RetrogeneDB ID: retro_eeur_683

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_66110:245..617(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: OSTF1
• Ensembl ID: ENSEEUG00000008320
• Aliases: None
• Description: osteoclast stimulating factor 1 [Source:HGNC Symbol;Acc:8510]

Sequence

>retro_eeur_683
CAAGTTAAAGCATTTAGAGCTCTGTGTACATTTGAACCCACAACTCCAGATGAATTGTACTTTGAAGAAGGCGATATTAT
TTACATTACTGACATGAGTGACACCACTTGGTGGAAAGGCACCTCCAAGGGAAGGACGGAATTAATCCCAAGCAACTATA
TGGCTGAGCAAGCAGAATCCATCGACAATCCGTTGCATGAGGCTGCAAAGAGAGGCAACTTGAGCTGGCTGAGGGAGTGT
CTGGACAACCGGGTTGGTGTGAACGGTTTGGACAAAGCAGGAAGCACTGCCTTGTACTGGGCTTGTCACGGGGGCCACAA
AGATATCGTGGGAATGCTATTTACTCAACCAAACATTGAACTGAACCAACAG

Alignment

ORF - retro_eeur_683 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.65 %
• Parental protein coverage: 61.39 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QVKVFRALYTFEPRTXXXXXXXXXXXXXXXXXSDTNWWKGTSKGRTGLIPSNYVAEQAESIDNPLHEAAK
          QVK.FRAL.TFEP.T.................SDT.WWKGTSKGRT.LIPSNY.AEQAESIDNPLHEAAK
Retrocopy QVKAFRALCTFEPTTPDELYFEEGDIIYITDMSDTTWWKGTSKGRTELIPSNYMAEQAESIDNPLHEAAK

Parental  RGNLSWLRECLDNRVGVNGLDKAGSTALYWACHGGHKDIVEMLFTQPNIELNQQ
          RGNLSWLRECLDNRVGVNGLDKAGSTALYWACHGGHKDIV.MLFTQPNIELNQQ
Retrocopy RGNLSWLRECLDNRVGVNGLDKAGSTALYWACHGGHKDIVGMLFTQPNIELNQQ

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	11.44 RPM	16.11 RPM
SRP017611_kidney	16.50 RPM	27.01 RPM
SRP017611_liver	9.49 RPM	12.38 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_683 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 15 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012808	1 retrocopy	retro_cjac_3249,
Cavia porcellus	ENSCPOG00000007226	1 retrocopy	retro_cpor_1049,
Dipodomys ordii	ENSDORG00000002933	1 retrocopy	retro_dord_698,
Erinaceus europaeus	ENSEEUG00000008320	2 retrocopies	retro_eeur_545, retro_eeur_683 ,
Felis catus	ENSFCAG00000022374	1 retrocopy	retro_fcat_1869,
Homo sapiens	ENSG00000134996	1 retrocopy	retro_hsap_1058,
Gorilla gorilla	ENSGGOG00000011920	1 retrocopy	retro_ggor_836,
Macaca mulatta	ENSMMUG00000010401	1 retrocopy	retro_mmul_836,
Nomascus leucogenys	ENSNLEG00000001854	1 retrocopy	retro_nleu_2502,
Otolemur garnettii	ENSOGAG00000002603	1 retrocopy	retro_ogar_2962,
Pongo abelii	ENSPPYG00000019300	1 retrocopy	retro_pabe_883,
Pan troglodytes	ENSPTRG00000021031	1 retrocopy	retro_ptro_720,
Rattus norvegicus	ENSRNOG00000012156	2 retrocopies	retro_rnor_936, retro_rnor_937,
Sus scrofa	ENSSSCG00000005273	1 retrocopy	retro_sscr_979,
Tursiops truncatus	ENSTTRG00000003081	1 retrocopy	retro_ttru_492,