RetrogeneDB ID: retro_eeur_303

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_247159:89..1481(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: POLD2
• Ensembl ID: ENSEEUG00000006258
• Aliases: None
• Description: polymerase (DNA directed), delta 2, accessory subunit [Source:HGNC Symbol;Acc:9176]

Sequence

>retro_eeur_303
TCTGAGCAGGGTGCCCAGAGGGCCCAGAATCTGCTGTCTCCACTTCCACCAACAATGCCACTTTTGCCCGTGTGCCTGTG
GTTACCTACAGCAACTCTTCCCAGCCCTTCCGCTTGGGCGAGCGCAGCTTTATCCGCCAATATGCTCACATCTATGCCAC
CTGCGTTGTCTAGATGCGGCCTTTCTTGGAGAGCCGCGCCCAGCAGCACTGGGCGCACTGAGGTGCAAATCAAGAAGCTG
TGTGAGCTGCAGCCTGCAGAGAAGTGTTGTGTGGTGGGGACCCTCTTTAAGGCCATGCTGCTCCAGCCCTCCATCCTGCG
GGAGGTCAGTGAGGAGCACAACTTGGTCCCCCAACCCCCTCGGGGCAAATACATCTACCCGGACCATGAGCTGGTCCTGG
AGGACAAGCTGCAGCGCATCAAGCTAGAGGGCAACATCGCCGTGTCCCAGCTGGTGACAGGGACTGTGCTAGCTGTACTG
GGCTCTGTGCGTGACGACGGCAAGTTCCTGGTGGAGGACCACTGCTTTGCAGAACTTGCGCCCCAGAAGCCCGCACCCAC
CCTGGACTTGGACCGGTTCGTGCTCCTGGTATCTGGCCTGGGGCTGGGTGGTGGCGGCGGTGAGAGCCTGCTGGGCACCC
AGCTGCCGATGGACGTGGTGACAGGGCAGCTGGGGGATGAGGGAGAGCAGCGCAGTGCCGCCCAAGTGTCCTGCGTCATC
CTGGCTAGGAACCTGCTGAGCCACAGCACCCAGAGCCGGGACTCCATCAACAAGGCCAAGTACCTGACCAAGAAAACCCA
GGCAGCCAGCGTGGAGGCTGTCAAGATGCTGGATGAGATCCTCCTGCAGCTGAGTGCCTCAGTGCCCGTGGATGTGATGC
CAGGAGAATTTGACCCCACCAACTACACGCTCCCCCAGCAGCCCCTGCACCCCTGCATGTTCCCCCTGGCCACAGCCTAC
TCCACCCTCCAGCTGGTCACCAACCCCTACCAGGCCACCATTGATGGAATCAGATTCCTGGGGACATCAGGACAGAACGT
GAGTAACATCTTCAGGTACAGCAGCATGGAGGACCACCTGGAAATTCTGGAGTGGACGTTACGGGTCCGTCACATCAGCC
CCACAGCCCCTGACACACTTGGTTGCTACCCCTTCTACAAAACTGACCCATTTGTCTTCCCTGAGTGCCCACATGTCTAC
TTCTGTGGCAGCGCCCCCAGCTTTGGCTCCAAAGTCATACGAGGTCCTGAGGGCCAGACGGTGCTGCTGGTGGCTGTCCC
GGACTTCAGCACCATGCAGACGGCCTGCCTGGTGAACCTGCATGGCCTGGCTTGCCAACCCATTAGCTTCTCAGGCTTTG
GAGCTGATGAGGACCTGGGAGACCTGGGCCCC

Alignment

ORF - retro_eeur_303 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.42 %
• Parental protein coverage: 99.57 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SEQAAQRAQTLLSP-PSTNNATFARVPVVTYSNSSQPFRLGERSFNRQYAHIYATRLVQMRPFLESRAQQ
          SEQ.AQRAQ.LLSP..STNNATFARVPVVTYSNSSQPFRLGERSF.RQYAHIYAT..V.MRPFLESRAQQ
Retrocopy SEQGAQRAQNLLSP<TSTNNATFARVPVVTYSNSSQPFRLGERSFIRQYAHIYATCVV*MRPFLESRAQQ

