RetrogeneDB ID: retro_eeur_441

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_304947:10846..11826(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSEEUG00000002955
• Aliases: None
• Description: None

Sequence

>retro_eeur_441
ATGAGGGAAATCATGCACACCCAGGCCGGTCAGTGTGGCAACCAGATCAGTGCTAAGTTCTGGGAGGTGATCAGTGATGA
GCATGGCATTGACCCCACCAGCACCTACCACAGGAACAGCAACCTGCAGCTGGACCACATTTATGTGTATTACTATGAAG
GCACAGGTGCAAATATGTTCCTTGTGCTATCTTGGTGAATCTAGAACCCGGTACCACGGACTCTGTTCTCTCAGGTCCTT
TTGGTCAGATCTTCAAAACACATGACTTCTTTGTTGGTCAGTTTGGGACAGGCAAACAACTGGGCCAAGGGCCACTATAC
AGAAGGAGCTGAGCTGGTTGACTCTATCCTGGATGTGGTATGGAAGGAAGCAGAGAGCTGTGACTGCCTACAGGGCTTCC
AGCTGAACCACTCACTGGGTGGGGGCACAGGCTCTGGAATGGGCACCCTACTTATCAGCAAGATCAGAGAAGAGTACCCT
GACAGAATCATGAATGCCTTCAGTGTGGTTCCCTCACCTAAAGTGTCTGACACTGTAGTTGAGCCCTACAATGCAACCCT
CTTTGTTCATCAGTTAGTAGAGAACACTGATGAAACTTACTGTATTGACAATGAGGCCCTTTATGATATCTGCTTCCATA
CGCTCAAGCTGACCACTACAATCTATGGAGACCTGAACAACCTCATCTCAGCCACCATGAGCAGTGTCACCACCTACCTC
CACTTCCCTGGCAAGCTCAATGCTGACCTCCGCAAGCTGGCATTCAACATGGTGCCTCCCCTCGTCTTCATTTCTTCATG
CCTGGTTTTGCCCCCCTCACAAGCCATTAAAACCAGCAATATCAGGCTCTCACTGTGCCCAAACTCACACAGCAGGTCTT
TGATGCCAAGAATATGATGGCTGCCTGAGATCCTTGCCTCAGCCGCTACCTCACTATGACTGCTGTCTTCCATAGGTGGA
TGTCCATGAAGGAGGTGGAT

Alignment

ORF - retro_eeur_441 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.61 %
• Parental protein coverage: 73.42 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEAAGN-KYVPRAILVDLE
          MREI.H.QAGQCGNQI.AKFWEVISDEHGIDPT..YH..S.LQL..I.VYY.E..G..KYVP.AILV.LE
Retrocopy MREIMHTQAGQCGNQISAKFWEVISDEHGIDPTSTYHRNSNLQLDHIYVYYYEGTGA<KYVPCAILVNLE

Parental  PGTMDSVRSGPFGQIFRP-DFVFGQSGAG-NNWAKGHYTEGAELVDSVLDVVRKESESCDCLQGFQLTHS
          PGT.DSV.SGPFGQIF...DF..GQ.G.G.NNWAKGHYTEGAELVDS.LDVV.KE.ESCDCLQGFQL.HS
Retrocopy PGTTDSVLSGPFGQIFKTHDFFVGQFGTG>NNWAKGHYTEGAELVDSILDVVWKEAESCDCLQGFQLNHS

Parental  LGGGTGSGMGTLLISKIREEYPDRIMNTFSVMPSPKVSDTVVEPYNATLSVHQLVENTDETYCIDNEALY
          LGGGTGSGMGTLLISKIREEYPDRIMN.FSV.PSPKVSDTVVEPYNATL.VHQLVENTDETYCIDNEALY
Retrocopy LGGGTGSGMGTLLISKIREEYPDRIMNAFSVVPSPKVSDTVVEPYNATLFVHQLVENTDETYCIDNEALY

Parental  DICFRTLKLTTPTYGDLNHLVSATMSGVTTCLRFPGQLNADLRKLAVNMVP-FPRLHFFMPGFAPLTSRG
          DICF.TLKLTT..YGDLN.L.SATMS.VTT.L.FPG.LNADLRKLA.NMVP..PRLHFFMPGFAPLTS..
Retrocopy DICFHTLKLTTTIYGDLNNLISATMSSVTTYLHFPGKLNADLRKLAFNMVP<SPRLHFFMPGFAPLTSH*

Parental  SQQYRALTVPELTQQMFDSKNMMAACDPRHGRYLTVAAIFRGRMSMKEVD
          .QQY.ALTVP.LTQQ.FD.KNMMAA.DP...RYLT..A.F...MSMKEVD
Retrocopy NQQYQALTVPKLTQQVFDAKNMMAA*DPCLSRYLTMTAVFHRWMSMKEVD

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	1.45 RPM	446.37 RPM
SRP017611_kidney	0.56 RPM	23.44 RPM
SRP017611_liver	0.32 RPM	32.48 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_441 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 4 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000002955	1 retrocopy	retro_eeur_441 ,
Myotis lucifugus	ENSMLUG00000016179	1 retrocopy	retro_mluc_401,
Tupaia belangeri	ENSTBEG00000004854	9 retrocopies	retro_tbel_2291, retro_tbel_3456, retro_tbel_3944, retro_tbel_4113, retro_tbel_413, retro_tbel_4390, retro_tbel_4439, retro_tbel_961, retro_tbel_962,
Tursiops truncatus	ENSTTRG00000006144	1 retrocopy	retro_ttru_1393,