RetrogeneDB ID: retro_pabe_3080

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 7:101957978..101958266(+)
• Located in intron of: ENSPPYG00000017889

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPLP1
• Ensembl ID: ENSPPYG00000006601
• Aliases: None
• Description: ribosomal protein, large, P1 [Source:HGNC Symbol;Acc:10372]

Sequence

>retro_pabe_3080
GAGTTCGCCTGCATCTACTCCACCCTCATTCTTCACTATGAATGAGGTGACCGTCACAGAGGATAAATCAAGGCCCTAAT
TAAAGTAAGTGGTGTAAATGTTGAACCTTTTCAGCCTGGTTTGTTGGCAAAGGCCCTGGCCTATGTTGACATCGAGAGAC
TCATCCTAATGTAGGGGTTGGTGGACCTGCTCCAGCAGCTGCTGCTGCCATCAACAGTAGGTCCTGCCCTGTCCAGAGCA
GCTGCTCCAGCTGAGGAGAAGAAAGTGTAAGCAAAGAAAAAAGAATCT

Alignment

ORF - retro_pabe_3080 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.0 %
• Parental protein coverage: 84.21 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  ELACIYSALILHDD-EVTVTEDK-INALIKAAGVNVEPFWPGLFAKALANVNIGSLIC-NVGAGGPAPAA
          E.ACIYS.LILH...EVTVTEDK.I.ALIK..GVNVEPF.PGL.AKALA.V.I..LI..NVG.GGPAPAA
Retrocopy EFACIYSTLILHYE>EVTVTEDK<IKALIKVSGVNVEPFQPGLLAKALAYVDIERLIL<NVGVGGPAPAA

Parental  GAA-PAGGPAPSTAAAPAEEKKVEAKKEES
          .AA....GPA.S.AAAPAEEKKV.AKK.ES
Retrocopy AAA>STVGPALSRAAAPAEEKKV*AKKKES

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	56.12 RPM
SRP007412_cerebellum	0.00 RPM	51.56 RPM
SRP007412_heart	0.00 RPM	134.65 RPM
SRP007412_kidney	0.00 RPM	166.40 RPM
SRP007412_liver	0.00 RPM	207.42 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3080 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3080 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3080 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3768
Gorilla gorilla	retro_ggor_2534

---

Parental genes homology:

