RetrogeneDB ID: retro_eeur_23

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_213937:4462..5629(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSEEUG00000009813
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSEEUG00000008602
• Aliases: None
• Description: None

Sequence

>retro_eeur_23
ATGTCTGTTCTCAAGATTCATGCCAGAGAGATCTTTGACTCCAGGGGGAACCCCACTGTGGAGGTTGATCTCTACACCAA
CAAAGGTCTCTTCAGAGCTGCTGTGCCCAGTGGTGCCTCAACTGGCATCTATGAGGCACTTGAGCTTTGGGACAATGACA
AGACCGGCTATATGGGGAAAGGTGTCTCACAGGCTGTTGAGCACATCAATAACACTATTGCGCCTGCCCTGGTTAGCAAG
AAGCTGAACGTTGTGGAGCAGGAGAAGATTGACAAGCTGTTGATAGAGATGGATGGGACAGAGAATAAATCTAAATTTGG
GGCAAATGCCATTTTGGGTGTGTCCCTGGCAGTCTGCAAGGCTGGTGCTGTTGAGAAGGGAGTGCCCCTGTATCACCACG
TCGCTGATTTGGCTGGCAACCCTGAAGTCATTCTTCCAGTTCCCGCTTTCAGTGTTATCAACGGAGGTTCTCATGCTGGC
AACAAGTTGGCCATGCAGGAGTTTATGATCCTCCCTGCTGGGGCAGCAAACTTCAAGGAAGCCATGCGCACTGGAGCCGA
GGTTTACCACAACCTGAAGAATGTCATCAAGGAGAAATATGGAAAGGATGCCACCAACGTGGGGGATGAAGGAGGATTTG
CTCCCAACATCCTGGAAAATAAAGAAGCCCTGGAGCTGCTGAAAAACGCCATCGCAAAGGCTGGCTACACCTACAAGGTT
GTCATCGGCATGGATGTGGCTGCTTCTGAGTTCTTCCGGTCAGGAAAGTATGACCTGGACTTCAAGTCACCCGATGATCC
CAGCAGGTACATCTCAGCCAGTGAGCTGGGCAACCTGTACAAGTCTTTCATCAGTGACTACCCAGTGGTGTCTATTGAAG
ATCCCTTCGACCAGGATGACTGGGAAGCTTGGCGGGACTTCACTGCCACTGCAGGCATCCAGGTGGTAGGGGATGACCTC
ACAGTGACCAACCCGAAGCGGATTGCCAAGGCTATAGAAGAGAAGTCCTGCAACTGCCTGCTGCTGAAAGTGAACCAGAT
TGGCTCTGTGACTGAATCTCTGCAGGCGTGCAAACTGGCCCAGTCCAATGGGTGGGGCGTCATGGTATCTCATCGCTCTG
GGGAGACTGAGGACACCTTCATTGCTGACCTGGTGGTGGGGCTCTGC

Alignment

ORF - retro_eeur_23 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.17 %
• Parental protein coverage: 89.63 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSILKIHAREIFDSRGNPTVEVDLYTNKGLFRAAVPSGASTGIYEALELRDNDKTRYMGKGVSQAVEHIN
          MS.LKIHAREIFDSRGNPTVEVDLYTNKGLFRAAVPSGASTGIYEALEL.DNDKT.YMGKGVSQAVEHIN
Retrocopy MSVLKIHAREIFDSRGNPTVEVDLYTNKGLFRAAVPSGASTGIYEALELWDNDKTGYMGKGVSQAVEHIN

Parental  NTIAPALVSKKLNVVEQEKIDKLMIEMDGTENKSKFGANAILGVSLAVCKAGAVEKGVPLYRHIADLAGN
          NTIAPALVSKKLNVVEQEKIDKL.IEMDGTENKSKFGANAILGVSLAVCKAGAVEKGVPLY.H.ADLAGN
Retrocopy NTIAPALVSKKLNVVEQEKIDKLLIEMDGTENKSKFGANAILGVSLAVCKAGAVEKGVPLYHHVADLAGN

