RetrogeneDB ID: retro_eeur_123

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: GeneScaffold_7679:19458..20170(-)
• Located in intron of: ENSEEUG00000001461

Retrocopy information

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

Parental gene information

• Parental gene symbol: MTERFD1
• Ensembl ID: ENSEEUG00000004188
• Aliases: None
• Description: MTERF domain containing 1 [Source:HGNC Symbol;Acc:24258]

Sequence

>retro_eeur_123
TTCAACTCAACTAAATTGAGTAACTTTGTCAATATTATACAGCTCAGAAAATGTCTGCAGAGACAAGGACAAACATTGTT
GTGTAGCCTTTCTGCTCAGCCTCAGGTGTCCTCTGACAATTGTTGTCTCCAGTGGGGACTTAAGACATACAACACTTTCT
TTTTGAGGAATATTTCCCAGTCTCCCACCTCTACTAGGTAGAAGAATAATTCTGCCCAGAGTACTCTGCTTTCCTCTGTG
ATTTAACAGTCACAGAAGACACAAAAGATACCCAGCTTTGATTCTAAACTGTCTCTAGAAGAATTGGATGATTTGCCTCC
AATGTCTCCATTGCAGGCAGTATCTGAGGAAGAGGTTGTCTGAATTATTGCAAGCCCACCACTGCGCTCAGATTCATCCA
CACTTCGAGATTATGTGGATCATTCTGAGACTCTGTAGAAGTTAATGCTTCTAGGAGTGGATTTGTCCAAGATAGAAAAA
CATCCAGATGCTGCCAACCTCCTCCTGAAACTGGATTCTGAGAAAGACATTAAACACATACTCTGATTTCTAAAGATTTG
GGAATAGAGGATAAGAAACTTGATGCATTCTTAACCAAAAATTGTTACCTTTTCTGAAGAGCTTGGAAATCTTCAGACCA
TAGTGGCTTATCTACAGTCAAAAAAATTTCAGTAAAGCAGATATTACACAGATGGTAAAAAATGCACCATTT

Alignment

ORF - retro_eeur_123 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.08 %
• Parental protein coverage: 58.77 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FDSIKSSNFINIMQLRKRLPRPRKTVLCGLSAQPQVSSDNCFLQWGFKTYSTSSLWNSSQSPTCTRQENN
          F.S.K.SNF.NI.QLRK.L.R...T.LC.LSAQPQVSSDNC.LQWG.KTY.T..L.N.SQSPT.TR..NN
Retrocopy FNSTKLSNFVNIIQLRKCLQRQGQTLLCSLSAQPQVSSDNCCLQWGLKTYNTFFLRNISQSPTSTR*KNN

Parental  SAQSTLLPSVIEQSEKTQQIPSFDSELSLEELDDLPPLSPLQPVSEEEAIRIIANPPLPPVSSTLRVYVD
          SAQSTLL.SVI.QS.KTQ.IPSFDS.LSLEELDDLPP.SPLQ.VSEEE...IIA.PPL...SSTLR.YVD
Retrocopy SAQSTLLSSVI*QSQKTQKIPSFDSKLSLEELDDLPPMSPLQAVSEEEVV*IIASPPLRSDSSTLRDYVD

Parental  HSETLQKLVLLGVDLSKIEKHPDAANLLLRLDFEKHIKHILLFL-KDLGIEDNQLGAFLTKNYAI-FSED
          HSETL.KL.LLGVDLSKIEKHPDAANLLL.LD.EK.IKHIL.FL.KDLGIED..L.AFLTKN....F...
Retrocopy HSETL*KLMLLGVDLSKIEKHPDAANLLLKLDSEKDIKHIL*FL<KDLGIEDKKLDAFLTKNCYL<FLKS

Parental  LENLQTRVAYLQSKNFSKADITQMVTKAPF
          LE...........KNFSKADITQMV..APF
Retrocopy LEIFRP*WLIYSQKNFSKADITQMVKNAPF

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	0.16 RPM	12.25 RPM
SRP017611_kidney	0.00 RPM	12.38 RPM
SRP017611_liver	0.00 RPM	10.61 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_123 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.

---

Parental genes homology:

Parental genes homology involve 3 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007893	3 retrocopies	retro_chof_1333, retro_chof_1757, retro_chof_2268,
Erinaceus europaeus	ENSEEUG00000004188	1 retrocopy	retro_eeur_123 ,
Otolemur garnettii	ENSOGAG00000004303	1 retrocopy	retro_ogar_3409,