Parental genes homology involve 20 parental genes, and 191 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000018320	4 retrocopies	retro_btau_1131, retro_btau_1717, retro_btau_186, retro_btau_615,
Callithrix jacchus	ENSCJAG00000032919	19 retrocopies	retro_cjac_1125, retro_cjac_1150, retro_cjac_1222, retro_cjac_1375, retro_cjac_1413, retro_cjac_1666, retro_cjac_1809, retro_cjac_183, retro_cjac_2090, retro_cjac_2626, retro_cjac_267, retro_cjac_2765, retro_cjac_306, retro_cjac_3131, retro_cjac_458, retro_cjac_469, retro_cjac_694, retro_cjac_750, retro_cjac_984,
Equus caballus	ENSECAG00000008542	4 retrocopies	retro_ecab_380, retro_ecab_677, retro_ecab_820, retro_ecab_958,
Homo sapiens	ENSG00000137818	18 retrocopies	retro_hsap_1325, retro_hsap_1366, retro_hsap_1719, retro_hsap_1835, retro_hsap_2014, retro_hsap_2079, retro_hsap_2348, retro_hsap_2897, retro_hsap_2936, retro_hsap_3169, retro_hsap_3382, retro_hsap_3392, retro_hsap_3523, retro_hsap_3768, retro_hsap_3939, retro_hsap_472, retro_hsap_533, retro_hsap_679,
Gorilla gorilla	ENSGGOG00000003980	13 retrocopies	retro_ggor_1033, retro_ggor_118, retro_ggor_1276, retro_ggor_1458, retro_ggor_1628, retro_ggor_2036, retro_ggor_2163, retro_ggor_2269, retro_ggor_2381, retro_ggor_2534, retro_ggor_585, retro_ggor_73, retro_ggor_94,
Latimeria chalumnae	ENSLACG00000012630	1 retrocopy	retro_lcha_7,
Macropus eugenii	ENSMEUG00000015277	6 retrocopies	retro_meug_1096, retro_meug_1283, retro_meug_1312, retro_meug_1401, retro_meug_1515, retro_meug_793,
Myotis lucifugus	ENSMLUG00000010542	33 retrocopies	retro_mluc_10, retro_mluc_1064, retro_mluc_1122, retro_mluc_1234, retro_mluc_136, retro_mluc_1374, retro_mluc_1412, retro_mluc_1424, retro_mluc_1654, retro_mluc_1670, retro_mluc_1751, retro_mluc_1810, retro_mluc_1832, retro_mluc_1850, retro_mluc_1944, retro_mluc_197, retro_mluc_2025, retro_mluc_2255, retro_mluc_2265, retro_mluc_2294, retro_mluc_2489, retro_mluc_2578, retro_mluc_433, retro_mluc_472, retro_mluc_570, retro_mluc_577, retro_mluc_61, retro_mluc_732, retro_mluc_791, retro_mluc_858, retro_mluc_916, retro_mluc_945, retro_mluc_95,
Monodelphis domestica	ENSMODG00000009209	1 retrocopy	retro_mdom_1022,
Mustela putorius furo	ENSMPUG00000000204	13 retrocopies	retro_mputfur_1018, retro_mputfur_113, retro_mputfur_122, retro_mputfur_1265, retro_mputfur_129, retro_mputfur_1334, retro_mputfur_1450, retro_mputfur_1598, retro_mputfur_1613, retro_mputfur_304, retro_mputfur_628, retro_mputfur_635, retro_mputfur_709,
Mus musculus	ENSMUSG00000007892	6 retrocopies	retro_mmus_180, retro_mmus_206, retro_mmus_2060, retro_mmus_2180, retro_mmus_247, retro_mmus_2525,
Oryctolagus cuniculus	ENSOCUG00000015087	8 retrocopies	retro_ocun_1009, retro_ocun_1464, retro_ocun_1655, retro_ocun_1735, retro_ocun_48, retro_ocun_551, retro_ocun_647, retro_ocun_884,
Otolemur garnettii	ENSOGAG00000029641	19 retrocopies	retro_ogar_1078, retro_ogar_1259, retro_ogar_1363, retro_ogar_1430, retro_ogar_1670, retro_ogar_2215, retro_ogar_2413, retro_ogar_2603, retro_ogar_2683, retro_ogar_2942, retro_ogar_3053, retro_ogar_3222, retro_ogar_3393, retro_ogar_363, retro_ogar_474, retro_ogar_500, retro_ogar_574, retro_ogar_607, retro_ogar_961,
Ochotona princeps	ENSOPRG00000001163	11 retrocopies	retro_opri_1010, retro_opri_130, retro_opri_214, retro_opri_245, retro_opri_38, retro_opri_530, retro_opri_645, retro_opri_768, retro_opri_784, retro_opri_96, retro_opri_972,
Procavia capensis	ENSPCAG00000014595	7 retrocopies	retro_pcap_107, retro_pcap_118, retro_pcap_124, retro_pcap_315, retro_pcap_32, retro_pcap_36, retro_pcap_83,
Pongo abelii	ENSPPYG00000006601	5 retrocopies	retro_pabe_1506, retro_pabe_160, retro_pabe_182, retro_pabe_261, retro_pabe_3080 ,
Rattus norvegicus	ENSRNOG00000011955	6 retrocopies	retro_rnor_1042, retro_rnor_1402, retro_rnor_1827, retro_rnor_2175, retro_rnor_2678, retro_rnor_493,
Rattus norvegicus	ENSRNOG00000013874	3 retrocopies	retro_rnor_2432, retro_rnor_2700, retro_rnor_2934,
Sarcophilus harrisii	ENSSHAG00000014818	6 retrocopies	retro_shar_182, retro_shar_234, retro_shar_449, retro_shar_550, retro_shar_614, retro_shar_742,
Ictidomys tridecemlineatus	ENSSTOG00000027893	8 retrocopies	retro_itri_1589, retro_itri_1698, retro_itri_1842, retro_itri_1856, retro_itri_226, retro_itri_409, retro_itri_796, retro_itri_976,