RetrogeneDB ID: retro_eeur_88

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: GeneScaffold_5494:91972..92515(-)
• Located in intron of: ENSEEUG00000002428

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNF2
• Ensembl ID: ENSEEUG00000014091
• Aliases: None
• Description: ring finger protein 2 [Source:HGNC Symbol;Acc:10061]

Sequence

>retro_eeur_88
ATGTCTCAGGAGGTGCAGACCAATGGAACGTTGTAACCATTAAGCAAAACATGGGAACTCAGTTTGTATGAATTACAACG
AAGACCTCAGGAGGCAATAACAGATGGCTTGGAAATTGTGGTTTCACCTCGAAGTCTACACAGTGAATTAATGTGTCCAA
TTTGTCTGGATATGTTGAAAAATACCATGACTACAAAGGAGTGTTTATATCGCTTTTGTGCGGACTGCATCATCACAGCC
CTCAGAAGTGGCAATAGAGAATGTCCTACCTGTCGGAAAAAGCTGGTTTCCAAAAGATCACTGAGACCAGATCCACACTT
CGCTGCACTCATCAGCAAAATCTATCCAAGTTGTGATGAGAATGAAGTTCATCGAGAAGGAGTACTAGCCAGGATCAACA
AGCACAACAACTAGCACGCACTCAGCCATAACACTGAGGAGGGGCTGAAGATACAGGCCATGAACAGATTACAGGGAGGC
AAGAAGCAACAGATTGAAAATGGTAGGGGTGCAGAAGATAATGGTGACAGTTCCCACTGCAGT

Alignment

ORF - retro_eeur_88 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.5 %
• Parental protein coverage: 53.57 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSQAVQTNGTQ-PLSKTWELSLYELQRTPQEAITDGLEIVVSPRSLHSELMCPICLDMLKNTMTTKECLH
          MSQ.VQTNGT..PLSKTWELSLYELQR.PQEAITDGLEIVVSPRSLHSELMCPICLDMLKNTMTTKECL.
Retrocopy MSQEVQTNGTL*PLSKTWELSLYELQRRPQEAITDGLEIVVSPRSLHSELMCPICLDMLKNTMTTKECLY

Parental  RFCADCIITALRSGNKECPTCRKKLVSKRSLRPDPNFDALISKIYPSRDEYEAHQERVLARINKHNNQQA
          RFCADCIITALRSGN.ECPTCRKKLVSKRSLRPDP.F.ALISKIYPS.DE.E.H.E.VLARINKHNN..A
Retrocopy RFCADCIITALRSGNRECPTCRKKLVSKRSLRPDPHFAALISKIYPSCDENEVHREGVLARINKHNN*HA

Parental  LSHSIEEGLKIQAMNRLQRGKKQQIENGSGAEDNGDSSHCS
          LSH..EEGLKIQAMNRLQ.GKKQQIENG.GAEDNGDSSHCS
Retrocopy LSHNTEEGLKIQAMNRLQGGKKQQIENGRGAEDNGDSSHCS

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	0.16 RPM	24.82 RPM
SRP017611_kidney	0.00 RPM	13.88 RPM
SRP017611_liver	0.00 RPM	6.75 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_88 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 17 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000011199	3 retrocopies	retro_chof_1450, retro_chof_2217, retro_chof_2251,
Callithrix jacchus	ENSCJAG00000005442	1 retrocopy	retro_cjac_4198,
Erinaceus europaeus	ENSEEUG00000014091	1 retrocopy	retro_eeur_88 ,
Echinops telfairi	ENSETEG00000015824	1 retrocopy	retro_etel_2081,
Felis catus	ENSFCAG00000009609	1 retrocopy	retro_fcat_1725,
Homo sapiens	ENSG00000121481	2 retrocopies	retro_hsap_4056, retro_hsap_4226,
Gorilla gorilla	ENSGGOG00000014400	1 retrocopy	retro_ggor_2724,
Loxodonta africana	ENSLAFG00000021357	1 retrocopy	retro_lafr_407,
Myotis lucifugus	ENSMLUG00000001129	1 retrocopy	retro_mluc_2187,
Monodelphis domestica	ENSMODG00000007422	1 retrocopy	retro_mdom_857,
Nomascus leucogenys	ENSNLEG00000018029	2 retrocopies	retro_nleu_1042, retro_nleu_554,
Oryctolagus cuniculus	ENSOCUG00000004892	1 retrocopy	retro_ocun_838,
Pongo abelii	ENSPPYG00000000417	2 retrocopies	retro_pabe_3331, retro_pabe_3374,
Pan troglodytes	ENSPTRG00000001775	2 retrocopies	retro_ptro_2749, retro_ptro_2871,
Ictidomys tridecemlineatus	ENSSTOG00000006625	3 retrocopies	retro_itri_1646, retro_itri_1794, retro_itri_410,
Tupaia belangeri	ENSTBEG00000016387	4 retrocopies	retro_tbel_1757, retro_tbel_3368, retro_tbel_3892, retro_tbel_4061,
Tarsius syrichta	ENSTSYG00000006109	6 retrocopies	retro_tsyr_1344, retro_tsyr_1647, retro_tsyr_2063, retro_tsyr_2083, retro_tsyr_227, retro_tsyr_474,