Parental  PEVILPVPAFNVINGGSHAGNKLAMQEFMILPAGAANFKEAMRIGAEVYHNLKNVIKEKYGKDATNVGDE
          PEVILPVPAF.VINGGSHAGNKLAMQEFMILPAGAANFKEAMR.GAEVYHNLKNVIKEKYGKDATNVGDE
Retrocopy PEVILPVPAFSVINGGSHAGNKLAMQEFMILPAGAANFKEAMRTGAEVYHNLKNVIKEKYGKDATNVGDE

Parental  GGFAPNILENKEALELLKNAIAKAGYADKVVIGMDVAASEFFRSGKYDLDFKSPDDPSRYISASELGNLY
          GGFAPNILENKEALELLKNAIAKAGY..KVVIGMDVAASEFFRSGKYDLDFKSPDDPSRYISASELGNLY
Retrocopy GGFAPNILENKEALELLKNAIAKAGYTYKVVIGMDVAASEFFRSGKYDLDFKSPDDPSRYISASELGNLY

Parental  KSFISDYPVVSIEDPFDQDDWEAWRDFTATAGIQVVGDDLTVTNPKRIAKAVEEKSCNCLLLKVNQIGSV
          KSFISDYPVVSIEDPFDQDDWEAWRDFTATAGIQVVGDDLTVTNPKRIAKA.EEKSCNCLLLKVNQIGSV
Retrocopy KSFISDYPVVSIEDPFDQDDWEAWRDFTATAGIQVVGDDLTVTNPKRIAKAIEEKSCNCLLLKVNQIGSV

Parental  TESLQACKLAQSNGWGVMVSHRSGETEDTFIADLVVGLC
          TESLQACKLAQSNGWGVMVSHRSGETEDTFIADLVVGLC
Retrocopy TESLQACKLAQSNGWGVMVSHRSGETEDTFIADLVVGLC

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	52.37 RPM	335.99 RPM
SRP017611_kidney	79.52 RPM	489.29 RPM
SRP017611_liver	52.57 RPM	307.24 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_23 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	ENSCHOG00000003483	2 retrocopies	retro_chof_1289, retro_chof_1811,
Callithrix jacchus	ENSCJAG00000000359	4 retrocopies	retro_cjac_1963, retro_cjac_2238, retro_cjac_3891, retro_cjac_438,
Erinaceus europaeus	ENSEEUG00000008602	2 retrocopies	retro_eeur_23 , retro_eeur_243,
Homo sapiens	ENSG00000074800	1 retrocopy	retro_hsap_325,
Macropus eugenii	ENSMEUG00000005942	11 retrocopies	retro_meug_1445, retro_meug_1521, retro_meug_353, retro_meug_472, retro_meug_494, retro_meug_652, retro_meug_664, retro_meug_765, retro_meug_794, retro_meug_874, retro_meug_888,
Macropus eugenii	ENSMEUG00000007840	1 retrocopy	retro_meug_96,
Monodelphis domestica	ENSMODG00000009521	1 retrocopy	retro_mdom_1794,
Mustela putorius furo	ENSMPUG00000006382	2 retrocopies	retro_mputfur_1162, retro_mputfur_547,
Mus musculus	ENSMUSG00000063524	1 retrocopy	retro_mmus_109,
Oryctolagus cuniculus	ENSOCUG00000010086	1 retrocopy	retro_ocun_933,
Otolemur garnettii	ENSOGAG00000004001	1 retrocopy	retro_ogar_1059,
Ochotona princeps	ENSOPRG00000009492	1 retrocopy	retro_opri_969,
Pan troglodytes	ENSPTRG00000000109	1 retrocopy	retro_ptro_261,
Pteropus vampyrus	ENSPVAG00000005030	1 retrocopy	retro_pvam_317,
Rattus norvegicus	ENSRNOG00000017895	1 retrocopy	retro_rnor_112,
Sarcophilus harrisii	ENSSHAG00000005522	1 retrocopy	retro_shar_304,
Tarsius syrichta	ENSTSYG00000002509	1 retrocopy	retro_tsyr_2011,