RetrogeneDB ID: retro_eeur_190

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_202746:492..852(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PCBD2
• Ensembl ID: ENSEEUG00000007051
• Aliases: None
• Description: pterin-4 alpha-carbinolamine dehydratase/dimerization cofactor of hepatocyte nuclear factor 1 alpha (TCF1) 2 [Source:HGNC Symbol;Acc:24474]

Sequence

>retro_eeur_190
GCGGCGCTGTGCTTGCTCTGGGGGCTGCGGGGTCGCAGCCCGAGCTTCGCAGCCATGTCAACAGATGCTCACTGGTTGAC
TGCAGAGAAGAATCAAGTTATACTTGACCTTACAGCAGCAGGATGGTTGGAATTAAGTGATAGAAATGCTGTCTACAAAG
AGTTCATCTTTAAAAATTTTAATCAGGCATTTGGCTTTATGTCCAGAGTTGCTCTACAAGCAGAGAAGATGAATCATCAC
TCAGAATGGTTTCATGTGTACAACAAGGTCCAGATAACTCTCACCTCACATGACTGCGGTGGACTGACCAAAAGAGATGT
GAAACTGGCCAATTTTATTGAAAAAGCAGCTGCCTCTATG

Alignment

ORF - retro_eeur_190 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.39 %
• Parental protein coverage: 93.75 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AALCLLRALRGRSPSFAAMSTDAHWLTAEERNQVILDLTAAGWLELSDRDAVYKEFIFKNFNQAFGFMSR
          AALCLL..LRGRSPSFAAMSTDAHWLTAE..NQVILDLTAAGWLELSDR.AVYKEFIFKNFNQAFGFMSR
Retrocopy AALCLLWGLRGRSPSFAAMSTDAHWLTAE-KNQVILDLTAAGWLELSDRNAVYKEFIFKNFNQAFGFMSR

Parental  VALQAEKMNHH-PWFNVYNKVQITLTSHDCGGLTKRDVKLANFIEKAAASM
          VALQAEKMNHH..WF.VYNKVQITLTSHDCGGLTKRDVKLANFIEKAAASM
Retrocopy VALQAEKMNHHSEWFHVYNKVQITLTSHDCGGLTKRDVKLANFIEKAAASM

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	1.29 RPM	3.55 RPM
SRP017611_kidney	3.94 RPM	21.57 RPM
SRP017611_liver	2.57 RPM	9.32 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_190 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 9 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000019125	2 retrocopies	retro_dnov_645, retro_dnov_660,
Equus caballus	ENSECAG00000015810	2 retrocopies	retro_ecab_489, retro_ecab_871,
Erinaceus europaeus	ENSEEUG00000007051	1 retrocopy	retro_eeur_190 ,
Echinops telfairi	ENSETEG00000016658	2 retrocopies	retro_etel_1252, retro_etel_75,
Macropus eugenii	ENSMEUG00000003784	1 retrocopy	retro_meug_1185,
Myotis lucifugus	ENSMLUG00000012638	1 retrocopy	retro_mluc_1445,
Monodelphis domestica	ENSMODG00000014351	1 retrocopy	retro_mdom_1369,
Pteropus vampyrus	ENSPVAG00000000384	2 retrocopies	retro_pvam_63, retro_pvam_750,
Tursiops truncatus	ENSTTRG00000016874	3 retrocopies	retro_ttru_1135, retro_ttru_359, retro_ttru_511,