RetrogeneDB ID: retro_pabe_2167

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2b:128909998..128910899(-)
• Located in intron of: ENSPPYG00000013305

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL3
• Ensembl ID: ENSPPYG00000011837
• Aliases: None
• Description: ribosomal protein L3 [Source:HGNC Symbol;Acc:10332]

Sequence

>retro_pabe_2167
CCTCAAGGCCTCCAGACCTTCAAGACCATCTTCTCTAAGCACATCAGCGATGAGTGCAAAAAGCACTTCTCTAAGAACAG
GCATAAATCTAAGAAGAAGGCCTTTACCAATTACTGCAAGAAATGGCAGAATAAGGATGGCAAGAAGCAGCTGGAGCAGG
ACTTCAGCAGCGTGAAGAAGCACTGCCAAGTCATCCACGTCACTGCCCACACCCACATGCACCTGCTTCCTCCACGCCAG
AAGAAGGCCCGGCTGATGGAGATCTAGGTGAACAGAGGCACCGTGTCCAAGAAGCTGGAATGGGGCCGGGAGAGGCTAGA
GCAGCAGGTACCTATGAACCAAGTGTTTGGGCAGGACGAGATGATTGACGTCTTCAAGGTGACCAAGGGCAAAGACTACA
AAGGGGTCACGAGTCATTGACACACCAAGAAGCTACCCTGCAAGACCCACTGAGGCTTGTGCAAGGTGGCCTGGATTGGG
GCATGGCATACTGCCTGTGTGGCCTTCTCTGTGGCATGTGCTGGGCAGAAAGGGTACCATCACCGCACTGAGATCAACAA
GAAGATTGACCTGTAAGATCGGCCAGGGCTACCTTATCAAGGACGACCAACTGATCAAGAACAGTGCCTCCACTGACCAT
GACCTGCCTGACAAGAGCATCAACTCTCTGGGTGGCTTTGTCCTATATGGTGAAGTGACCAGTGGCTTTGTCATGCTGAA
GGAATGTGTGGTGGGAACCAAGAAGCGAGTGCTCACCCTCCACAAGTCTTTGCTGGCTGAGACCAAACGGCGAGCTCTGG
AGAAGACTGACCTTAAGTTCATTGACACCACTGCCAAGTTTGGCCATGGCTGCTCCCAGACCATGGAAGAGAAGAAAGTA
TTCATTGAAAGTATTCGTGAA

Alignment

ORF - retro_pabe_2167 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.75 %
• Parental protein coverage: 74.19 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PRGLRTFKTVFAEHISDECKRRFYKNWHKSKKKAFTKYCKKWQDEDGKKQLEKDFSSMKKYCQVIRVIAH
          P.GL.TFKT.F..HISDECK..F.KN.HKSKKKAFT.YCKKWQ..DGKKQLE.DFSS.KK.CQVI.V.AH
Retrocopy PQGLQTFKTIFSKHISDECKKHFSKNRHKSKKKAFTNYCKKWQNKDGKKQLEQDFSSVKKHCQVIHVTAH

Parental  TQMRLLPLRQKKAHLMEIQVNGGTVAEKLDWARERLEQQVPVNQVFGQDEMIDVIGVTKGKGYKGVTSRW
          T.M.LLP.RQKKA.LMEI.VN.GTV..KL.W.RERLEQQVP.NQVFGQDEMIDV..VTKGK.YKGVTS..
Retrocopy THMHLLPPRQKKARLMEI*VNRGTVSKKLEWGRERLEQQVPMNQVFGQDEMIDVFKVTKGKDYKGVTSH*

Parental  HTKKLPRKTHRGLRKVACIGAWHPARVAFSVARA-GQKGYHHRTEINKKIY-KIGQGYLIKDGKLIKNNA
          HTKKLP.KTH.GL.KVA.IGAWH.A.VAFSVA.A.G.KG.............KIGQGYLIKD..LIKN.A
Retrocopy HTKKLPCKTH*GLCKVAWIGAWHTACVAFSVACA>GRKGTITALRSTRRLTCKIGQGYLIKDDQLIKNSA

