RetrogeneDB ID: retro_eeur_521

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_336321:6145..6937(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KRT5
• Ensembl ID: ENSEEUG00000009412
• Aliases: None
• Description: keratin 5 [Source:HGNC Symbol;Acc:6442]

Sequence

>retro_eeur_521
AACAAGTATGAAGATGAGATTAACAGGCGCACAGAGATGGAGAATGAATTTGTCCTCATCAAGAAGGATGTGGATGAAGC
ATACATGAACAAGGTGGAGCTGGAGTCTCGCCTGAAAGGACTGACAGATGAGATCAACTTTTTCAGGCAGCTGTATGAAG
TGGAGATCCAAGAGCTGCAGTCCCAGATCTCGGACACGTCCATGGACAACAACCGCTCCCTGGACCTGGACGGCATCATC
GCTGATGTCAAGGCCCAGTACAAGGAGATGACAACCGCAACCGGGCTGAGGCCAAGTCCATGTGCCAGATCAAGTATGAG
GAGCTGCAGACTTTGGCTGGGAAGCATGGGGATGACCTCCATCGCAGGAAGACGGAGATTTCTAACACGAACCGGAACAT
CAGCCAGCTCCAGGCAGAGATCGAGAACCTCAAAGGCCAGTGGGCTTCCCTGGAGGCCGCCATTGCTGATGCTGAGCAGC
ACGGGGAGCTGGCCATCAAGGACGCCAACTCCAAGCTGGCGGAACTGGAGGCCGCCCTGCAGCGGGCCAAGCAGCACATG
GCGCGGCAGCTGCGCGAGTACCAGGGAGCTCATGAACGTGAAGCTGGCCCTGGACATCGAGATCGCCACCTACAGGAAGC
TGCTGAAGGGCGAGGAGAGCAGGTTGGAATCTGGGATGCAGAATATGAGCATCCACACCAAGACCACCAGCGGCTACTCC
AGTGGGCTGAGCTCGGCCTACTGGGGCCTCCCCAGTCCCGGCCTCACCTACGGCCTGAATGCCAGTTTCGGC

Alignment

ORF - retro_eeur_521 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.68 %
• Parental protein coverage: 51.23 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NKYEDEINKRTTAENEFVMLKKDVDAAYMNKVELEARVDALMDKINFMKMFFEAELSQIQTHVSDTSVVL
          NKYEDEIN.RT..ENEFV..KKDVD.AYMNKVELE.R...L.D.INF.....E.E....Q...SDT....
Retrocopy NKYEDEINRRTEMENEFVLIKKDVDEAYMNKVELESRLKGLTDEINFFRQLYEVEIQELQSQISDT----

Parental  SMDNNRSLDLDSIIAEVKAQYEDIA-NRSRTEAESWYQTKYEELQQTAGRHGDDLRNTKHEISEMNRMIQ
          SMDNNRSLDLD.IIA.VKAQY.....NR.R.EA.S..Q.KYEELQ..AG.HGDDL...K.EIS..NR.I.
Retrocopy SMDNNRSLDLDGIIADVKAQYKEMT<NRNRAEAKSMCQIKYEELQTLAGKHGDDLHRRKTEISNTNRNIS

Parental  RLRAEIDNVKKQCANLQNAIADAEQRGELALKDARNKLAELEDALQKAKQDMARLLREYQ-ELMNVKLAL
          .L.AEI.N.K.Q.A.L..AIADAEQ.GELA.KDA..KLAELE.ALQ.AKQ.MAR.LREYQ.ELMNVKLAL
Retrocopy QLQAEIENLKGQWASLEAAIADAEQHGELAIKDANSKLAELEAALQRAKQHMARQLREYQ>ELMNVKLAL

Parental  DVEIATYRKLLEGEEYRLSGEGVGPVNISVVTNSVSSGYGGG--SGFGGGLGGGLGSGLGSGLG
          D.EIATYRKLL.GEE.RL.....G..N.S..T....SGY..G..S...G....GL..GL....G
Retrocopy DIEIATYRKLLKGEESRLES---GMQNMSIHTKT-TSGYSSGLSSAYWGLPSPGLTYGLNASFG

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	0.32 RPM	0.00 RPM
SRP017611_kidney	52.14 RPM	5.63 RPM
SRP017611_liver	199.36 RPM	0.00 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_521 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 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000011913	4 retrocopies	retro_chof_1848, retro_chof_2381, retro_chof_2385, retro_chof_778,
Erinaceus europaeus	ENSEEUG00000009412	1 retrocopy	retro_eeur_521 ,
Echinops telfairi	ENSETEG00000007907	1 retrocopy	retro_etel_1586,
Nomascus leucogenys	ENSNLEG00000017746	5 retrocopies	retro_nleu_2270, retro_nleu_2596, retro_nleu_354, retro_nleu_457, retro_nleu_852,
Pongo abelii	ENSPPYG00000004548	1 retrocopy	retro_pabe_1103,
Vicugna pacos	ENSVPAG00000011707	3 retrocopies	retro_vpac_334, retro_vpac_551, retro_vpac_555,