.00 RPM	48.76 RPM
SRP017611_liver	0.00 RPM	33.76 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_254 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 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000006017	1 retrocopy	retro_cfam_1658,
Choloepus hoffmanni	ENSCHOG00000007449	4 retrocopies	retro_chof_1039, retro_chof_2342, retro_chof_355, retro_chof_883,
Erinaceus europaeus	ENSEEUG00000002084	1 retrocopy	retro_eeur_254 ,
Monodelphis domestica	ENSMODG00000014543	1 retrocopy	retro_mdom_290,
Otolemur garnettii	ENSOGAG00000013964	1 retrocopy	retro_ogar_2142,
Sarcophilus harrisii	ENSSHAG00000006597	2 retrocopies	retro_shar_485, retro_shar_56,