RetrogeneDB ID: retro_ptro_1657

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 2B:162305897..162306359(+)
• Located in intron of: ENSPTRG00000012556

Retrocopy information

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

Parental gene information

• Parental gene symbol: PTP4A1
• Ensembl ID: ENSPTRG00000018314
• Aliases: None
• Description: Pan troglodytes protein tyrosine phosphatase type IVA, member 1 (PTP4A1), mRNA. [Source:RefSeq mRNA;Acc:NM_001246639]

Sequence

>retro_ptro_1657
ATGGCTCAAATGAACCGTCCAGCTCCTGTGGAAGTCACATACAAGAACATGAGGATTTCTTACTACACACAACCCAACCA
ATGTGACCTTAAACAAATTCGTAGAGGAACTTAAGAAGTATGGAGTTTTCACAATAGATAAGAGTATGTAAAGCAACTTA
TGACACTACTCTTCTGGAGAAAGAAGGTACCCATGTTCTCGATTGGCCTTTTGATGACGGTGCACCACCATCCAACCAGA
TTGATGACTGGTTAAGTCTTGTGAAAATTAAGTTTCATAAAGAACCTCATTGTTGTACTGCTGTTCATTGCATTGCAGGC
CTTGGGAGAGCTCCAGTACTTGTTGCCCTAGCATTAATTGAAGGCAAAATGAAAGATGATGATGCAGTACAATTCGCAAG
AAAAAAGCAGTGTGGAGCTTTTGACAGCAAGTTAACTTTTGTATTTGGAGAAGTGTCGTCCT

Alignment

ORF - retro_ptro_1657 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.17 %
• Parental protein coverage: 89.02 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MARMNRPAPVEVTYKNMR-FLITHNPTNATLNKFIEELKKYGVTTI-VRVCEATYDTTLVEKEGIHVLDW
          MA.MNRPAPVEVTYKNMR.FL.THNPTN.TLNKF.EELKKYGV.TI..RVC.ATYDTTL.EKEG.HVLDW
Retrocopy MAQMNRPAPVEVTYKNMR>FLTTHNPTNVTLNKFVEELKKYGVFTI>IRVCKATYDTTLLEKEGTHVLDW

Parental  PFDDGAPPSNQIVDDWLSLVKIKFREEPGCCIAVHCVAGLGRAPVLVALALIEGGMKYEDAVQFIRQKRR
          PFDDGAPPSNQI.DDWLSLVKIKF..EP.CC.AVHC.AGLGRAPVLVALALIEG.MK..DAVQF.R.K..
Retrocopy PFDDGAPPSNQI-DDWLSLVKIKFHKEPHCCTAVHCIAGLGRAPVLVALALIEGKMKDDDAVQFARKKQC

Parental  GAFNSKQ-LLYLEKYRP
          GAF.SK..LLYLEK.RP
Retrocopy GAFDSKL>LLYLEKCRP

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
SRP007412_brain_prefrontal_cortex	0.02 RPM	53.78 RPM
SRP007412_cerebellum	0.00 RPM	31.73 RPM
SRP007412_heart	0.00 RPM	67.44 RPM
SRP007412_kidney	0.00 RPM	57.51 RPM
SRP007412_liver	0.03 RPM	128.42 RPM
SRP007412_testis	0.00 RPM	127.51 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1657 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1657 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1657 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2171
Gorilla gorilla	retro_ggor_1723
Pongo abelii	retro_pabe_2058
Callithrix jacchus	retro_cjac_2812

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Parental genes homology:

Parental genes homology involve 27 parental genes, and 122 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	ENSPTRG00000000467	4 retrocopies	retro_ptro_1212, retro_ptro_562, retro_ptro_654, retro_ptro_727,
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,