Parental  HWG-TEVQIKKLCELQPAEKCCVVGTLFKAMLLQPSILREVSEEHNLVPQPPRSKYIHPDDELVLEDELQ
          HW..TEVQIKKLCELQPAEKCCVVGTLFKAMLLQPSILREVSEEHNLVPQPPR.KYI.PD.ELVLED.LQ
Retrocopy HWA>TEVQIKKLCELQPAEKCCVVGTLFKAMLLQPSILREVSEEHNLVPQPPRGKYIYPDHELVLEDKLQ

Parental  RIKLEGNIAVSRLVTGTVLAVLGSVRDDGKFLVEDHCFAELAPQKPAPTLDSDRFVLLVSGLGLGGGGGE
          RIKLEGNIAVS.LVTGTVLAVLGSVRDDGKFLVEDHCFAELAPQKPAPTLD.DRFVLLVSGLGLGGGGGE
Retrocopy RIKLEGNIAVSQLVTGTVLAVLGSVRDDGKFLVEDHCFAELAPQKPAPTLDLDRFVLLVSGLGLGGGGGE

Parental  SLLGTQLLVDVVTGQLGDEGEQRSAAQVSRVILAGNLLSHSTQSRDSINKAKYLTKKTQAASVEAVKMLD
          SLLGTQL..DVVTGQLGDEGEQRSAAQVS.VILA.NLLSHSTQSRDSINKAKYLTKKTQAASVEAVKMLD
Retrocopy SLLGTQLPMDVVTGQLGDEGEQRSAAQVSCVILARNLLSHSTQSRDSINKAKYLTKKTQAASVEAVKMLD

Parental  EILLQLSASVPVDVMPGEFDPTNYTLPQQPLHPCMFPLATAYSTLQLVTNPYQATIDGVRFLGTSGQNVS
          EILLQLSASVPVDVMPGEFDPTNYTLPQQPLHPCMFPLATAYSTLQLVTNPYQATIDG.RFLGTSGQNVS
Retrocopy EILLQLSASVPVDVMPGEFDPTNYTLPQQPLHPCMFPLATAYSTLQLVTNPYQATIDGIRFLGTSGQNVS

Parental  DIFRYSSMEDHLEILEWTLRVRHISPTARDTLGCYPFYKTDPFVFPECPHVYFCGSAPNFGSKVIRGPEG
          .IFRYSSMEDHLEILEWTLRVRHISPTA.DTLGCYPFYKTDPFVFPECPHVYFCGSAP.FGSKVIRGPEG
Retrocopy NIFRYSSMEDHLEILEWTLRVRHISPTAPDTLGCYPFYKTDPFVFPECPHVYFCGSAPSFGSKVIRGPEG

Parental  QTVLLVAVPDFSTTQTACLVNLRGLACQPISFSGFGADEDLGDLGP
          QTVLLVAVPDFST.QTACLVNL.GLACQPISFSGFGADEDLGDLGP
Retrocopy QTVLLVAVPDFSTMQTACLVNLHGLACQPISFSGFGADEDLGDLGP

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	5.80 RPM
SRP017611_kidney	2.81 RPM	21.94 RPM
SRP017611_liver	0.64 RPM	6.27 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_303 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 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000002933	1 retrocopy	retro_cfam_1870,
Callithrix jacchus	ENSCJAG00000007954	1 retrocopy	retro_cjac_700,
Erinaceus europaeus	ENSEEUG00000006258	1 retrocopy	retro_eeur_303 ,
Homo sapiens	ENSG00000106628	1 retrocopy	retro_hsap_3217,
Gorilla gorilla	ENSGGOG00000004424	2 retrocopies	retro_ggor_2183, retro_ggor_2184,
Pongo abelii	ENSPPYG00000017597	1 retrocopy	retro_pabe_2665,
Pan troglodytes	ENSPTRG00000019138	1 retrocopy	retro_ptro_2236,