RetrogeneDB ID:

retro_ptro_21

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:3:60198023..60198518(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSPTRG00000034348
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL12
Ensembl ID:ENSPTRG00000022808
Aliases:None
Description:Pan troglodytes ribosomal protein L12 (RPL12), mRNA. [Source:RefSeq mRNA;Acc:NM_001251929]


Retrocopy-Parental alignment summary:






>retro_ptro_21
ATGCCGCCGAAGTTCGACCCCAACGAGATCAAAGTCGTATACCTGAGGTGCACCGGAGGTGAAGTCGGTGCCACTTCCGC
CCTGGCCCCCAAGATCGGCCCCCTGGGTCTGTCTCCAAAAAAGGTTGGTGATGACATTGCCAAGGCAACGGGTGACTGGA
AGGGCCTGAGGATTACAGTGAAACTGACCATTCAGAACAGACAGGCCCAGATTGAGGTGGTGCCTTCTGCCTCTGCCCTG
ATCATCAAAGCCCTCAAGGAACCACCAAGAGACAGAAAGAAACAAAAAAACATTAAACACAGTGGGAATATCACTTTTGA
TGAGATCGTCAACATTGCTCGACAGATGCGGCACCGATCCTTAGCCAGAGAACTCTCTGGAACCATTAAAGAGATCCTGG
GGACTGCCCAGTCTGTGGGCTGTAATGTTGATGGCCGCCACCCTCATGACATCATCGATGACATCAACAGTGGTGCTGTG
GAATGCCCAGCCAGT

ORF - retro_ptro_21 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 100. %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMPPKFDPNEIKVVYLRCTGGEVGATSALAPKIGPLGLSPKKVGDDIAKATGDWKGLRITVKLTIQNRQAQ
MPPKFDPNEIKVVYLRCTGGEVGATSALAPKIGPLGLSPKKVGDDIAKATGDWKGLRITVKLTIQNRQAQ
RetrocopyMPPKFDPNEIKVVYLRCTGGEVGATSALAPKIGPLGLSPKKVGDDIAKATGDWKGLRITVKLTIQNRQAQ
ParentalIEVVPSASALIIKALKEPPRDRKKQKNIKHSGNITFDEIVNIARQMRHRSLARELSGTIKEILGTAQSVG
IEVVPSASALIIKALKEPPRDRKKQKNIKHSGNITFDEIVNIARQMRHRSLARELSGTIKEILGTAQSVG
RetrocopyIEVVPSASALIIKALKEPPRDRKKQKNIKHSGNITFDEIVNIARQMRHRSLARELSGTIKEILGTAQSVG
ParentalCNVDGRHPHDIIDDINSGAVECPAS
CNVDGRHPHDIIDDINSGAVECPAS
RetrocopyCNVDGRHPHDIIDDINSGAVECPAS

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
SRP007412_brain_prefrontal_cortex 0 .93 RPM 100 .33 RPM
SRP007412_cerebellum 0 .04 RPM 65 .89 RPM
SRP007412_heart 0 .00 RPM 81 .58 RPM
SRP007412_kidney 0 .10 RPM 221 .45 RPM
SRP007412_liver 0 .03 RPM 162 .53 RPM
SRP007412_testis 0 .11 RPM 20 .76 RPM

ChIP-Seq - click to see more details

Pan troglodytes was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_ptro_21 retrocopy.

TSS - click to see more details

Pan troglodytes was not studied using FANTOM5 data.

