RetrogeneDB ID: retro_ptro_1518

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 22:41390172..41390481(-)
• Located in intron of: ENSPTRG00000014461

Retrocopy information

• Ensembl ID: ENSPTRG00000040932
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ATP5L
• Ensembl ID: ENSPTRG00000004342
• Aliases: None
• Description: None

Sequence

>retro_ptro_1518
ATGGCTCCATTTGTCCGTAACCTTGTGGAGAAGACCCCAGCACTGGTGAATGCTGCTGTGACTTACTTGAAGCCTCGATT
GGCCGCATTTTGATACTACACCACGGTTGAGCTGGTTCCTCCCACCCCTGCTGAGATCCCTAGAGCTATTCAGAGCCTGA
AAAAAATAGTCAGTAGCGCTCAGACTGGTAGCTTCAAACAGCTCACAGTTAAGGAAGCTTTGCTGAATGGTTTGGTGGCC
ACTGAGGTATCGATGTGGTTTTATGTCAGAGAGATCATAGGCAAGCGTGGCATCATTGGCTAGAATGTT

Alignment

ORF - retro_ptro_1518 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.35 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAQFVRNLVEKTPALVNAAVTYSKPRLATFWYYAKVELVPPTPAEIPRAIQSLKKIVNSAQTGSFKQLTV
          MA.FVRNLVEKTPALVNAAVTY.KPRLA.F.YY..VELVPPTPAEIPRAIQSLKKIV.SAQTGSFKQLTV
Retrocopy MAPFVRNLVEKTPALVNAAVTYLKPRLAAF*YYTTVELVPPTPAEIPRAIQSLKKIVSSAQTGSFKQLTV

Parental  KEAVLNGLVATEVLMWFYVGEIIGKRGIIGYDV
          KEA.LNGLVATEV.MWFYV.EIIGKRGIIG..V
Retrocopy KEALLNGLVATEVSMWFYVREIIGKRGIIG*NV

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	0.05 RPM	70.66 RPM
SRP007412_cerebellum	0.14 RPM	40.65 RPM
SRP007412_heart	0.00 RPM	121.71 RPM
SRP007412_kidney	0.03 RPM	119.83 RPM
SRP007412_liver	0.10 RPM	44.32 RPM
SRP007412_testis	0.00 RPM	30.56 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1518 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1518 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1518 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_63
Pongo abelii	retro_pabe_1913

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Parental genes homology:

Parental genes homology involve 25 parental genes, and 127 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007332	2 retrocopies	retro_btau_105, retro_btau_245,
Choloepus hoffmanni	ENSCHOG00000010589	3 retrocopies	retro_chof_1454, retro_chof_1865, retro_chof_2204,
Callithrix jacchus	ENSCJAG00000013281	1 retrocopy	retro_cjac_283,
Dasypus novemcinctus	ENSDNOG00000019354	5 retrocopies	retro_dnov_1491, retro_dnov_1872, retro_dnov_2169, retro_dnov_2341, retro_dnov_344,
Equus caballus	ENSECAG00000023715	1 retrocopy	retro_ecab_434,
Erinaceus europaeus	ENSEEUG00000009863	7 retrocopies	retro_eeur_106, retro_eeur_111, retro_eeur_333, retro_eeur_495, retro_eeur_499, retro_eeur_589, retro_eeur_606,
Echinops telfairi	ENSETEG00000008755	11 retrocopies	retro_etel_1239, retro_etel_166, retro_etel_1884, retro_etel_1885, retro_etel_2183, retro_etel_241, retro_etel_254, retro_etel_355, retro_etel_822, retro_etel_876, retro_etel_995,
Felis catus	ENSFCAG00000011782	4 retrocopies	retro_fcat_1358, retro_fcat_1615, retro_fcat_1941, retro_fcat_371,
Homo sapiens	ENSG00000167283	5 retrocopies	retro_hsap_3029, retro_hsap_3110, retro_hsap_63, retro_hsap_860, retro_hsap_883,
Loxodonta africana	ENSLAFG00000030274	3 retrocopies	retro_lafr_1209, retro_lafr_135, retro_lafr_3,
Macropus eugenii	ENSMEUG00000015281	1 retrocopy	retro_meug_1774,
Microcebus murinus	ENSMICG00000015233	6 retrocopies	retro_mmur_1428, retro_mmur_237, retro_mmur_365, retro_mmur_513, retro_mmur_700, retro_mmur_725,
Macaca mulatta	ENSMMUG00000017604	4 retrocopies	retro_mmul_1333, retro_mmul_22, retro_mmul_25, retro_mmul_262,
Mus musculus	ENSMUSG00000038717	1 retrocopy	retro_mmus_139,
Nomascus leucogenys	ENSNLEG00000007362	6 retrocopies	retro_nleu_425, retro_nleu_608, retro_nleu_765, retro_nleu_81, retro_nleu_841, retro_nleu_846,
Oryctolagus cuniculus	ENSOCUG00000029455	4 retrocopies	retro_ocun_1140, retro_ocun_1156, retro_ocun_1418, retro_ocun_567,
Otolemur garnettii	ENSOGAG00000016298	10 retrocopies	retro_ogar_1097, retro_ogar_1102, retro_ogar_176, retro_ogar_3286, retro_ogar_3332, retro_ogar_352, retro_ogar_433, retro_ogar_444, retro_ogar_533, retro_ogar_573,
Pongo abelii	ENSPPYG00000003933	5 retrocopies	retro_pabe_1913, retro_pabe_2508, retro_pabe_2568, retro_pabe_2589, retro_pabe_688,
Pan troglodytes	ENSPTRG00000004342	5 retrocopies	retro_ptro_1518 , retro_ptro_2043, retro_ptro_2102, retro_ptro_2478, retro_ptro_597,
Rattus norvegicus	ENSRNOG00000028884	19 retrocopies	retro_rnor_1145, retro_rnor_1160, retro_rnor_1185, retro_rnor_1319, retro_rnor_1345, retro_rnor_1379, retro_rnor_1420, retro_rnor_1468, retro_rnor_1993, retro_rnor_2258, retro_rnor_2271, retro_rnor_2404, retro_rnor_2573, retro_rnor_2650, retro_rnor_2723, retro_rnor_2735, retro_rnor_2929, retro_rnor_660, retro_rnor_698,
Sus scrofa	ENSSSCG00000023777	5 retrocopies	retro_sscr_196, retro_sscr_270, retro_sscr_378, retro_sscr_463, retro_sscr_500,
Ictidomys tridecemlineatus	ENSSTOG00000014400	2 retrocopies	retro_itri_1649, retro_itri_332,
Tupaia belangeri	ENSTBEG00000009999	4 retrocopies	retro_tbel_1364, retro_tbel_4005, retro_tbel_857, retro_tbel_959,
Tarsius syrichta	ENSTSYG00000002686	4 retrocopies	retro_tsyr_1516, retro_tsyr_1688, retro_tsyr_2166, retro_tsyr_578,
Tursiops truncatus	ENSTTRG00000004284	9 retrocopies	retro_ttru_1088, retro_ttru_1125, retro_ttru_1255, retro_ttru_1537, retro_ttru_1781, retro_ttru_541, retro_ttru_716, retro_ttru_810, retro_ttru_972,