RetrogeneDB ID: retro_eeur_329

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_25622:52..892(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSEEUG00000003341
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSEEUG00000014870
• Aliases: None
• Description: None

Sequence

>retro_eeur_329
GGCACAGCTTGTGTCCTGATCGGGCAGCCCTTCGACACTGTCAAAGTCAAGATGCAGACGTTCCCTTACATGTACAAGGG
CCTCACCGACTGCTGCCGCCAGACCTACTCCCAAGTGGGCTTTCGGGGTTTCTACAGGGGGACTGGCCCCGCGCTCATGG
CCTACGTCGCCGAGAACTCAGTCCTCTTCATGTGCTTCGGCTTCTGCCAACAGTTCGTGAAGAAAGTGGTCGGGCTGCGC
AAGCATGAAAAGCTGAACGATCTGCAAACTGCAGCCGCCGGCTCACTGGCTTCTGCTTTTGCAGCTCTTGTCCTTTGCCC
CACCGAGCTGGTGAAGTGCCGGCTACAGACTATGTACGAAATGGAAATGTCAGGGAAGATCACAAAGAGGCAGAACACAG
TTTGGTCGGTGGTAAATGCTATCCTTAGGAAGGACGGTCTGCTAGGCTTCTACCATGGACTCTCCGGTACTCTACTTCAG
GAAGTACCGGGATATTTCTTCTTCTTTGGTGGCTATGAGGTAAGCCGCTCGATATTTGCCTCAGGGAGATCAAAAGATGA
CCTAAGTCCTGCCCACTTGATGATTAGTGGAGGGATTGCTGGGATTTGCCATTGGGTTGTTGTATACCCAGTGGATTGTA
TCAAATCCAGAATTCAGGTTCTTTCCATGTCTGGGAAGCAGGCAGGTTTTGCCAGAACTCTTAGAAATACTGTGAAAAAT
GAAGGGGTAGCAGTCTTATATTCTGGACTGAAAGTTACTTTGATTCGAGCAGTCCCTGCCAACGGGTCACTGTTTATAGT
CTATGAATACAGCAGGAAGATGATGATGAGCCGGTTTGAA

Alignment

ORF - retro_eeur_329 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.79 %
• Parental protein coverage: 99.29 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GTACDLTGQLFDTMKVKMQTFPDLYRGLTDCCLKTYSQVGFRGFYKGTSPALIANIAENSVLFMCYGFCQ
          GTAC.L.GQ.FDT.KVKMQTFP..Y.GLTDCC..TYSQVGFRGFY.GT.PAL.A..AENSVLFMC.GFCQ
Retrocopy GTACVLIGQPFDTVKVKMQTFPYMYKGLTDCCRQTYSQVGFRGFYRGTGPALMAYVAENSVLFMCFGFCQ

Parental  QVVRKVIGLDSQAKLSDLQNAAAGSFASAFAALVLCPTELVKCRLQTMYEMESSGKIARSQNTVWSVVKS
          Q.V.KV.GL....KL.DLQ.AAAGS.ASAFAALVLCPTELVKCRLQTMYEME.SGKI...QNTVWSVV..
Retrocopy QFVKKVVGLRKHEKLNDLQTAAAGSLASAFAALVLCPTELVKCRLQTMYEMEMSGKITKRQNTVWSVVNA

Parental  ILSKDGPLGFYHGLSSTLLREVPGYFFFFGGYELSRSFFASGRSKDELGPVPLMLSGGVGGICLWLAVYP
          IL.KDG.LGFYHGLS.TLL.EVPGYFFFFGGYE.SRS.FASGRSKD.L.P..LM.SGG..GIC.W..VYP
Retrocopy ILRKDGLLGFYHGLSGTLLQEVPGYFFFFGGYEVSRSIFASGRSKDDLSPAHLMISGGIAGICHWVVVYP

Parental  VDCIKSRIQVLSMSGKQAGFI-TFISVLKNEGVTALYSGLKPTMIRAFPANGALFLAYEYSRKLMMGQFE
          VDCIKSRIQVLSMSGKQAGF..T.....KNEGV..LYSGLK.T.IRA.PANG.LF..YEYSRK.MM..FE
Retrocopy VDCIKSRIQVLSMSGKQAGFARTLRNTVKNEGVAVLYSGLKVTLIRAVPANGSLFIVYEYSRKMMMSRFE

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	2.42 RPM	6.28 RPM
SRP017611_kidney	0.56 RPM	3.38 RPM
SRP017611_liver	0.16 RPM	147.91 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_329 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 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011723	1 retrocopy	retro_amel_5,
Bos taurus	ENSBTAG00000011647	1 retrocopy	retro_btau_1581,
Canis familiaris	ENSCAFG00000005955	1 retrocopy	retro_cfam_211,
Choloepus hoffmanni	ENSCHOG00000004899	3 retrocopies	retro_chof_1643, retro_chof_494, retro_chof_561,
Erinaceus europaeus	ENSEEUG00000014870	1 retrocopy	retro_eeur_329 ,
Mus musculus	ENSMUSG00000031482	1 retrocopy	retro_mmus_75,
Oryctolagus cuniculus	ENSOCUG00000016684	2 retrocopies	retro_ocun_192, retro_ocun_1927,
Ochotona princeps	ENSOPRG00000014616	1 retrocopy	retro_opri_7,
Rattus norvegicus	ENSRNOG00000011881	1 retrocopy	retro_rnor_130,
Sorex araneus	ENSSARG00000002472	1 retrocopy	retro_sara_30,
Sus scrofa	ENSSSCG00000009373	1 retrocopy	retro_sscr_688,