Lab - click to see more details

retro_ptro_21 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_21 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 19 parental genes, and 369 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000069633 retrocopies
retro_btau_102, retro_btau_2, retro_btau_5,
Callithrix jacchus ENSCJAG000000180821 retrocopy
retro_cjac_221,
Homo sapiens ENSG0000019795841 retrocopies
retro_hsap_1064, retro_hsap_117, retro_hsap_1210, retro_hsap_127, retro_hsap_1311, retro_hsap_1359, retro_hsap_137, retro_hsap_1401, retro_hsap_1592, retro_hsap_1644, retro_hsap_1790, retro_hsap_1850, retro_hsap_1880, retro_hsap_1895, retro_hsap_2005, retro_hsap_2031, retro_hsap_2099, retro_hsap_2123, retro_hsap_2202, retro_hsap_2311, retro_hsap_2381, retro_hsap_2428, retro_hsap_2436, retro_hsap_2456, retro_hsap_2642, retro_hsap_3388, retro_hsap_3405, retro_hsap_3458, retro_hsap_3544, retro_hsap_3578, retro_hsap_3709, retro_hsap_4107, retro_hsap_4121, retro_hsap_4746, retro_hsap_584, retro_hsap_643, retro_hsap_705, retro_hsap_719, retro_hsap_768, retro_hsap_868, retro_hsap_983,
Gorilla gorilla ENSGGOG0000000064834 retrocopies
retro_ggor_1024, retro_ggor_1059, retro_ggor_1086, retro_ggor_1207, retro_ggor_1242, retro_ggor_1377, retro_ggor_1389, retro_ggor_1449, retro_ggor_1511, retro_ggor_1516, retro_ggor_1530, retro_ggor_1645, retro_ggor_1740, retro_ggor_1753, retro_ggor_1806, retro_ggor_1845, retro_ggor_2158, retro_ggor_221, retro_ggor_2232, retro_ggor_2293, retro_ggor_2304, retro_ggor_232, retro_ggor_2334, retro_ggor_2394, retro_ggor_2414, retro_ggor_2506, retro_ggor_262, retro_ggor_2758, retro_ggor_2768, retro_ggor_2949, retro_ggor_541, retro_ggor_600, retro_ggor_637, retro_ggor_942,
Latimeria chalumnae ENSLACG000000153733 retrocopies
retro_lcha_31, retro_lcha_87, retro_lcha_92,
Macropus eugenii ENSMEUG0000000738012 retrocopies
retro_meug_1102, retro_meug_1107, retro_meug_1199, retro_meug_1357, retro_meug_1426, retro_meug_1611, retro_meug_1634, retro_meug_1691, retro_meug_1953, retro_meug_265, retro_meug_479, retro_meug_493,
Macaca mulatta ENSMMUG000000004222 retrocopies
retro_mmul_1823, retro_mmul_53,
Monodelphis domestica ENSMODG000000045719 retrocopies
retro_mdom_1061, retro_mdom_1177, retro_mdom_1192, retro_mdom_1526, retro_mdom_1719, retro_mdom_1871, retro_mdom_1947, retro_mdom_309, retro_mdom_925,
Mus musculus ENSMUSG000000389001 retrocopy
retro_mmus_28,
Oryctolagus cuniculus ENSOCUG000000049029 retrocopies
retro_ocun_1246, retro_ocun_1632, retro_ocun_1895, retro_ocun_318, retro_ocun_329, retro_ocun_520, retro_ocun_556, retro_ocun_677, retro_ocun_880,
Otolemur garnettii ENSOGAG00000000597120 retrocopies
retro_ogar_1002, retro_ogar_1010, retro_ogar_1049, retro_ogar_1069, retro_ogar_1106, retro_ogar_1117, retro_ogar_1137, retro_ogar_1140, retro_ogar_1181, retro_ogar_1188, retro_ogar_1189, retro_ogar_1192, retro_ogar_1230, retro_ogar_1247, retro_ogar_1263, retro_ogar_1295, retro_ogar_1331, retro_ogar_1341, retro_ogar_1408, retro_ogar_1409, retro_ogar_1427, retro_ogar_1457, retro_ogar_1464, retro_ogar_1489, retro_ogar_1503, retro_ogar_1534, retro_ogar_1536, retro_ogar_1550, retro_ogar_1569, retro_ogar_1570, retro_ogar_1579, retro_ogar_1606, retro_ogar_1621, retro_ogar_1709, retro_ogar_1717, retro_ogar_1739, retro_ogar_1789, retro_ogar_1803, retro_ogar_1810, retro_ogar_1825, retro_ogar_1836, retro_ogar_1881, retro_ogar_1885, retro_ogar_1916, retro_ogar_1923, retro_ogar_1937, retro_ogar_1941, retro_ogar_1948, retro_ogar_1969, retro_ogar_1975, retro_ogar_1987, retro_ogar_2055, retro_ogar_2115, retro_ogar_2134, retro_ogar_2172, retro_ogar_2179, retro_ogar_2180, retro_ogar_2208