RetrogeneDB ID: retro_eeur_64

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: GeneScaffold_3678:23485..23878(+)
• Located in intron of: ENSEEUG00000015714

Retrocopy information

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

Parental gene information

• Parental gene symbol: DNAJC15
• Ensembl ID: ENSEEUG00000008785
• Aliases: None
• Description: DnaJ (Hsp40) homolog, subfamily C, member 15 [Source:HGNC Symbol;Acc:20325]

Sequence

>retro_eeur_64
TCAGGAGAGGGGCTTCGTTGCACTGTGTACTCGCCACCCGTGAACAGACAGGTGGACTCAGACATCAACTGGTGCCTGGC
ACAAAGTGTGATAGCTGTTGGACTGGGTGTTGCAACACTTGCATTTGCAGGTCGCTATGCATTTCAGATTTGGAGACATC
TAGAACAAGTAATCACAGAAACTGCAAAGAAGATTTCAACTCCTATTCTTTTGTCCTACTACAAAGGAGGATTTGAACAT
AAAATGAGTAGACAAGAAGCTAGTCTTATTTTGGGTGTAAGCCCATCTGCTGGTAAAGCCAAGATTAGAACAGCTCACAG
AAGAATCATGATTTTGAACCTCCCAGATAATCCTTACTTAGCAACCAAAATAAATGAAACAAAAGACTTGCTA

Alignment

ORF - retro_eeur_64 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.84 %
• Parental protein coverage: 93.06 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SGEGLRYAEYSPPANRLADADIDRRLARSLIAVGLGVATLAFAGRYAFQIWKPLEQVITETAKKISTPSL
          SGEGLR...YSPP.NR..D.DI...LA.S.IAVGLGVATLAFAGRYAFQIW..LEQVITETAKKISTP.L
Retrocopy SGEGLRCTVYSPPVNRQVDSDINWCLAQSVIAVGLGVATLAFAGRYAFQIWRHLEQVITETAKKISTPIL

Parental  LSYYKGGFEQKMSRREASLILGVSPSAGKAKIRTAHRRIMILNHPDKGGSPYLATKINEAKDLL
          LSYYKGGFE.KMSR.EASLILGVSPSAGKAKIRTAHRRIMILN.PD....PYLATKINE.KDLL
Retrocopy LSYYKGGFEHKMSRQEASLILGVSPSAGKAKIRTAHRRIMILNLPD---NPYLATKINETKDLL

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	16.76 RPM
SRP017611_kidney	0.00 RPM	39.95 RPM
SRP017611_liver	0.00 RPM	26.53 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_64 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 25 parental genes, and 55 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000034785	1 retrocopy	retro_btau_1624,
Canis familiaris	ENSCAFG00000004664	1 retrocopy	retro_cfam_939,
Callithrix jacchus	ENSCJAG00000017589	2 retrocopies	retro_cjac_1663, retro_cjac_634,
Cavia porcellus	ENSCPOG00000003485	1 retrocopy	retro_cpor_327,
Equus caballus	ENSECAG00000007757	1 retrocopy	retro_ecab_561,
Erinaceus europaeus	ENSEEUG00000006955	9 retrocopies	retro_eeur_221, retro_eeur_230, retro_eeur_309, retro_eeur_455, retro_eeur_48, retro_eeur_511, retro_eeur_596, retro_eeur_74, retro_eeur_94,
Erinaceus europaeus	ENSEEUG00000008785	5 retrocopies	retro_eeur_360, retro_eeur_608, retro_eeur_64 , retro_eeur_93, retro_eeur_95,
Felis catus	ENSFCAG00000022632	1 retrocopy	retro_fcat_259,
Homo sapiens	ENSG00000120675	2 retrocopies	retro_hsap_3331, retro_hsap_4312,
Gorilla gorilla	ENSGGOG00000016338	2 retrocopies	retro_ggor_1294, retro_ggor_2882,
Loxodonta africana	ENSLAFG00000004343	2 retrocopies	retro_lafr_287, retro_lafr_942,
Myotis lucifugus	ENSMLUG00000008684	3 retrocopies	retro_mluc_1358, retro_mluc_1544, retro_mluc_520,
Macaca mulatta	ENSMMUG00000013689	1 retrocopy	retro_mmul_1169,
Mustela putorius furo	ENSMPUG00000001704	1 retrocopy	retro_mputfur_1065,
Nomascus leucogenys	ENSNLEG00000001759	4 retrocopies	retro_nleu_1408, retro_nleu_1464, retro_nleu_1675, retro_nleu_585,
Oryctolagus cuniculus	ENSOCUG00000001696	4 retrocopies	retro_ocun_1101, retro_ocun_487, retro_ocun_882, retro_ocun_936,
Ochotona princeps	ENSOPRG00000016191	5 retrocopies	retro_opri_1038, retro_opri_235, retro_opri_285, retro_opri_756, retro_opri_766,
Pongo abelii	ENSPPYG00000005323	1 retrocopy	retro_pabe_3508,
Pan troglodytes	ENSPTRG00000005831	2 retrocopies	retro_ptro_2148, retro_ptro_2920,
Pteropus vampyrus	ENSPVAG00000011281	1 retrocopy	retro_pvam_807,
Sorex araneus	ENSSARG00000007683	1 retrocopy	retro_sara_658,
Ictidomys tridecemlineatus	ENSSTOG00000012805	1 retrocopy	retro_itri_1710,
Taeniopygia guttata	ENSTGUG00000012364	2 retrocopies	retro_tgut_20, retro_tgut_45,
Tursiops truncatus	ENSTTRG00000015580	1 retrocopy	retro_ttru_1021,
Vicugna pacos	ENSVPAG00000001445	1 retrocopy	retro_vpac_113,