RetrogeneDB ID: retro_eeur_227

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_214361:7521..8037(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSEEUG00000003160
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PTP4A1
• Ensembl ID: ENSEEUG00000006477
• Aliases: None
• Description: protein tyrosine phosphatase type IVA, member 1 [Source:HGNC Symbol;Acc:9634]

Sequence

>retro_eeur_227
ATGGCGCGGATGAACCGGCCCGCGCCCGTGGAGGTGAGCTATAAGAACATGCGCTTCCTCATCACACACAACCCCACTGA
CGCCACCCTCAGCAGCTTCCTGGAGGACCTGAAGAAGTATGGAGCCACCACTGTGGTGTGTGTGTGTGAAGTGACGTACG
ACAAGGCACCCTTGGAGAAGGACGGCATCACCGTAGTGGACTGGCCATTTGATGATGGGGCACCCCCACCAGGCAAAGTG
GTGGAAGACTGGCTGAGCCTGCTGAAGGCCAAATTCTGTGATGATCCTGGCAGCTGTGTCGCTGTGCATTGTGTGGCTGG
CCTGGGGCGGGCGCCAGTCCTTGTGGCGCTGGCCCTCATCGAGAGCGGGATGAAGCATGAGGACACCATCCAATTCATTC
GACAGAAGCGGTGAGGTTCCATCAACAGCAAGCAGCTCACCTACTTGGAAAAGTACCGGCCTAAACAGAGACTGCGCTTC
AAAGACCCCCCCTCACACAAGACCAGATGCTGCGTC

Alignment

ORF - retro_eeur_227 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.93 %
• Parental protein coverage: 99.42 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MARMNRPAPVEVTYKNMRFLITHNPTNATLNKFIEELKKYGVTTIVRVCEATYDTTLVEKEGIHVLDWPF
          MARMNRPAPVEV.YKNMRFLITHNPT.ATL..F.E.LKKYG.T........TYD....EK.GI.V.DWPF
Retrocopy MARMNRPAPVEVSYKNMRFLITHNPTDATLSSFLEDLKKYGATXXXXXXXVTYDKAPLEKDGITVVDWPF

Parental  DDGAPPSNQIVDDWLSLVKIKFREEPGCCIAVHCVAGLGRAPVLVALALIEGGMKYEDAVQFIRQKRRGA
          DDGAPP....V.DWLSL.K.KF...PG.C.AVHCVAGLGRAPVLVALALIE.GMK.ED..QFIRQKR.G.
Retrocopy DDGAPPPGKVVEDWLSLLKAKFCDDPGSCVAVHCVAGLGRAPVLVALALIESGMKHEDTIQFIRQKR*GS

Parental  FNSKQLLYLEKYRPKMRLRFKDSNGHRNNCCI
          .NSKQL.YLEKYRPK.RLRFKD...H...CC.
Retrocopy INSKQLTYLEKYRPKQRLRFKDPPSHKTRCCV

