RetrogeneDB ID: retro_eeur_222

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_213135:3845..4452(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSEEUG00000002617
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: FTSJ1
• Ensembl ID: ENSEEUG00000001469
• Aliases: None
• Description: FtsJ RNA methyltransferase homolog 1 (E. coli) [Source:HGNC Symbol;Acc:13254]

Sequence

>retro_eeur_222
ATGGGATGGGCATCAAAATTCAAGCGTGATGTCTGCCGCCCAGCCCAGGAGAAGGGCTGGCGTGCCGAGAGCGCCTTTAA
ACTGCTACAACTTGATGAGGAATTCCATCTCCTCCAAGGCATCACACGGGCAGTTGACTTGTGTGCAGCCCCTGGCAGCT
GGAGCCAAGTGCTGATTCAGAAGATGGGGAGCCAAGGGTCTGGCCATGTGGTAGCTGTGGATCGTCAGGATATGGCTCCA
CTGCCAGGTGTGTTACAGATCAAGGGGGATATCACTCAGCTGTCCACTGCCAAGGCAGTTGTCCAGCACTTTGAGGGTTC
TCCTGCAGACCTGGTGGTATGTGACGGAGATCCTGATTTAACTGGCCTGCAAGATATTGATGAACATATGCGGACCCAGC
TCCTTTTGGCGGCTCTAAACATTGCTACACACATATTGAAGCCTGGGGGCTGTTTTGTGGCCAAGATCATCCGTGGCCGT
GATGTGGACCCTGACCTACAGCCAGCTTCGAGTTTTCTTTCTCCACTGTAGGTCTGTGCCCAGGCCCAGGAGCAGTCCCA
GCTCAAGCAGTGAAGCTTTTGCTGTCTGTCACAGGTATGATCCCCCT

Alignment

ORF - retro_eeur_222 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.49 %
• Parental protein coverage: 68.94 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGRTSKDKRDVYYRLAKENGWRARSAFKLLQLDEEFQLFQGVKRAVDLCAAPGSWSQVLSQKIGNQGSGH
          MG..SK.KRDV..R.A.E.GWRA.SAFKLLQLDEEF.L.QG..RAVDLCAAPGSWSQVL.QK.G.QGSGH
Retrocopy MGWASKFKRDVC-RPAQEKGWRAESAFKLLQLDEEFHLLQGITRAVDLCAAPGSWSQVLIQKMGSQGSGH

Parental  VVAVDLQAMAPLPGVIQIQGDITQLSTAKEIIRHFEGSSADLVVCDGAPDVTGLHDVDEYMQAQLLLAAL
          VVAVD.Q.MAPLPGV.QI.GDITQLSTAK....HFEGS.ADLVVCDG.PD.TGL.D.DE.M..QLLLAAL
Retrocopy VVAVDRQDMAPLPGVLQIKGDITQLSTAKAVVQHFEGSPADLVVCDGDPDLTGLQDIDEHMRTQLLLAAL

Parental  NIATHVLKPGGSFVAKIFRGRDV-TLLYSQLRVFFSNV-VCAKPRSSRNSSIEAFAVCRGYDPP
          NIATH.LKPGG.FVAKI.RGRDV.TL.YSQLRVFF........PRSS..SS.EAFAVC..YDPP
Retrocopy NIATHILKPGGCFVAKIIRGRDV>TLTYSQLRVFFLHCRSVPRPRSSPSSSSEAFAVCHRYDPP

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	31.10 RPM	48.99 RPM
SRP017611_kidney	13.50 RPM	4.13 RPM
SRP017611_liver	3.70 RPM	3.70 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_222 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 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000031829	1 retrocopy	retro_btau_27,
Canis familiaris	ENSCAFG00000015339	1 retrocopy	retro_cfam_544,
Erinaceus europaeus	ENSEEUG00000001469	1 retrocopy	retro_eeur_222 ,
Echinops telfairi	ENSETEG00000014092	3 retrocopies	retro_etel_1697, retro_etel_1803, retro_etel_1928,
Myotis lucifugus	ENSMLUG00000003977	1 retrocopy	retro_mluc_1329,
Oryctolagus cuniculus	ENSOCUG00000008009	1 retrocopy	retro_ocun_870,
Otolemur garnettii	ENSOGAG00000016174	1 retrocopy	retro_ogar_180,
Sorex araneus	ENSSARG00000007091	1 retrocopy	retro_sara_26,