RetrogeneDB ID: retro_eeur_643

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_373496:76428..77079(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MKRN1
• Ensembl ID: ENSEEUG00000001133
• Aliases: None
• Description: makorin ring finger protein 1 [Source:HGNC Symbol;Acc:7112]

Sequence

>retro_eeur_643
GCCACCGCGCAGGACTCAATGGCCTGGGAGGAATCAAAGAAAGAACAAGGAGCGGAGCAGCATTATCTCTGTGCTGAGGG
TGGAGAGTGCAGCAGTGTGTATCTCCACAATGACACATGTGACCTCTGTGGACTGCAGGTCCTCCATCCAAGGGATGCTG
CCCAGAGATCACAGCACGTACGATCTTGCGTTGAGGCCCACCAGAAGAAAATCTCACTGGCAATGGAGCTTAGTAGGGAC
AAGGTGTGTGGAATCTGCATGGAAGTGGTGTTGGCGAAGGCTAACCCCAAGGATCGATGCTTTGGGATTCTACCCAAATG
CAACCACATCTTCTGTTTCAAGTGTATTGGCAAGTGGAGGAAGGCCATACAATTTTTGAGGTCCATCAGAAAGTCCTGTC
CAACATGCCGGACCTTATCTCACTTTATCGTTCCCAGTGAATACTGGGTGGAGGAGGAAGAGGAGAAGATGAAACTCATT
GAGGAATACAAGAAGAAAATGAACAACATTGACTGCAAGTATTTTAATAAAGGACGTGGGAAATGTCCGTATGGAGCAAG
CTGTTTTTACAAGCATGGGTATCCTGATGGCCGAAGATTGGAGACACAGAAACAGCACAGAGCACCATTCAGCAGCTTCC
TAGCCCTACGA

Alignment

ORF - retro_eeur_643 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.71 %
• Parental protein coverage: 60.53 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  APLQGSVTKEESEKEQTAVETKKQLCPYAAVGECRYGENCVYLHGDSCDMCGLQVLHPMDAAQRSQHIKS
          A..Q.S...EES.K.....E....LC..A..GEC......VYLH.D.CD.CGLQVLHP.DAAQRSQH..S
Retrocopy ATAQDSMAWEES-KKEQGAE-QHYLC--AEGGEC----SSVYLHNDTCDLCGLQVLHPRDAAQRSQHVRS

Parental  CIEAHEKDMELSFAVQRSKDMVCGICMEVVYEKANPSERRFGILSNCNHTYCLKCIRKWRSAKQFESKII
          C.EAH.K....S.A...S.D.VCGICMEVV..KANP..R.FGIL..CNH..C.KCI.KWR.A.QF...I.
Retrocopy CVEAHQK--KISLAMELSRDKVCGICMEVVLAKANPKDRCFGILPKCNHIFCFKCIGKWRKAIQFLRSIR

Parental  KSCPECRITSNFVIPSEYWVEEKEEKQKLIQKYKEAMSNKACRYFDEGRGSCPFGGNCFYKHAYPDGRRE
          KSCP.CR..S.F..PSEYWVEE.EEK.KLI..YK..M.N..C.YF..GRG.CP.G..CFYKH.YPDGRR.
Retrocopy KSCPTCRTLSHFIVPSEYWVEEEEEKMKLIEEYKKKMNNIDCKYFNKGRGKCPYGASCFYKHGYPDGRRL

Parental  EPQRQKVGTSSRYRAQR
          E.Q.Q.....S...A.R
Retrocopy ETQKQHRAPFSSFLALR

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	97.01 RPM
SRP017611_kidney	0.00 RPM	65.08 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_643 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 8 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000008306	2 retrocopies	retro_btau_401, retro_btau_943,
Canis familiaris	ENSCAFG00000003953	2 retrocopies	retro_cfam_2157, retro_cfam_253,
Callithrix jacchus	ENSCJAG00000013474	2 retrocopies	retro_cjac_210, retro_cjac_2991,
Cavia porcellus	ENSCPOG00000000948	1 retrocopy	retro_cpor_109,
Erinaceus europaeus	ENSEEUG00000001133	1 retrocopy	retro_eeur_643 ,
Gorilla gorilla	ENSGGOG00000023977	4 retrocopies	retro_ggor_119, retro_ggor_2813, retro_ggor_3031, retro_ggor_381,
Macaca mulatta	ENSMMUG00000010420	3 retrocopies	retro_mmul_191, retro_mmul_2597, retro_mmul_76,
Pongo abelii	ENSPPYG00000018057	3 retrocopies	retro_pabe_3435, retro_pabe_3776, retro_pabe_947,