, retro_ogar_2209, retro_ogar_2230, retro_ogar_2291, retro_ogar_2323, retro_ogar_2387, retro_ogar_2483, retro_ogar_2495, retro_ogar_2511, retro_ogar_2570, retro_ogar_2620, retro_ogar_2622, retro_ogar_2624, retro_ogar_2749, retro_ogar_2768, retro_ogar_2809, retro_ogar_2904, retro_ogar_2935, retro_ogar_2945, retro_ogar_2953, retro_ogar_2980, retro_ogar_3004, retro_ogar_3017, retro_ogar_303, retro_ogar_3035, retro_ogar_3128, retro_ogar_3135, retro_ogar_3164, retro_ogar_3394, retro_ogar_3489, retro_ogar_395, retro_ogar_398, retro_ogar_412, retro_ogar_427, retro_ogar_452, retro_ogar_480, retro_ogar_512, retro_ogar_513, retro_ogar_538, retro_ogar_560, retro_ogar_587, retro_ogar_624, retro_ogar_636, retro_ogar_653, retro_ogar_655, retro_ogar_667, retro_ogar_668, retro_ogar_669, retro_ogar_683, retro_ogar_700, retro_ogar_734, retro_ogar_737, retro_ogar_744, retro_ogar_747, retro_ogar_775, retro_ogar_818, retro_ogar_853, retro_ogar_868, retro_ogar_901, retro_ogar_927, retro_ogar_956, retro_ogar_962, retro_ogar_964,
Ochotona princeps ENSOPRG0000001107821 retrocopies
retro_opri_100, retro_opri_1018, retro_opri_1066, retro_opri_1110, retro_opri_1210, retro_opri_1217, retro_opri_221, retro_opri_265, retro_opri_336, retro_opri_353, retro_opri_418, retro_opri_461, retro_opri_479, retro_opri_576, retro_opri_638, retro_opri_648, retro_opri_658, retro_opri_672, retro_opri_835, retro_opri_905, retro_opri_986,
Pongo abelii ENSPPYG0000001962244 retrocopies
retro_pabe_1009, retro_pabe_1084, retro_pabe_1095, retro_pabe_1127, retro_pabe_1159, retro_pabe_1223, retro_pabe_1246, retro_pabe_1309, retro_pabe_1361, retro_pabe_1471, retro_pabe_1509, retro_pabe_1577, retro_pabe_1659, retro_pabe_1660, retro_pabe_1736, retro_pabe_1794, retro_pabe_1806, retro_pabe_1820, retro_pabe_1969, retro_pabe_1982, retro_pabe_2000, retro_pabe_2149, retro_pabe_2328, retro_pabe_2531, retro_pabe_2802, retro_pabe_2859, retro_pabe_2928, retro_pabe_2947, retro_pabe_3002, retro_pabe_3146, retro_pabe_3185, retro_pabe_3276, retro_pabe_3363, retro_pabe_3405, retro_pabe_3482, retro_pabe_3693, retro_pabe_488, retro_pabe_521, retro_pabe_604, retro_pabe_620, retro_pabe_757, retro_pabe_815, retro_pabe_831, retro_pabe_904,
Pan troglodytes ENSPTRG00000022808 1 retrocopy
retro_ptro_21 ,
Pteropus vampyrus ENSPVAG0000000092515 retrocopies
retro_pvam_100, retro_pvam_1026, retro_pvam_1193, retro_pvam_209, retro_pvam_239, retro_pvam_483, retro_pvam_572, retro_pvam_590, retro_pvam_617, retro_pvam_630, retro_pvam_687, retro_pvam_747, retro_pvam_787, retro_pvam_846, retro_pvam_888,
Rattus norvegicus ENSRNOG000000162204 retrocopies
retro_rnor_166, retro_rnor_236, retro_rnor_247, retro_rnor_312,
Sarcophilus harrisii ENSSHAG000000178648 retrocopies
retro_shar_140, retro_shar_266, retro_shar_284, retro_shar_335, retro_shar_346, retro_shar_453, retro_shar_508, retro_shar_646,
Sus scrofa ENSSSCG0000000561214 retrocopies
retro_sscr_1111, retro_sscr_127, retro_sscr_189, retro_sscr_28, retro_sscr_439, retro_sscr_526, retro_sscr_551, retro_sscr_71, retro_sscr_715, retro_sscr_772, retro_sscr_773, retro_sscr_828, retro_sscr_832, retro_sscr_911,
Vicugna pacos ENSVPAG0000000512327 retrocopies
retro_vpac_158, retro_vpac_181, retro_vpac_189, retro_vpac_191, retro_vpac_194, retro_vpac_236, retro_vpac_268, retro_vpac_276, retro_vpac_291, retro_vpac_306, retro_vpac_323, retro_vpac_36, retro_vpac_37, retro_vpac_377, retro_vpac_413, retro_vpac_43, retro_vpac_432, retro_vpac_465, retro_vpac_482, retro_vpac_494, retro_vpac_506, retro_vpac_55, retro_vpac_569, retro_vpac_615, retro_vpac_80, retro_vpac_83, retro_vpac_90,


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