RetrogeneDB ID: retro_ocun_225

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 1:130235323..130235845(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000027723
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: PTP4A1
• Ensembl ID: ENSOCUG00000006311
• Aliases: None
• Description: protein tyrosine phosphatase type IVA, member 1 [Source:HGNC Symbol;Acc:9634]

Sequence

>retro_ocun_225
ATGGCTCCGATGAACCGCCCGGCTCCTGTGGAAGTCACATACAGGAACATGAGATTCCTTATTACACACAACCCAACCAC
TGCAACCTTAAACAGGTTTATAGAGGAACTTAAGAAATTCGGAGTTACCACAATAGTGAGAGTGTGTGAAGCAACTTACG
ACACCGCCCTCATGGAGAAAGAAGGTATCCAGGTTCTGGATTGGCCTTTTGATGATGGATCATCTCCTTCCAATCAGATT
GTTGATGACTGGTTAAGTCTTGTAAACATTAAATTCCGTGAAGAACCTGGTTGTTGTATTGCTGTCCACTGTGTTGCGGG
TCTTGGGAGAACCCCAGTGCTTGTTGCCTTAGCGTTAATTGAAAGTGGAATGAAAAATGAAGATGCAGTGCAGTTTATTA
GACAAAAGCGGCGTGGAGCTTTTAACAGCAAACAACTTTTGTATTTGGAGAAATACCGTTCTAAAATGCGGCTGCGCTTC
AAAGACTCCAGTGGTCACAGAAACAACTGTTGCATTCAATAA

Alignment

ORF - retro_ocun_225 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.75 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MARMNRPAPVEVTYKNMRFLITHNPTNATLNKFIEELKKYGVTTIVRVCEATYDTTLVEKEGIHVLDWPF
          MA.MNRPAPVEVTY.NMRFLITHNPT.ATLN.FIEELKK.GVTTIVRVCEATYDT.L.EKEGI.VLDWPF
Retrocopy MAPMNRPAPVEVTYRNMRFLITHNPTTATLNRFIEELKKFGVTTIVRVCEATYDTALMEKEGIQVLDWPF

Parental  DDGAPPSNQIVDDWLSLVKIKFREEPGCCIAVHCVAGLGRAPVLVALALIEGGMKYEDAVQFIRQKRRGA
          DDG..PSNQIVDDWLSLV.IKFREEPGCCIAVHCVAGLGR.PVLVALALIE.GMK.EDAVQFIRQKRRGA
Retrocopy DDGSSPSNQIVDDWLSLVNIKFREEPGCCIAVHCVAGLGRTPVLVALALIESGMKNEDAVQFIRQKRRGA

Parental  FNSKQLLYLEKYRPKMRLRFKDSNGHRNNCCIQ
          FNSKQLLYLEKYR.KMRLRFKDS.GHRNNCCIQ
Retrocopy FNSKQLLYLEKYRSKMRLRFKDSSGHRNNCCIQ

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	0.06 RPM	7.12 RPM
SRP017611_kidney	0.10 RPM	8.62 RPM
SRP017611_liver	0.00 RPM	6.63 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_225 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_225 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_225 has 10 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_807
Pan troglodytes	retro_ptro_562
Gorilla gorilla	retro_ggor_662
Pongo abelii	retro_pabe_721
Callithrix jacchus	retro_cjac_910
Mus musculus	retro_mmus_3053
Rattus norvegicus	retro_rnor_612
Bos taurus	retro_btau_1186
Canis familiaris	retro_cfam_206
Equus caballus	retro_ecab_20

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Parental genes homology:

Parental genes homology involve 34 parental genes, and 157 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,
Cavia porcellus	ENSCPOG00000025759	5 retrocopies	retro_cpor_1137, retro_cpor_1233, retro_cpor_1392, retro_cpor_552, retro_cpor_58,
Dasypus novemcinctus	ENSDNOG00000018507	4 retrocopies	retro_dnov_1850, retro_dnov_278, retro_dnov_692, retro_dnov_996,
Dipodomys ordii	ENSDORG00000009960	6 retrocopies	retro_dord_148, retro_dord_244, retro_dord_355, retro_dord_375, retro_dord_696, retro_dord_92,
Equus caballus	ENSECAG00000022483	6 retrocopies	retro_ecab_10, retro_ecab_1075, retro_ecab_20, retro_ecab_425, retro_ecab_783, retro_ecab_869,
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	ENSOCUG00000002060	1 retrocopy	retro_ocun_1673,
Oryctolagus cuniculus	ENSOCUG00000006311	4 retrocopies	retro_ocun_225 , retro_ocun_226, retro_ocun_24, retro_ocun_26,
Ochotona princeps	ENSOPRG00000004938	4 retrocopies	retro_opri_246, retro_opri_511, retro_opri_692, retro_opri_973,
Procavia capensis	ENSPCAG00000001271	8 retrocopies	retro_pcap_183, retro_pcap_249, retro_pcap_291, retro_pcap_338, retro_pcap_367, retro_pcap_425, retro_pcap_431, retro_pcap_76,
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,
Pteropus vampyrus	ENSPVAG00000015225	2 retrocopies	retro_pvam_487, retro_pvam_848,
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,
Vicugna pacos	ENSVPAG00000004277	9 retrocopies	retro_vpac_167, retro_vpac_201, retro_vpac_275, retro_vpac_427, retro_vpac_476, retro_vpac_496, retro_vpac_535, retro_vpac_560, retro_vpac_583,