RetrogeneDB ID: retro_eeur_97

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: GeneScaffold_6006:246544..247162(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FDFT1
• Ensembl ID: ENSEEUG00000013655
• Aliases: None
• Description: farnesyl-diphosphate farnesyltransferase 1 [Source:HGNC Symbol;Acc:3629]

Sequence

>retro_eeur_97
CAGAAAACAAATATAATACATGATTATCTAGAAGACCAGCAAGAAGGAAGACAAGTTTGGCCTCAAGAGGTTTGGAGCAA
GTATGTTAAGAAGTTAGGTGATTTTGCTAAGCCTGAGAAGACTGATGTGGCTGTGCAGTCCCTGAATGAACTGATCACCA
ATGCACTCCAGCACATTCCAGATGTCATTACCTGCCTCTCAAGACTGAGGAACCAGAGTGTGTTCAACTTCTGTGCTACC
CCACAGGTCATGGCCATTGCCACTTTGGCTGCCTGTTATAACAACCAACAGGCGTTTCGAGGGGTTGTGAATATTCAAAA
GGGACAGGTTGTTACCCTGATGATGGATGCCACCAATATGCCAGCTATTAAAGCTATCATACACCACTACATGGAGGAGA
TCTATCATAGAATCCCCAACTCCGACCCATATGTTAGGAAAACACGGAAGATCATTACCACTGTGCGGACACAGAACCTG
TCCACCTGCCAGCTAGTCTCCTGGAGCCACTACTCCCCTATCTACCTGACATTTGTCATGCTGCAGGCATCCCTGTGCTG
GCAGTACCTAAGCACACTGTCACAAGTCACAGAAGACATTGTTCAGAGTGGAGAGCAC

Alignment

ORF - retro_eeur_97 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.35 %
• Parental protein coverage: 53.65 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QKTNIIRDYLEDQQEGREFWPQEVWSKYVKKLGDFTKPENIDLAVQCLNELITNALQHIPDVITYLSRLR
          QKTNII.DYLEDQQEGR..WPQEVWSKYVKKLGDF.KPE..D.AVQ.LNELITNALQHIPDVIT.LSRLR
Retrocopy QKTNIIHDYLEDQQEGRQVWPQEVWSKYVKKLGDFAKPEKTDVAVQSLNELITNALQHIPDVITCLSRLR

Parental  NQSVFNFCAIPQVMAIATLAACYNNQQVFRGVVKIRKGQAVTLMMDATNMPAVKAIIHQYMEEIYHRIPN
          NQSVFNFCA.PQVMAIATLAACYNNQQ.FRGVV.I.KGQ.VTLMMDATNMPA.KAIIH.YMEEIYHRIPN
Retrocopy NQSVFNFCATPQVMAIATLAACYNNQQAFRGVVNIQKGQVVTLMMDATNMPAIKAIIHHYMEEIYHRIPN

Parental  SDPSVSKTRKIISTVRTQNLSTCQLASRSHYSPIYLTFVMLLAALSWQYLSTLSQVTEDIVQSGEH
          SDP.V.KTRKII.TVRTQNLSTCQL.S.SHYSPIYLTFVML.A.L.WQYLSTLSQVTEDIVQSGEH
Retrocopy SDPYVRKTRKIITTVRTQNLSTCQLVSWSHYSPIYLTFVMLQASLCWQYLSTLSQVTEDIVQSGEH

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	0.48 RPM	56.24 RPM
SRP017611_kidney	0.56 RPM	36.38 RPM
SRP017611_liver	0.16 RPM	47.27 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_97 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000003988	2 retrocopies	retro_cjac_1945, retro_cjac_2761,
Erinaceus europaeus	ENSEEUG00000013655	1 retrocopy	retro_eeur_97 ,
Loxodonta africana	ENSLAFG00000007372	1 retrocopy	retro_lafr_772,
Mus musculus	ENSMUSG00000021273	1 retrocopy	retro_mmus_1182,
Vicugna pacos	ENSVPAG00000006183	1 retrocopy	retro_vpac_463,