RetrogeneDB ID: retro_ptro_1639

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 2B:130254088..130254580(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPIA
• Ensembl ID: ENSPTRG00000023064
• Aliases: None
• Description: Peptidyl-prolyl cis-trans isomerase A [Source:UniProtKB/Swiss-Prot;Acc:Q0ZQL1]

Sequence

>retro_ptro_1639
ATGGTCAACCCCACTGTGTTCTTCGACATTGCCATTGACAGCGAGCCCTTGGGCCACGTCTCCTTCAAGCTGTTTGCAGA
CAAGTTTCCAAAGACAGCAGAAAACTTTTGTGCTCTGAGCACTGGAGAGAAAGCATTTGGTTATAAGGGTTCCTGCTTTC
ACAGAATTATTCCAGGGTTTATGTATCAGGGTGGTGACTTCACACACCATAACAGCACTGATGGCAAGTCCATCTATGGG
GAGAAATTTGATGATGAAAACTTCATCCTAAAGCATACAGGTCATGGCATCTTGTCCATGGCAAATGCTGGACCCAGCAC
AAATGGTTCCCAGTTTTTCATCTGCACTGCCAAGAGTGAGTGGTTGGATGGCAAGCATGTGGTCTTTGGCAAGATGAAAG
AAGGCATGAATATTGTGGAGGCCACGTAGTGCTTTGGGTCCAGGAATGGCAAGACAAGCAAGAAGATCACCATTGCTGAC
TATGGACAACTC

Alignment

ORF - retro_ptro_1639 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.8 %
• Parental protein coverage: 99.39 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVNPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTRH
          MVNPTVFFDIA.D.EPLG.VSF.LFADK.PKTAENF.ALSTGEK.FGYKGSCFHRIIPGFM.QGGDFT.H
Retrocopy MVNPTVFFDIAIDSEPLGHVSFKLFADKFPKTAENFCALSTGEKAFGYKGSCFHRIIPGFMYQGGDFTHH

Parental  NGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVE
          N.T.GKSIYGEKF.DENFILKHTG.GILSMANAGP.TNGSQFFICTAK.EWLDGKHVVFGK.KEGMNIVE
Retrocopy NSTDGKSIYGEKFDDENFILKHTGHGILSMANAGPSTNGSQFFICTAKSEWLDGKHVVFGKMKEGMNIVE

Parental  AMERFGSRNGKTSKKITIADCGQL
          A...FGSRNGKTSKKITIAD.GQL
Retrocopy AT*CFGSRNGKTSKKITIADYGQL

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	0.00 RPM	473.80 RPM
SRP007412_cerebellum	0.04 RPM	137.73 RPM
SRP007412_heart	0.03 RPM	52.38 RPM
SRP007412_kidney	0.00 RPM	185.81 RPM
SRP007412_liver	0.10 RPM	155.29 RPM
SRP007412_testis	0.11 RPM	52.38 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1639 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1639 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1639 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2154

---

Parental genes homology:

Parental genes homology involve 19 parental genes, and 375 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012003	12 retrocopies	retro_btau_1005, retro_btau_1448, retro_btau_155, retro_btau_1696, retro_btau_1806, retro_btau_272, retro_btau_334, retro_btau_335, retro_btau_345, retro_btau_414, retro_btau_751, retro_btau_934,
Callithrix jacchus	ENSCJAG00000011969	54 retrocopies	retro_cjac_1065, retro_cjac_1080, retro_cjac_1083, retro_cjac_1092, retro_cjac_1097, retro_cjac_11, retro_cjac_1193, retro_cjac_1213, retro_cjac_1310, retro_cjac_1326, retro_cjac_1347, retro_cjac_1451, retro_cjac_147, retro_cjac_1678, retro_cjac_1710, retro_cjac_1760, retro_cjac_1782, retro_cjac_1982, retro_cjac_1989, retro_cjac_2043, retro_cjac_2060, retro_cjac_2062, retro_cjac_2118, retro_cjac_2286, retro_cjac_2327, retro_cjac_2376, retro_cjac_2425, retro_cjac_2426, retro_cjac_2479, retro_cjac_2540, retro_cjac_2688, retro_cjac_2863, retro_cjac_2881, retro_cjac_2977, retro_cjac_3073, retro_cjac_3077, retro_cjac_3101, retro_cjac_3196, retro_cjac_384, retro_cjac_4202, retro_cjac_4203, retro_cjac_501, retro_cjac_646, retro_cjac_649, retro_cjac_695, retro_cjac_704, retro_cjac_710, retro_cjac_714, retro_cjac_717, retro_cjac_755, retro_cjac_827, retro_cjac_834, retro_cjac_871, retro_cjac_971,
Echinops telfairi	ENSETEG00000002186	21 retrocopies	retro_etel_115, retro_etel_1188, retro_etel_1292, retro_etel_1322, retro_etel_1670, retro_etel_1827, retro_etel_1875, retro_etel_1886, retro_etel_208, retro_etel_25, retro_etel_288, retro_etel_371, retro_etel_430, retro_etel_447, retro_etel_485, retro_etel_537, retro_etel_551, retro_etel_568, retro_etel_595, retro_etel_937, retro_etel_998,
Gorilla gorilla	ENSGGOG00000026298	4 retrocopies	retro_ggor_138, retro_ggor_15, retro_ggor_165, retro_ggor_28,
Macropus eugenii	ENSMEUG00000002016	20 retrocopies	retro_meug_1024, retro_meug_1055, retro_meug_1089, retro_meug_1133, retro_meug_1269, retro_meug_1391, retro_meug_1576, retro_meug_1746, retro_meug_1880, retro_meug_1975, retro_meug_2013, retro_meug_2037, retro_meug_260, retro_meug_297, retro_meug_301, retro_meug_437, retro_meug_478, retro_meug_510, retro_meug_713, retro_meug_73,
Macaca mulatta	ENSMMUG00000016638	10 retrocopies	retro_mmul_1, retro_mmul_13, retro_mmul_132, retro_mmul_141, retro_mmul_161, retro_mmul_195, retro_mmul_245, retro_mmul_5, retro_mmul_56, retro_mmul_8,
Monodelphis domestica	ENSMODG00000016089	9 retrocopies	retro_mdom_1373, retro_mdom_1524, retro_mdom_1856, retro_mdom_1884, retro_mdom_215, retro_mdom_272, retro_mdom_29, retro_mdom_730, retro_mdom_85,
Mus musculus	ENSMUSG00000071866	2 retrocopies	retro_mmus_242, retro_mmus_285,
Oryctolagus cuniculus	ENSOCUG00000016662	3 retrocopies	retro_ocun_113, retro_ocun_1406, retro_ocun_237,
Otolemur garnettii	ENSOGAG00000027997	31 retrocopies	retro_ogar_1090, retro_ogar_1201, retro_ogar_1305, retro_ogar_1329, retro_ogar_1336, retro_ogar_1562, retro_ogar_1634, retro_ogar_1741, retro_ogar_1889, retro_ogar_1893, retro_ogar_1920, retro_ogar_1973, retro_ogar_1974, retro_ogar_1999, retro_ogar_21, retro_ogar_2246, retro_ogar_2265, retro_ogar_2397, retro_ogar_2401, retro_ogar_2440, retro_ogar_2484, retro_ogar_2794, retro_ogar_2907, retro_ogar_2924, retro_ogar_2938, retro_ogar_2948, retro_ogar_3072, retro_ogar_3187, retro_ogar_3210, retro_ogar_357, retro_ogar_743,
Pongo abelii	ENSPPYG00000017586	12 retrocopies	retro_pabe_1065, retro_pabe_1330, retro_pabe_186, retro_pabe_221, retro_pabe_2267, retro_pabe_2469, retro_pabe_2633, retro_pabe_2730, retro_pabe_2812, retro_pabe_3474, retro_pabe_631, retro_pabe_995,
