RetrogeneDB ID: retro_eeur_159

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_112045:19..701(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DCP2
• Ensembl ID: ENSEEUG00000005752
• Aliases: None
• Description: decapping mRNA 2 [Source:HGNC Symbol;Acc:24452]

Sequence

>retro_eeur_159
AATATTGAGTGGTTCTCCATTGTGAAATTGCCCTGCTATAGAAATGATATGACCCCAAAGTCTAAACTTAGTTTGGCACC
TAACAAATTTTTTATGGACATTCCCTTTATCAGACCTTTAAGGGACTGGCTTTCTCAGAGATTTGAAGATTCTTCAGACA
GTGACAATGGATTTTCTTCAACTGGTAGCACTCCAGCTAAGCCTACATGTGGAAAAATTGAGTCGAACCAAATTTCACCA
ATGTCAGCAATTATTTCCTGAAGGTTCTCCTGGTGACCAGTGGGTAAAGCACAAGAAGGCACTTTAGCAAAAGCCATATA
ATAATCATTAGGAGATGTCTGACCTTTTTAAAGCAAGGAATCAGAGTATGAAGGGAAACGGCAGAAAACAGTACCAGGAC
TCACCTAAATAAAAAGAAAAGAACAAATGGGGTCCACAGCCAGCCAGCCAAGCAGCAGAATTCCTTGATGAAATGTGAAA
AAAAATTCATCCACAAAAACTTCAGGATAATTTTGAAACAGATGCTGTATACGACTTATCTTGCTCCAGTGAAGACCAGT
CGCTTGAACATGCCGAGGGACAGTCATCTGTGGCATGTAATGGACATTGTAAGTTTCCCTTTTAATCCAGAGCCTTTTTG
AGTGTCAAGTTTGATCATAATGCTATAATGAAAAAATTTGAA

Alignment

ORF - retro_eeur_159 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.65 %
• Parental protein coverage: 53.66 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  NIEWFSIEKLPCHRNDMTPKSKLGLAPNKFFMAIPFIRPLKDWLSRRFGDSSDSDNGFSSTGSTPAKPT-
          NIEWFSI.KLPC.RNDMTPKSKL.LAPNKFFM.IPFIRPL.DWLS.RF.DSSDSDNGFSSTGSTPAKPT.
Retrocopy NIEWFSIVKLPCYRNDMTPKSKLSLAPNKFFMDIPFIRPLRDWLSQRFEDSSDSDNGFSSTGSTPAKPT>

Parental  VEKLSRTKFRHCQQLFPEGSPGDQWVKHKQPLQQKPYNNHSEMFDLFKAKNQSMKGNGRKQYQDSP-NQK
          VEKLSRTKF..CQQLFPEGSPGDQWVKHK..L.QKPYNNH.EM.DLFKA.NQSMKGNGRKQYQDSP.N.K
Retrocopy VEKLSRTKFHQCQQLFPEGSPGDQWVKHKKAL*QKPYNNH*EMSDLFKARNQSMKGNGRKQYQDSP>NKK

Parental  KRTNGVHSQPTKQQNSLMKCEKKL-HPRKLQDNFETDAVYELSCSSEDQLLEHAEGQPSVACNGHCKFPF
          KRTNGVHSQP.KQQNSLMKC.....HP.KLQDNFETDAVY.LSCSSEDQ.LEHAEGQ.SVACNGHCKFPF
Retrocopy KRTNGVHSQPAKQQNSLMKCXXXF<HPQKLQDNFETDAVYDLSCSSEDQSLEHAEGQSSVACNGHCKFPF

Parental  SSRAFLSFKFDHNAIMKNLD
          .SRAFLS.KFDHNAIMK...
Retrocopy *SRAFLSVKFDHNAIMKKFE

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	22.08 RPM
SRP017611_kidney	0.38 RPM	5.63 RPM
SRP017611_liver	0.16 RPM	5.14 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_159 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000005752	1 retrocopy	retro_eeur_159 ,