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	4.67 RPM	41.90 RPM
SRP017611_kidney	17.63 RPM	19.88 RPM
SRP017611_liver	1.77 RPM	56.75 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_227 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 26 parental genes, and 118 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002438	3 retrocopies	retro_amel_1102, retro_amel_1344, retro_amel_1590,
Bos taurus	ENSBTAG00000002275	3 retrocopies	retro_btau_1051, retro_btau_1186, retro_btau_859,
Canis familiaris	ENSCAFG00000002490	3 retrocopies	retro_cfam_1832, retro_cfam_206, retro_cfam_593,
Callithrix jacchus	ENSCJAG00000001743	3 retrocopies	retro_cjac_2812, retro_cjac_4144, retro_cjac_910,
Dipodomys ordii	ENSDORG00000009960	6 retrocopies	retro_dord_148, retro_dord_244, retro_dord_355, retro_dord_375, retro_dord_696, retro_dord_92,
Erinaceus europaeus	ENSEEUG00000006477	3 retrocopies	retro_eeur_227 , retro_eeur_626, retro_eeur_687,
Echinops telfairi	ENSETEG00000008183	6 retrocopies	retro_etel_1485, retro_etel_1681, retro_etel_1698, retro_etel_18, retro_etel_2153, retro_etel_668,
Felis catus	ENSFCAG00000001199	3 retrocopies	retro_fcat_1439, retro_fcat_335, retro_fcat_969,
Homo sapiens	ENSG00000112245	5 retrocopies	retro_hsap_2171, retro_hsap_3212, retro_hsap_479, retro_hsap_4798, retro_hsap_807,
Gorilla gorilla	ENSGGOG00000022521	7 retrocopies	retro_ggor_1723, retro_ggor_2180, retro_ggor_2251, retro_ggor_2986, retro_ggor_452, retro_ggor_662, retro_ggor_763,
Latimeria chalumnae	ENSLACG00000007183	1 retrocopy	retro_lcha_90,
Loxodonta africana	ENSLAFG00000006572	8 retrocopies	retro_lafr_1054, retro_lafr_1120, retro_lafr_1133, retro_lafr_328, retro_lafr_670, retro_lafr_7, retro_lafr_780, retro_lafr_939,
Myotis lucifugus	ENSMLUG00000001162	1 retrocopy	retro_mluc_264,
Macaca mulatta	ENSMMUG00000002777	1 retrocopy	retro_mmul_1720,
Monodelphis domestica	ENSMODG00000018701	5 retrocopies	retro_mdom_1630, retro_mdom_1864, retro_mdom_363, retro_mdom_729, retro_mdom_927,
Mustela putorius furo	ENSMPUG00000003118	1 retrocopy	retro_mputfur_17,
Mus musculus	ENSMUSG00000026064	10 retrocopies	retro_mmus_1192, retro_mmus_1830, retro_mmus_1874, retro_mmus_1891, retro_mmus_2138, retro_mmus_2876, retro_mmus_2985, retro_mmus_3053, retro_mmus_3527, retro_mmus_575,
Nomascus leucogenys	ENSNLEG00000000440	6 retrocopies	retro_nleu_1111, retro_nleu_1159, retro_nleu_1681, retro_nleu_169, retro_nleu_407, retro_nleu_893,
Oryctolagus cuniculus	ENSOCUG00000006311	4 retrocopies	retro_ocun_225, retro_ocun_226, retro_ocun_24, retro_ocun_26,
Pongo abelii	ENSPPYG00000016743	5 retrocopies	retro_pabe_2058, retro_pabe_255, retro_pabe_2660, retro_pabe_3732, retro_pabe_721,
Pan troglodytes	ENSPTRG00000018314	4 retrocopies	retro_ptro_1657, retro_ptro_2239, retro_ptro_3190, retro_ptro_360,
Rattus norvegicus	ENSRNOG00000011771	4 retrocopies	retro_rnor_1591, retro_rnor_2798, retro_rnor_494, retro_rnor_827,
Rattus norvegicus	ENSRNOG00000046370	4 retrocopies	retro_rnor_2349, retro_rnor_2868, retro_rnor_612, retro_rnor_971,
Tupaia belangeri	ENSTBEG00000009956	14 retrocopies	retro_tbel_1216, retro_tbel_1392, retro_tbel_2167, retro_tbel_2236, retro_tbel_23, retro_tbel_2549, retro_tbel_2570, retro_tbel_2611, retro_tbel_3144, retro_tbel_3295, retro_tbel_3424, retro_tbel_4074, retro_tbel_4123, retro_tbel_869,
Tarsius syrichta	ENSTSYG00000004632	2 retrocopies	retro_tsyr_1011, retro_tsyr_1152,
Tursiops truncatus	ENSTTRG00000004129	6 retrocopies	retro_ttru_34, retro_ttru_450, retro_ttru_571, retro_ttru_642, retro_ttru_643, retro_ttru_69,