RetrogeneDB ID: retro_eeur_151

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_103091:59..636(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSEEUG00000009626
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: EPCAM
• Ensembl ID: ENSEEUG00000009462
• Aliases: None
• Description: epithelial cell adhesion molecule [Source:HGNC Symbol;Acc:11529]

Sequence

>retro_eeur_151
CACCACAAGATGACTGTGTGCAACCGGGACGGCCCGGGTGGACTGTGCCAGTGCGCGCCATCGGCTCGGCTTCGCGGTCA
ACTGCTCCACCCTCACCTCCAAGTGCCTGCTGCTCAAGGCGCGCATGAGCGCCCCCAAGAACGGCCGCGGGCTGGTGCGC
CCCAGCGAGCACGCGATCACCGACAACGATGGGCTGTACGACCCGGACTGCGACCACGAGGGGCGCTTCAAGGCTCGCCA
GTGCAACCAGACTTCCGAGTGCTGGTGCGTGAACTCGGTGGGCGTGCGGCGCACGGACAAGGGCGACCAGCACCTGCGCT
GCGACGAGCTGGTGCGCACCTACCACATCCTCATCGACCTCCGCCACCGCCCAGCATCCCGCGCCTTCAACCACTCGGAC
CTGGATGCCGAGCTGCGCCGGCTGTTCCGCGAGCGCTACCGGCTGCACCCCAAGTTCGTGGCGGCCGTGCACTACGAGCA
ACCCACCATCCAGATCGAGCTGCTCCAGAACGCGTCGCAAAAGGCCCCCGGCGACGTGGACATCGCCGATGCCGCCTACT
ACTTCGAGAGAGACGTC

Alignment

ORF - retro_eeur_151 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.28 %
• Parental protein coverage: 76.92 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NYKLTTNCSENDNGQCQCT-SIGTQH-TVTCSKLASKCLVMKAEMNGSKSGRR-VRP-EGAIQNNDGLYD
          ..K.T........G.CQC...IG.....V.CS.L.SKCL..KA.M...K.GR..VRP.E.AI..NDGLYD
Retrocopy HHKMTVCNRDGPGGLCQCA<AIGSAS<AVNCSTLTSKCLLLKARMSAPKNGRGLVRPSEHAITDNDGLYD

Parental  PDCDEMGLFKAKQCNGTTACWCVNTAGVRRTDK-DSEIICSERVRTYWIIIELKHKARETPFEVESLKSA
          PDCD..G.FKA.QCN.T..CWCVN..GVRRTDK.D....C.E.VRTY.I.I.L.H......F....L...
Retrocopy PDCDHEGRFKARQCNQTSECWCVNSVGVRRTDKGDQHLRCDELVRTYHILIDLRHRPASRAFNHSDLDAE

Parental  LKQVITSRYQLDPKYITNIVYENDIITIDLVQNSSQKTQSDVDIADVAYYFEKDV
          L......RY.L.PK......YE...I.I.L.QN.SQK...DVDIAD.AYYFE.DV
Retrocopy LRRLFRERYRLHPKFVAAVHYEQPTIQIELLQNASQKAPGDVDIADAAYYFERDV

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	7.25 RPM
SRP017611_kidney	12.75 RPM	173.29 RPM
SRP017611_liver	0.80 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_151 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 17 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006474	1 retrocopy	retro_btau_66,
Choloepus hoffmanni	ENSCHOG00000013834	1 retrocopy	retro_chof_258,
Callithrix jacchus	ENSCJAG00000000624	1 retrocopy	retro_cjac_3006,
Dasypus novemcinctus	ENSDNOG00000011799	1 retrocopy	retro_dnov_345,
Erinaceus europaeus	ENSEEUG00000009462	1 retrocopy	retro_eeur_151 ,
Macropus eugenii	ENSMEUG00000015074	2 retrocopies	retro_meug_1984, retro_meug_474,
Microcebus murinus	ENSMICG00000000151	1 retrocopy	retro_mmur_739,
Macaca mulatta	ENSMMUG00000012390	1 retrocopy	retro_mmul_34,
Monodelphis domestica	ENSMODG00000001077	1 retrocopy	retro_mdom_104,
Mus musculus	ENSMUSG00000045394	1 retrocopy	retro_mmus_185,
Ochotona princeps	ENSOPRG00000004301	1 retrocopy	retro_opri_1225,
Pelodiscus sinensis	ENSPSIG00000015680	1 retrocopy	retro_psin_22,
Pan troglodytes	ENSPTRG00000011902	1 retrocopy	retro_ptro_92,
Rattus norvegicus	ENSRNOG00000015667	1 retrocopy	retro_rnor_252,
Sus scrofa	ENSSSCG00000008429	1 retrocopy	retro_sscr_69,
Ictidomys tridecemlineatus	ENSSTOG00000008631	1 retrocopy	retro_itri_106,
Tursiops truncatus	ENSTTRG00000004235	2 retrocopies	retro_ttru_21, retro_ttru_394,