RetrogeneDB ID: retro_eeur_13

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_281792:5598..6318(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSEEUG00000002650
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSEEUG00000001433
• Aliases: None
• Description: None

Sequence

>retro_eeur_13
TTTGGTAAGAACACTCTAAGCCGGAGAGGAAGAGTAGTGCCAGGAAAGAGACGTCCTTACGGAGTTATAACTGGTCTTGC
GGCTAGAAAAGCAGCTGGGATTCGGAAAGGGGTTAGTCCTATGAATCGGCCACCTCTGAGTGACAAGAATATAGAACGAT
ATTTTCCAGTGTTAAAGAGGAAGGCAAATCTTCTTAGACAAAATGAAGTGCAGAGGAAACCAGTTACAGTTCTTAAGAGA
TCTAACCAGCTAAATAGAAAAAATAACATTCCAGCCAATTTTACCAGGAGTGGAAATAAATTAAGTCATCAGAAAGACAG
TCGCCAGGCAACTTTTCTTTTCAGAAGAGGGCTGAAGGTTCAGGCCCAGGTGAACACAGAGCAGCTGATGAATGATGTCG
TAGTAAAGAGAGCTCGTCCATGGCGGACTTCTACCACAAATGGAGGAATATTGACTGTCTCCATTGACAATCCTGGAGCA
GTGCAGTGCCCAGTAACTCAGAAGCCACGATTAACTCGTACTGCTGTTCCCTCATTCTTGACAAAACGGGAGCAATCAGA
TGTAAAGAAAGTTCCTAAAGGTGTTCTCCTACAATTTGACATAAATAGTGTTGGAAAACAGACGGGGATGACTCTGAATG
AGCGATTTGGGATCCTAAAGGAGCAGAGCGCCGCTCTCACGTTCAACAAAAGAGGAAGTCGCTTTGTAACCCTAGGATAG

Alignment

ORF - retro_eeur_13 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.65 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FGKNTLSRRGRVVPGKRRPYGVITGLAARKAAGIRKGVSPMNRPPLSDKNIEQYFPVLKRKANLLRQNEV
          FGKNTLSRRGRVVPGKRRPYGVITGLAARKAAGIRKGVSPMNRPPLSDKNIE.YFPVLKRKANLLRQNEV
Retrocopy FGKNTLSRRGRVVPGKRRPYGVITGLAARKAAGIRKGVSPMNRPPLSDKNIERYFPVLKRKANLLRQNEV

Parental  QRKPVTVLKRSNQLNRKNNIPANFTRSGNKLSHQKDSRQATFLFRRGLKVQAQVNTEQLMDDVVAKRARP
          QRKPVTVLKRSNQLNRKNNIPANFTRSGNKLSHQKDSRQATFLFRRGLKVQAQVNTEQLM.DVV.KRARP
Retrocopy QRKPVTVLKRSNQLNRKNNIPANFTRSGNKLSHQKDSRQATFLFRRGLKVQAQVNTEQLMNDVVVKRARP

Parental  WRTSTTNGGILTVSIDNPGAVQCPVTQKPRLTRTAVPSFLTKREQSDVKKVPKGVPLQFDINSVGKQTGM
          WRTSTTNGGILTVSIDNPGAVQCPVTQKPRLTRTAVPSFLTKREQSDVKKVPKGV.LQFDINSVGKQTGM
Retrocopy WRTSTTNGGILTVSIDNPGAVQCPVTQKPRLTRTAVPSFLTKREQSDVKKVPKGVLLQFDINSVGKQTGM

Parental  TLNERFGILKEQRAALTFNKGGGRFVTVG
          TLNERFGILKEQ.AALTFNK.G.RFVT.G
Retrocopy TLNERFGILKEQSAALTFNKRGSRFVTLG

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	15.95 RPM
SRP017611_kidney	3.94 RPM	27.01 RPM
SRP017611_liver	1.45 RPM	9.97 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_13 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 31 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014874	1 retrocopy	retro_btau_1572,
Canis familiaris	ENSCAFG00000029695	1 retrocopy	retro_cfam_70,
Choloepus hoffmanni	ENSCHOG00000002881	2 retrocopies	retro_chof_1068, retro_chof_114,
Callithrix jacchus	ENSCJAG00000016488	2 retrocopies	retro_cjac_1639, retro_cjac_623,
Cavia porcellus	ENSCPOG00000011463	2 retrocopies	retro_cpor_1039, retro_cpor_586,
Dasypus novemcinctus	ENSDNOG00000007807	6 retrocopies	retro_dnov_1010, retro_dnov_1224, retro_dnov_1311, retro_dnov_2013, retro_dnov_442, retro_dnov_570,
Erinaceus europaeus	ENSEEUG00000001433	1 retrocopy	retro_eeur_13 ,
Echinops telfairi	ENSETEG00000000700	1 retrocopy	retro_etel_765,
Homo sapiens	ENSG00000122068	2 retrocopies	retro_hsap_4291, retro_hsap_476,
Gorilla gorilla	ENSGGOG00000011665	1 retrocopy	retro_ggor_450,
Macaca mulatta	ENSMMUG00000006626	1 retrocopy	retro_mmul_577,
Nomascus leucogenys	ENSNLEG00000015547	2 retrocopies	retro_nleu_1047, retro_nleu_889,
Pongo abelii	ENSPPYG00000014456	2 retrocopies	retro_pabe_258, retro_pabe_3497,
Pan troglodytes	ENSPTRG00000015796	1 retrocopy	retro_ptro_357,
Sorex araneus	ENSSARG00000009996	1 retrocopy	retro_sara_148,
Sarcophilus harrisii	ENSSHAG00000005704	1 retrocopy	retro_shar_242,
Tupaia belangeri	ENSTBEG00000005595	4 retrocopies	retro_tbel_2469, retro_tbel_2943, retro_tbel_4257, retro_tbel_791,