RetrogeneDB ID: retro_eeur_585

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_349276:41235..42073(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RRM2
• Ensembl ID: ENSEEUG00000009755
• Aliases: None
• Description: ribonucleotide reductase M2 [Source:HGNC Symbol;Acc:10452]

Sequence

>retro_eeur_585
CCCGCTCACCCCCATCGTGGACCCCAAACAGCTGCAGCTCTCACCCCTGAAAAAGCTCTTCCTGGCGGACTGGACTAGGA
GAACACGCCCCCGAGCCTCAGCGCGAGGAGGATCCTGCAGGAGGAGCCCGAGCCGAAAACCTAGGCCCCTGTCCCCAGCC
TCGAAGAGGAGCCACTCCTAAGAGAAAACCCCCGTCGCTTTGTCATCTTTCCCATCGAATACCATGATATCTGGCAGATG
TATAAGAAGGCCGAGGCCTCATTTTGGACAGCTGAGGAGGTGGACCTTTCCAGGGACATCCAGCACTGGGAGGCCCCTGA
AACCTGAGGAGAGATATTTTATATCCCATGTCCTGGCTTTCTTCGCAGCCAGTGATGGCATAGTGAGTGAAAACTTGGTG
GAGCGGTTTAGCCAAGAAGTTCAGATTACAGAAGCCTGCTGTTTCTATGGCTTCCAGATTGCCATGGAAAACATACACTC
TGAAATGTACAGTCTCCTCATCGATACTTACGTTAAAGATTCCAAAGAGAGGGAATTCCTCTTCAACGCTATTGAGACAA
TGCCTTGTGTAAAGAAGAAGGCAGATTGGGCCTTGTGTTGGATTGGGGACAAAGAAGCCACCCATGGAGAATGTGTAGTA
GCCTTTGCAGCAGTTGAAGGAATCTTCTTTTCTGGTTCTTTTGCATCCATATTCTGGCTCAAGAAACGAGGACTGATGCC
CGGTCTTACATTTTCGAATGAGCTAATTAGCAGAGATGAGGGACTCCATTGTGATTTTGCGTGTTTAATGTTCAAACATC
TGCTACATAAACCTTCGGAGCAGAGAGTCAGAGAAATA

Alignment

ORF - retro_eeur_585 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.79 %
• Parental protein coverage: 62.7 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PKQLQLSPLKKLCLADKENTPPSLSATRVLASKTARRILQEEPEPKTEAPVPSLEEEPLLRENPRRFVIF
          P......P.....L......P..L.......S..ARRILQEEPEPKT.APVPSLEEEPLLRENPRRFVIF
Retrocopy PAHPHRGPQTAAALTPEKALPGGLD*ENTPPSLSARRILQEEPEPKT*APVPSLEEEPLLRENPRRFVIF

Parental  PIEYHDIWQMYKKAEASFWTAEEVDLSKDIQHWEA-LKPEERYFISHVLAFFAASDGIVNENLVERFSQE
          PIEYHDIWQMYKKAEASFWTAEEVDLS.DIQHWEA.LKPEERYFISHVLAFFAASDGIV.ENLVERFSQE
Retrocopy PIEYHDIWQMYKKAEASFWTAEEVDLSRDIQHWEA>LKPEERYFISHVLAFFAASDGIVSENLVERFSQE

Parental  VQITEARCFYGFQIAMENIHSEMYSLLIDTYIKDSKEREFLFNAIETMPCVKKKADWALRWIGDKEATYG
          VQITEA.CFYGFQIAMENIHSEMYSLLIDTY.KDSKEREFLFNAIETMPCVKKKADWAL.WIGDKEAT.G
Retrocopy VQITEACCFYGFQIAMENIHSEMYSLLIDTYVKDSKEREFLFNAIETMPCVKKKADWALCWIGDKEATHG

Parental  ERVVAFAAVEGIFFSGSFASIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMFKHLLHKPSEQRVREI
          E.VVAFAAVEGIFFSGSFASIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMFKHLLHKPSEQRVREI
Retrocopy ECVVAFAAVEGIFFSGSFASIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMFKHLLHKPSEQRVREI

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	0.64 RPM
SRP017611_kidney	0.00 RPM	0.19 RPM
SRP017611_liver	0.00 RPM	1.45 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_585 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 18 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000003409	1 retrocopy	retro_cfam_2113,
Callithrix jacchus	ENSCJAG00000006533	3 retrocopies	retro_cjac_2134, retro_cjac_2950, retro_cjac_3851,
Cavia porcellus	ENSCPOG00000008652	1 retrocopy	retro_cpor_8,
Erinaceus europaeus	ENSEEUG00000009755	2 retrocopies	retro_eeur_421, retro_eeur_585 ,
Echinops telfairi	ENSETEG00000015797	2 retrocopies	retro_etel_640, retro_etel_691,
Homo sapiens	ENSG00000171848	1 retrocopy	retro_hsap_4815,
Macropus eugenii	ENSMEUG00000000121	3 retrocopies	retro_meug_1450, retro_meug_199, retro_meug_277,
Microcebus murinus	ENSMICG00000012789	1 retrocopy	retro_mmur_1384,
Myotis lucifugus	ENSMLUG00000010596	1 retrocopy	retro_mluc_794,
Macaca mulatta	ENSMMUG00000002057	1 retrocopy	retro_mmul_2568,
Monodelphis domestica	ENSMODG00000014763	1 retrocopy	retro_mdom_775,
Mus musculus	ENSMUSG00000020649	2 retrocopies	retro_mmus_2472, retro_mmus_3073,
Nomascus leucogenys	ENSNLEG00000013733	2 retrocopies	retro_nleu_2190, retro_nleu_3040,
Otolemur garnettii	ENSOGAG00000007075	1 retrocopy	retro_ogar_2665,
Pongo abelii	ENSPPYG00000012656	1 retrocopy	retro_pabe_3743,
Rattus norvegicus	ENSRNOG00000023272	1 retrocopy	retro_rnor_331,
Sus scrofa	ENSSSCG00000021742	1 retrocopy	retro_sscr_901,
Tursiops truncatus	ENSTTRG00000017209	1 retrocopy	retro_ttru_603,