RetrogeneDB ID: retro_eeur_506

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_331103:327..1045(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PDCL3
• Ensembl ID: ENSEEUG00000000224
• Aliases: None
• Description: phosducin-like 3 [Source:HGNC Symbol;Acc:28860]

Sequence

>retro_eeur_506
ATGCAGAACCCTAATTCAGACACTGAGTAGAATGACATCTTGTGGAAAAGGGCATCTTGACCTCAAAGGATAATTTGAAA
GAACGGGAAAAGAAGCAAAAGAAGAGGAACAGTTAATCCTTCAGCAATCAATCGTGAAGACATCTGAAGATATTACTTTG
CAAGAACTAGAGGATAATGAAGATGAATTTAATGAGGCAGGTGAACATGTTATTGAAATGTACAGACAGCAAAGACTAGT
AGAATGGAAAGCAACTAAATTGAAGAATAAATTTGGTGAAGTTTTAGAGATCTCAGGAAAGGATTATGTTCAATAAATTA
CCAAAGCCTGTGAGGGCCTGTGGGTAATCTTGCATCTTTACAAATAAAGGATTTCCCTCTGTGCCCTGATAAATCAGCAC
TTCAGTGGACTTACCAGGAAGTTTGCCAGTGTCAAATTTATCATAGCTATCTCAACAATCTGCATACACAATTACCCTGA
TAGAAACCTGCCCACAGTATTTGTTTACCTTGAAGGTGATAGCAAGACTCACTTTATTGGGCCTTTAGTGTTTGTAGGCA
TGAACCTGACAAGAGATGAATTGGAGTGGAAGTTGTCTGAATCTGGAGCCATCAAGACTGACCTAGAGGAAAACCTTAGG
AAACCAATTGAAGACACATTACTGTCCTCAGTGTGATGCTCAGTGCCCATGAGGAGCGGCAGTGATTCTGAGAATGAC

Alignment

ORF - retro_eeur_506 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.06 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MQDPNADTEWNDILRK-KGILPSKNNLEELEK-EAEEEEQLILQQSIVKTYEDMTLQELEDNEDEFNEED
          MQ.PN.DTE.NDIL.K.KGIL.SK.NL.E.EK.EA.EEEQLILQQSIVKT.ED.TLQELEDNEDEFNE..
Retrocopy MQNPNSDTE*NDILWK<KGILTSKDNLKEREK<EAKEEEQLILQQSIVKTSEDITLQELEDNEDEFNEAG

Parental  ERAIEMYRQQRLAEWKATKLKNKFGEVLEISGKDYVQEVTKAGEGLWVILHLYKQGIPLCALINQHFSEL
          E..IEMYRQQRL.EWKATKLKNKFGEVLEISGKDYVQ..TKA.EGLWVILHLYK..I.LCALINQHFS.L
Retrocopy EHVIEMYRQQRLVEWKATKLKNKFGEVLEISGKDYVQ*ITKACEGLWVILHLYK*RISLCALINQHFSGL

Parental  AKKFPSVKFIKAISTTCIPNYPDRNLPTIFVYLEGDIKAQFIGPLVFGGMNLTRDELEWKLSESGAIKTD
          ..KF.SVKFI.AIST.CI.NYPDRNLPT.FVYLEGD.K..FIGPLVF.GMNLTRDELEWKLSESGAIKTD
Retrocopy TRKFASVKFIIAISTICIHNYPDRNLPTVFVYLEGDSKTHFIGPLVFVGMNLTRDELEWKLSESGAIKTD

Parental  LEENPRKPVEDTLLSSVRCSVPMRSSSDSEDD
          LEEN.RKP.EDTLLSSV.CSVPMRS.SDSE.D
Retrocopy LEENLRKPIEDTLLSSV*CSVPMRSGSDSEND

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	0.00 RPM	30.94 RPM
SRP017611_kidney	0.00 RPM	71.83 RPM
SRP017611_liver	0.00 RPM	37.94 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_506 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 14 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000002226	1 retrocopy	retro_cfam_1740,
Callithrix jacchus	ENSCJAG00000010160	3 retrocopies	retro_cjac_1486, retro_cjac_1599, retro_cjac_2055,
Dipodomys ordii	ENSDORG00000012397	1 retrocopy	retro_dord_702,
Erinaceus europaeus	ENSEEUG00000000224	1 retrocopy	retro_eeur_506 ,
Homo sapiens	ENSG00000115539	7 retrocopies	retro_hsap_1132, retro_hsap_151, retro_hsap_2684, retro_hsap_2757, retro_hsap_3535, retro_hsap_3961, retro_hsap_4102,
Microcebus murinus	ENSMICG00000000657	1 retrocopy	retro_mmur_899,
Myotis lucifugus	ENSMLUG00000016446	1 retrocopy	retro_mluc_1443,
Monodelphis domestica	ENSMODG00000001489	1 retrocopy	retro_mdom_734,
Mus musculus	ENSMUSG00000026078	1 retrocopy	retro_mmus_2284,
Nomascus leucogenys	ENSNLEG00000014393	8 retrocopies	retro_nleu_1499, retro_nleu_1575, retro_nleu_2741, retro_nleu_2891, retro_nleu_538, retro_nleu_571, retro_nleu_778, retro_nleu_926,
Oryctolagus cuniculus	ENSOCUG00000001469	2 retrocopies	retro_ocun_1035, retro_ocun_920,
Otolemur garnettii	ENSOGAG00000015138	2 retrocopies	retro_ogar_1147, retro_ogar_2959,
Ochotona princeps	ENSOPRG00000011600	2 retrocopies	retro_opri_1070, retro_opri_289,
Tursiops truncatus	ENSTTRG00000006242	1 retrocopy	retro_ttru_1184,