Pongo abelii	ENSPPYG00000017587	4 retrocopies	retro_pabe_1118, retro_pabe_2202, retro_pabe_3311, retro_pabe_3602,
Pan troglodytes	ENSPTRG00000002669	1 retrocopy	retro_ptro_979,
Pan troglodytes	ENSPTRG00000023064	77 retrocopies	retro_ptro_1116, retro_ptro_1122, retro_ptro_1124, retro_ptro_1213, retro_ptro_1277, retro_ptro_1328, retro_ptro_1377, retro_ptro_1399, retro_ptro_1401, retro_ptro_1423, retro_ptro_1449, retro_ptro_1463, retro_ptro_1529, retro_ptro_1531, retro_ptro_1544, retro_ptro_1596, retro_ptro_1626, retro_ptro_1639 , retro_ptro_1672, retro_ptro_1717, retro_ptro_1779, retro_ptro_1787, retro_ptro_1835, retro_ptro_1843, retro_ptro_1889, retro_ptro_1890, retro_ptro_1891, retro_ptro_1916, retro_ptro_1925, retro_ptro_195, retro_ptro_1952, retro_ptro_2012, retro_ptro_2014, retro_ptro_210, retro_ptro_2136, retro_ptro_2138, retro_ptro_2161, retro_ptro_2260, retro_ptro_2272, retro_ptro_2425, retro_ptro_2546, retro_ptro_2562, retro_ptro_2611, retro_ptro_2642, retro_ptro_2663, retro_ptro_2689, retro_ptro_2692, retro_ptro_278, retro_ptro_2806, retro_ptro_2899, retro_ptro_2904, retro_ptro_2914, retro_ptro_293, retro_ptro_2945, retro_ptro_2967, retro_ptro_3010, retro_ptro_3033, retro_ptro_3049, retro_ptro_326, retro_ptro_394, retro_ptro_458, retro_ptro_472, retro_ptro_477, retro_ptro_498, retro_ptro_518, retro_ptro_521, retro_ptro_527, retro_ptro_541, retro_ptro_567, retro_ptro_585, retro_ptro_783, retro_ptro_825, retro_ptro_853, retro_ptro_879, retro_ptro_889, retro_ptro_905, retro_ptro_921,
Rattus norvegicus	ENSRNOG00000006423	2 retrocopies	retro_rnor_360, retro_rnor_387,
Sarcophilus harrisii	ENSSHAG00000017062	3 retrocopies	retro_shar_164, retro_shar_383, retro_shar_750,
Ictidomys tridecemlineatus	ENSSTOG00000010215	10 retrocopies	retro_itri_1073, retro_itri_1576, retro_itri_1683, retro_itri_1897, retro_itri_499, retro_itri_667, retro_itri_7, retro_itri_731, retro_itri_802, retro_itri_978,
Tupaia belangeri	ENSTBEG00000017484	77 retrocopies	retro_tbel_1014, retro_tbel_1098, retro_tbel_1104, retro_tbel_1106, retro_tbel_1180, retro_tbel_1661, retro_tbel_1689, retro_tbel_1808, retro_tbel_1813, retro_tbel_1831, retro_tbel_1895, retro_tbel_1904, retro_tbel_1913, retro_tbel_1918, retro_tbel_1936, retro_tbel_1938, retro_tbel_2013, retro_tbel_2014, retro_tbel_204, retro_tbel_2054, retro_tbel_2098, retro_tbel_2144, retro_tbel_2175, retro_tbel_221, retro_tbel_2557, retro_tbel_267, retro_tbel_2681, retro_tbel_2691, retro_tbel_2714, retro_tbel_2824, retro_tbel_2834, retro_tbel_2851, retro_tbel_2897, retro_tbel_2938, retro_tbel_3004, retro_tbel_3054, retro_tbel_3104, retro_tbel_3142, retro_tbel_3153, retro_tbel_3311, retro_tbel_3337, retro_tbel_3421, retro_tbel_3423, retro_tbel_3477, retro_tbel_3639, retro_tbel_3691, retro_tbel_3767, retro_tbel_3847, retro_tbel_3880, retro_tbel_3890, retro_tbel_3979, retro_tbel_4019, retro_tbel_415, retro_tbel_4155, retro_tbel_4325, retro_tbel_4332, retro_tbel_4364, retro_tbel_4391, retro_tbel_4534, retro_tbel_4537, retro_tbel_4568, retro_tbel_4581, retro_tbel_4683, retro_tbel_4699, retro_tbel_521, retro_tbel_541, retro_tbel_618, retro_tbel_64, retro_tbel_764, retro_tbel_80, retro_tbel_831, retro_tbel_832, retro_tbel_887, retro_tbel_900, retro_tbel_910, retro_tbel_922, retro_tbel_946,
Tarsius syrichta	ENSTSYG00000008973	23 retrocopies	retro_tsyr_1106, retro_tsyr_1266, retro_tsyr_1277, retro_tsyr_1530, retro_tsyr_1643, retro_tsyr_1816, retro_tsyr_1909, retro_tsyr_2040, retro_tsyr_2072, retro_tsyr_2097, retro_tsyr_388, retro_tsyr_400, retro_tsyr_408, retro_tsyr_430, retro_tsyr_459, retro_tsyr_478, retro_tsyr_481, retro_tsyr_507, retro_tsyr_641, retro_tsyr_705, retro_tsyr_760, retro_tsyr_847, retro_tsyr_924,