RetrogeneDB ID: retro_eeur_209

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_208787:2670..3277(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SIRT5
• Ensembl ID: ENSEEUG00000005650
• Aliases: None
• Description: sirtuin 5 [Source:HGNC Symbol;Acc:14933]

Sequence

>retro_eeur_209
CAGAGCAAGGACCCAAACCCTGGGCACCTTGCCATCGCTGAATGTGAGGCCTGGCTGCACAAGCAGGGCCGACAGGTCAT
GGTTATCACTCAGAACATTGATGAGCTGCACCACAAGGCCGGTACCAAGAATCTTCTGGAAATCCATGGTAGCTTATTTA
AAACTCAATGTACCTCTTGTGGAGTTGTGACTGAAAATTACAAGAGTCCAATTTGTCCAGCTTTAGCAGGAAAAGGTGCT
CCAGAACCCGAAGCTCAAGATGCCAGAATCCCAGAGGAGAAGCTTCCCAGGTGTGAAGAGGCAGGTTGTGGGGGCCTACT
GCGACCTCACGTAGTCTGGTTTGGTGAAAACCTGGATCCAACCATTTTGGAAGAAGTTGACAGAGAGCTGTCTCTCTGTG
ATTTGTGTCTCATGGTGGGGATTTTCTCTGTGGTTTATCCTGCTGCCATGTTTGCCCCACAGGTATCTTCAAGGGGGGGG
GGGGTCCCAGTAGCTGAATTTAACATGGAAACCACTCCAGCCACCAACCGATTCAGGTTTCATTTCCAAGGGCCCTGTGG
TACAACTTCCTGAAGCCCTGGCTCTTCATGAAACTGAAACTATTTCT

Alignment

ORF - retro_eeur_209 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.22 %
• Parental protein coverage: 64.84 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QSKEPNPGHLAIAECEARLHKQGRRVMVITQNIDELHRKAGTKNLLEIHGSLFKTRCTSCGVVTENYKSP
          QSK.PNPGHLAIAECEA.LHKQGR.VMVITQNIDELH.KAGTKNLLEIHGSLFKT.CTSCGVVTENYKSP
Retrocopy QSKDPNPGHLAIAECEAWLHKQGRQVMVITQNIDELHHKAGTKNLLEIHGSLFKTQCTSCGVVTENYKSP

Parental  VCPALAGKGAPEPEAQDARIPVEKLPRCEEAGCGGLLRPHVVWFGENLDPTILEEVDRELSLCDLCLVVG
          .CPALAGKGAPEPEAQDARIP.EKLPRCEEAGCGGLLRPHVVWFGENLDPTILEEVDRELSLCDLCL.VG
Retrocopy ICPALAGKGAPEPEAQDARIPEEKLPRCEEAGCGGLLRPHVVWFGENLDPTILEEVDRELSLCDLCLMVG

Parental  TSSVVYPAAMFAPQVSARGV--PVAEFNMETTPATNRFRFHFQ-GPCGTTLPEALAPHETETIS
          ..SVVYPAAMFAPQVS......PVAEFNMETTPATNRFRFHFQ.GP....LPEALA.HETETIS
Retrocopy IFSVVYPAAMFAPQVSSXXXXXPVAEFNMETTPATNRFRFHFQ>GPV-VQLPEALALHETETIS

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	0.32 RPM	12.41 RPM
SRP017611_kidney	0.19 RPM	24.01 RPM
SRP017611_liver	0.16 RPM	19.78 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_209 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000019802	1 retrocopy	retro_cjac_2923,
Erinaceus europaeus	ENSEEUG00000005650	1 retrocopy	retro_eeur_209 ,
Homo sapiens	ENSG00000124523	1 retrocopy	retro_hsap_167,
Macropus eugenii	ENSMEUG00000008671	1 retrocopy	retro_meug_733,
Nomascus leucogenys	ENSNLEG00000000843	1 retrocopy	retro_nleu_977,
Pan troglodytes	ENSPTRG00000017736	1 retrocopy	retro_ptro_158,
Tursiops truncatus	ENSTTRG00000007786	1 retrocopy	retro_ttru_944,