RetrogeneDB ID: retro_eeur_274

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_234148:22..763(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSEEUG00000008133
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SLC25A4
• Ensembl ID: ENSEEUG00000001021
• Aliases: None
• Description: solute carrier family 25 (mitochondrial carrier; adenine nucleotide translocator), member 4 [Source:HGNC Symbol;Acc:10990]

Sequence

>retro_eeur_274
ATGACAGACTCCGCCTTGTCCTTCTTGCAAGGACTTCCTGGCAGGGGGGTGGCCGCTGCCATCTCCAAGACCGCCATGGC
GCCCATGGAGTGGGTTAAACTGCTGCTGCAGGTGCAACATGCCAGCAAGCACATCACCGCTGACAAGCAATATAAGGGCA
TCATGGACTGTGTGGTCCCTATCCCCAAGGAACAGGGTGTGCTGCCCTTCTGGAATGGGAACCTAGACAATGTCATCAGA
CACTTCCCCACCCAGGCCCTCAACTTTGCCTTCAAAGATAAATACAAACAGATCTTCCTGGGAGGGGTGGACAAGAGGAC
CCAGTTGTGGCGCTACTTTGCCGGCAATCTGGCATCAGGTGGTGCAGCTGGGGCCACGTCCCTGTGCTTCGTGTACCCTC
TCGATTTTGCCCGTACCCGTCTAGCTGCTGATGTGGGCAAAGCCAGAGCTGAGCGAGAATTCAAAGGCCCGGTGACTGTC
TGGTTAAAATCTACAAATTGGATGGGATTAAGGGCCTGTACCAGGGCTTTAACGTGACTGTGCAGGGAATTATCATCTAC
CGGGCTGCCTACTTTGGTATCTCTGACACGGCACAGGGAATGCTCCCCCACCCCAAGAACATGCACATGTTTGTCAGCTG
GATGATCGCTCGCTCAGTCAGTCACAGCCCTGGCCGGCCTGGCTTCCTACCCATTTGATACTGTCCGATGTAGAATGATG
ATGCTGTCAGGGCGCAAAGGA

Alignment

ORF - retro_eeur_274 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.89 %
• Parental protein coverage: 82.55 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MSDQALSFV-KDFLAGG-VAAAVSKTAVAPIERVKLLLQVQHASKQISAEKQYKGIIDCIVRIPKEQGFV
          M.D.ALSF..KDFLAGG.VAAA.SKTA.AP.E.VKLLLQVQHASK.I.A.KQYKGI.DC.V.IPKEQG..
Retrocopy MTDSALSFL>KDFLAGG<VAAAISKTAMAPMEWVKLLLQVQHASKHITADKQYKGIMDCVVPIPKEQGVL

Parental  SFWRGNLANVIRYFPTQALNFAFKDKYKQIFLGGVDRHKQFWRYFAGNLASGGAAGATSLCFVYPLDFAR
          .FW.GNL.NVIR.FPTQALNFAFKDKYKQIFLGGVD...Q.WRYFAGNLASGGAAGATSLCFVYPLDFAR
Retrocopy PFWNGNLDNVIRHFPTQALNFAFKDKYKQIFLGGVDKRTQLWRYFAGNLASGGAAGATSLCFVYPLDFAR

Parental  TRLAADVGKGSAQREFNGL-GDCLTKIFKSDGLKGLYQGFSVSVQGIIIYRAAYFGVYDTAKGML-PDPK
          TRLAADVGK..A.REF.G..GDCL.KI.K.DG.KGLYQGF.V.VQGIIIYRAAYFG..DTA.GML.P.P.
Retrocopy TRLAADVGKARAEREFKGP<GDCLVKIYKLDGIKGLYQGFNVTVQGIIIYRAAYFGISDTAQGML>PTPR

Parental  NVHIIVSW-MIAQSVTAVAGLVSYPFDTVRRRMMMQSGRKG
          ...........AQSVTA.AGL.SYPFDTVR.RMMM.SGRKG
Retrocopy TCTCLSAG*SLAQSVTALAGLASYPFDTVRCRMMMLSGRKG

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	2.58 RPM	134.39 RPM
SRP017611_kidney	20.63 RPM	128.46 RPM
SRP017611_liver	4.50 RPM	0.00 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_274 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 13 parental genes, and 34 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013208	1 retrocopy	retro_btau_1592,
Choloepus hoffmanni	ENSCHOG00000010542	3 retrocopies	retro_chof_1117, retro_chof_1777, retro_chof_807,
Dasypus novemcinctus	ENSDNOG00000007258	3 retrocopies	retro_dnov_1531, retro_dnov_1800, retro_dnov_390,
Dipodomys ordii	ENSDORG00000013787	1 retrocopy	retro_dord_268,
Erinaceus europaeus	ENSEEUG00000001021	2 retrocopies	retro_eeur_274 , retro_eeur_36,
Macropus eugenii	ENSMEUG00000008508	4 retrocopies	retro_meug_222, retro_meug_549, retro_meug_6, retro_meug_921,
Microcebus murinus	ENSMICG00000010865	1 retrocopy	retro_mmur_1356,
Oryctolagus cuniculus	ENSOCUG00000002594	1 retrocopy	retro_ocun_102,
Ochotona princeps	ENSOPRG00000005957	6 retrocopies	retro_opri_1154, retro_opri_146, retro_opri_377, retro_opri_517, retro_opri_543, retro_opri_685,
Pan troglodytes	ENSPTRG00000016646	9 retrocopies	retro_ptro_146, retro_ptro_1588, retro_ptro_2143, retro_ptro_2364, retro_ptro_2388, retro_ptro_2517, retro_ptro_2525, retro_ptro_2819, retro_ptro_2882,
Pteropus vampyrus	ENSPVAG00000015279	1 retrocopy	retro_pvam_892,
Sarcophilus harrisii	ENSSHAG00000000932	1 retrocopy	retro_shar_160,
Tarsius syrichta	ENSTSYG00000004233	1 retrocopy	retro_tsyr_27,