RetrogeneDB ID: retro_eeur_171

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_139668:574..942(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSEEUG00000011007
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PAM16
• Ensembl ID: ENSEEUG00000007432
• Aliases: None
• Description: presequence translocase-associated motor 16 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:29679]

Sequence

>retro_eeur_171
GCCAGTTACCTCGCCCAGATCATCATGATGGGGGGTGCAGGTGGTGGGCAGGGCCTTCATGTATGGCCTGCAGGAGGAGT
TTGCAGTCAGGCTGGCCACAGCTGATGCTCAGGGGCCGGGCCGGACACCAGTCTGCAACTGCCTCCAACCTCATTTGGCC
TCAGCCTCCAGGAGGCCCAGCAGATTCTCAATGTCTCCAAGCTGAACCTGAGGAGATCCAAAAGAACTGTGAACACTTGT
TCAAGGTGAACATCAAGTCAGTAGGTGGCTCCTTCTACCTGCAGTCAAAGGTGGGCCGGGCAAAGGAGCACCTGGACGAG
GAGCTGAGGATCCAGGCCCAGGAGGACAGAGGAAAAGAACCCAAAACA

Alignment

ORF - retro_eeur_171 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.95 %
• Parental protein coverage: 99.19 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  ARYLAQIIVMGA-QVVGRAFARALREEFAASRAAADA-RGRAGHQSAAASNLT-GLSLQEAQQILNVSKL
          A.YLAQII.MG..QVVGRAF...L.EEFA...A.ADA.RGRAGHQSA.ASNL..GLSLQEAQQILNVSKL
Retrocopy ASYLAQIIMMGG>QVVGRAFMYGLQEEFAVRLATADA>RGRAGHQSATASNLI>GLSLQEAQQILNVSKL

Parental  N-PEEIQKNYQHLFKVNDKSVGGSFYLQSKVVRAKERLDEELRIRAQEDRGKEPQT
          N.PEEIQKN..HLFKVN.KSVGGSFYLQSKV.RAKE.LDEELRI.AQEDRGKEP.T
Retrocopy N<PEEIQKNCEHLFKVNIKSVGGSFYLQSKVGRAKEHLDEELRIQAQEDRGKEPKT

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	11.44 RPM
SRP017611_kidney	0.00 RPM	25.69 RPM
SRP017611_liver	0.00 RPM	16.88 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_171 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 16 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009200	1 retrocopy	retro_btau_1664,
Canis familiaris	ENSCAFG00000019226	1 retrocopy	retro_cfam_1967,
Callithrix jacchus	ENSCJAG00000019772	1 retrocopy	retro_cjac_1148,
Dasypus novemcinctus	ENSDNOG00000010921	2 retrocopies	retro_dnov_1361, retro_dnov_8,
Dipodomys ordii	ENSDORG00000014888	1 retrocopy	retro_dord_81,
Equus caballus	ENSECAG00000019387	1 retrocopy	retro_ecab_302,
Erinaceus europaeus	ENSEEUG00000007432	7 retrocopies	retro_eeur_138, retro_eeur_171 , retro_eeur_213, retro_eeur_234, retro_eeur_273, retro_eeur_440, retro_eeur_673,
Echinops telfairi	ENSETEG00000006416	1 retrocopy	retro_etel_2070,
Felis catus	ENSFCAG00000027971	1 retrocopy	retro_fcat_520,
Myotis lucifugus	ENSMLUG00000008921	6 retrocopies	retro_mluc_2446, retro_mluc_2447, retro_mluc_2448, retro_mluc_2516, retro_mluc_2517, retro_mluc_429,
Mus musculus	ENSMUSG00000014301	1 retrocopy	retro_mmus_73,
Rattus norvegicus	ENSRNOG00000004608	1 retrocopy	retro_rnor_713,
Sus scrofa	ENSSSCG00000007947	2 retrocopies	retro_sscr_1090, retro_sscr_468,
Ictidomys tridecemlineatus	ENSSTOG00000003461	1 retrocopy	retro_itri_1732,
Tupaia belangeri	ENSTBEG00000001347	1 retrocopy	retro_tbel_3190,
Tarsius syrichta	ENSTSYG00000009306	1 retrocopy	retro_tsyr_282,