RetrogeneDB ID: retro_eeur_243

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_221421:4932..5675(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

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

Sequence

>retro_eeur_243
ATGTCTATTCTCAAGATTCATGCCAGAGAGATCTTTGACTCGAGGGGGAACCCCACTGTGGAGGTTGATCTCTACACCAA
CAAAGGTCTCTTCAGAGCTGCTGTGCCCAGTGGTGCCTCGACTGGCATCTATGAGGCACTTGAGCTTCGGGACAATGACA
AGACCCGCTATATGGGGAAAGGTGTCTCACAGGCTGTTTAGCACATCAATAACACTATTGCGCCTGCCCTGGTTAGCAAG
AAGCTGAATGTTGTGGAGCAGGAGAAGATTGACAAGCTGATGATAGAGATGAATGGGACAGAGAATAAATCTAAATTTGG
GGCAAATGCCATTTTGGGTGTGTCCCTGGCAGTCTGCAAGGCTGGTGCTGTGGCGAAGGGAGTGCCCCTGTATCGCCACA
TCGCTGATTTGGCTGGCAACCCTGAAGTCATTCTTCCAGTTCCCGCTTTCAATGTTATCAACGGAGGCTCTCATGCTGGC
AACAAGTTGGCCATGCAGGAGTTTATGATCCTCCCTGCTGGGGCAGCAAACTTCAAGGAAGCCATATATATTGGAGCAGA
GGTTTACCACAACCTGAAGAATGTCATCAAGGAGAAATATGGAAAGGATGCCACCAACGTGGGGGATGAAGGTGGATTTG
CTCCCAGCATCCTGGAAAATAATAGAGCCATGGAGTAGCTGAAAAATGCCATCGCAAAGGCTGGCTACGCGACAAGGTGT
CATCGGCATGGGATGTGGCTGCT

Alignment

ORF - retro_eeur_243 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.98 %
• Parental protein coverage: 57.14 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSILKIHAREIFDSRGNPTVEVDLYTNKGLFRAAVPSGASTGIYEALELRDNDKTRYMGKGVSQAVEHIN
          MSILKIHAREIFDSRGNPTVEVDLYTNKGLFRAAVPSGASTGIYEALELRDNDKTRYMGKGVSQAV.HIN
Retrocopy MSILKIHAREIFDSRGNPTVEVDLYTNKGLFRAAVPSGASTGIYEALELRDNDKTRYMGKGVSQAV*HIN

Parental  NTIAPALVSKKLNVVEQEKIDKLMIEMDGTENKSKFGANAILGVSLAVCKAGAVEKGVPLYRHIADLAGN
          NTIAPALVSKKLNVVEQEKIDKLMIEM.GTENKSKFGANAILGVSLAVCKAGAV.KGVPLYRHIADLAGN
Retrocopy NTIAPALVSKKLNVVEQEKIDKLMIEMNGTENKSKFGANAILGVSLAVCKAGAVAKGVPLYRHIADLAGN

Parental  PEVILPVPAFNVINGGSHAGNKLAMQEFMILPAGAANFKEAMRIGAEVYHNLKNVIKEKYGKDATNVGDE
          PEVILPVPAFNVINGGSHAGNKLAMQEFMILPAGAANFKEA..IGAEVYHNLKNVIKEKYGKDATNVGDE
Retrocopy PEVILPVPAFNVINGGSHAGNKLAMQEFMILPAGAANFKEAIYIGAEVYHNLKNVIKEKYGKDATNVGDE

Parental  GGFAPNILENKEALELLKNAIAKAGYA-DKVVIGMDVAA
          GGFAP.ILEN..A.E.LKNAIAKAGYA.DKV....DVAA
Retrocopy GGFAPSILENNRAME*LKNAIAKAGYA<DKVSSAWDVAA

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	42.22 RPM	335.99 RPM
SRP017611_kidney	57.20 RPM	489.29 RPM
SRP017611_liver	38.91 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_243 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.

---

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,