RetrogeneDB ID: retro_eeur_147

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_100289:192..615(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RHOA
• Ensembl ID: ENSEEUG00000013063
• Aliases: None
• Description: ras homolog family member A [Source:HGNC Symbol;Acc:667]

Sequence

>retro_eeur_147
GTCGAGCTGGATTTGTGGGACACCTGTGGGCCGCCGGTTTACGACAGCTGGAGGCCCTTTTCCTACCTCGACACAGATGT
GATCCTCATGTGCTTCTCCATTGACAACCCCGACAGTTTGGATAACATCCCACTGAAATGGATGCCGGAAGTCAGGCATT
TCTGTCCGGACGTGCCCATCATCCTGGTCGGGAACAAGAAGGATCTTTGGGATGACGGCAGCACAAGGCTGGTGCTCAGC
AAGATGAAGCAGGCGCCAGTCAAGCCGGAAGAAGGCAGAGCTATGGCAAAGAAGATCCATGCTTTTGAGTTCGTGGAGTG
TTCAGCGAAGACCAGAGATGGGGTGAGGGAGGTGTTTGAAATAGCCACAAGAGCTGCTCTGCGGGCCAGGCGTGGGAAGA
AGAGATCTGGGTGCCTTGTCTTG

Alignment

ORF - retro_eeur_147 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.31 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VELALWDTAGQEDYDRLRPLSYPDTDVILMCFSIDSPDSLENIPEKWTPEVKHFCPNVPIILVGNKKDLR
          VEL.LWDT.G...YD..RP.SY.DTDVILMCFSID.PDSL.NIP.KW.PEV.HFCP.VPIILVGNKKDL.
Retrocopy VELDLWDTCGPPVYDSWRPFSYLDTDVILMCFSIDNPDSLDNIPLKWMPEVRHFCPDVPIILVGNKKDLW

Parental  NDEHTRRELAKMKQWGGTPVKPEEGRDMANRIGAFGYMECSAKTKDGVREVFEMATRAALQARRGKKKSG
          .D..TR..L.KMKQ....PVKPEEGR.MA..I.AF...ECSAKT.DGVREVFE.ATRAAL.ARRGKK.SG
Retrocopy DDGSTRLVLSKMKQ---APVKPEEGRAMAKKIHAFEFVECSAKTRDGVREVFEIATRAALRARRGKKRSG

Parental  CLVL
          CLVL
Retrocopy CLVL

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	89.76 RPM
SRP017611_kidney	0.00 RPM	187.73 RPM
SRP017611_liver	0.00 RPM	99.36 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_147 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 23 parental genes, and 48 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000008297	1 retrocopy	retro_acar_41,
Anas platyrhynchos	ENSAPLG00000014687	1 retrocopy	retro_apla_10,
Canis familiaris	ENSCAFG00000023066	2 retrocopies	retro_cfam_1652, retro_cfam_186,
Callithrix jacchus	ENSCJAG00000003904	3 retrocopies	retro_cjac_1306, retro_cjac_2010, retro_cjac_411,
Dipodomys ordii	ENSDORG00000003382	3 retrocopies	retro_dord_1, retro_dord_18, retro_dord_538,
Erinaceus europaeus	ENSEEUG00000013063	1 retrocopy	retro_eeur_147 ,
Gasterosteus aculeatus	ENSGACG00000005670	1 retrocopy	retro_gacu_9,
Gallus gallus	ENSGALG00000003806	1 retrocopy	retro_ggal_5,
Gadus morhua	ENSGMOG00000008188	1 retrocopy	retro_gmor_18,
Latimeria chalumnae	ENSLACG00000016941	1 retrocopy	retro_lcha_15,
Meleagris gallopavo	ENSMGAG00000002280	1 retrocopy	retro_mgal_2,
Myotis lucifugus	ENSMLUG00000013911	6 retrocopies	retro_mluc_108, retro_mluc_193, retro_mluc_1976, retro_mluc_2553, retro_mluc_2554, retro_mluc_2555,
Macaca mulatta	ENSMMUG00000012962	1 retrocopy	retro_mmul_977,
Monodelphis domestica	ENSMODG00000012981	2 retrocopies	retro_mdom_19, retro_mdom_294,
Mus musculus	ENSMUSG00000007815	9 retrocopies	retro_mmus_178, retro_mmus_191, retro_mmus_2041, retro_mmus_2507, retro_mmus_3728, retro_mmus_3729, retro_mmus_3964, retro_mmus_3965, retro_mmus_3966,
Oreochromis niloticus	ENSONIG00000018884	1 retrocopy	retro_onil_32,
Pelodiscus sinensis	ENSPSIG00000015328	1 retrocopy	retro_psin_7,
Rattus norvegicus	ENSRNOG00000050519	3 retrocopies	retro_rnor_127, retro_rnor_2899, retro_rnor_408,
Sorex araneus	ENSSARG00000008509	2 retrocopies	retro_sara_137, retro_sara_325,
Ictidomys tridecemlineatus	ENSSTOG00000004561	2 retrocopies	retro_itri_39, retro_itri_96,
Tupaia belangeri	ENSTBEG00000002417	1 retrocopy	retro_tbel_26,
Takifugu rubripes	ENSTRUG00000011944	1 retrocopy	retro_trub_19,
Tarsius syrichta	ENSTSYG00000008220	3 retrocopies	retro_tsyr_1604, retro_tsyr_413, retro_tsyr_593,