Parental  STDYDLSDKSINPLGGFVHYGEVTNDFVMLKGCVVGTKKRVLTLRKSLLVQTKRRALEKIDLKFIDTTSK
          STD.DL.DKSIN.LGGFV.YGEVT..FVMLK.CVVGTKKRVLTL.KSLL..TKRRALEK.DLKFIDTT.K
Retrocopy STDHDLPDKSINSLGGFVLYGEVTSGFVMLKECVVGTKKRVLTLHKSLLAETKRRALEKTDLKFIDTTAK

Parental  FGHGRFQTMEEKKAFMGPLKK
          FGHG..QTMEEKK.F......
Retrocopy FGHGCSQTMEEKKVFIESIRE

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	0.17 RPM	169.41 RPM
SRP007412_cerebellum	0.36 RPM	139.11 RPM
SRP007412_heart	0.03 RPM	60.51 RPM
SRP007412_kidney	0.13 RPM	379.03 RPM
SRP007412_liver	0.03 RPM	256.93 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2167 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2167 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2167 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2403
Pan troglodytes	retro_ptro_1753
Gorilla gorilla	retro_ggor_1822
Macaca mulatta	retro_mmul_973

---

Parental genes homology:

Parental genes homology involve 29 parental genes, and 143 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010853	1 retrocopy	retro_amel_1115,
Bos taurus	ENSBTAG00000003228	3 retrocopies	retro_btau_1644, retro_btau_281, retro_btau_341,
Canis familiaris	ENSCAFG00000001346	1 retrocopy	retro_cfam_97,
Callithrix jacchus	ENSCJAG00000016276	6 retrocopies	retro_cjac_1198, retro_cjac_1972, retro_cjac_2157, retro_cjac_2264, retro_cjac_3079, retro_cjac_823,
Dasypus novemcinctus	ENSDNOG00000001121	4 retrocopies	retro_dnov_1359, retro_dnov_1641, retro_dnov_652, retro_dnov_788,
Equus caballus	ENSECAG00000020665	1 retrocopy	retro_ecab_897,
Erinaceus europaeus	ENSEEUG00000014661	2 retrocopies	retro_eeur_488, retro_eeur_557,
Echinops telfairi	ENSETEG00000011380	5 retrocopies	retro_etel_1646, retro_etel_2199, retro_etel_2212, retro_etel_657, retro_etel_972,
Felis catus	ENSFCAG00000005820	1 retrocopy	retro_fcat_1809,
Homo sapiens	ENSG00000100316	9 retrocopies	retro_hsap_1341, retro_hsap_2403, retro_hsap_2529, retro_hsap_3328, retro_hsap_3448, retro_hsap_3638, retro_hsap_3889, retro_hsap_4081, retro_hsap_4749,
Gorilla gorilla	ENSGGOG00000002326	10 retrocopies	retro_ggor_1043, retro_ggor_1295, retro_ggor_1582, retro_ggor_1822, retro_ggor_2329, retro_ggor_2616, retro_ggor_2713, retro_ggor_2736, retro_ggor_2955, retro_ggor_36,
Macropus eugenii	ENSMEUG00000009789	26 retrocopies	retro_meug_1045, retro_meug_118, retro_meug_1210, retro_meug_1403, retro_meug_1452, retro_meug_1492, retro_meug_1516, retro_meug_1554, retro_meug_1589, retro_meug_1604, retro_meug_1698, retro_meug_1856, retro_meug_2150, retro_meug_2151, retro_meug_221, retro_meug_367, retro_meug_412, retro_meug_461, retro_meug_592, retro_meug_677, retro_meug_683, retro_meug_831, retro_meug_851, retro_meug_886, retro_meug_889, retro_meug_898,
Microcebus murinus	ENSMICG00000015832	1 retrocopy	retro_mmur_1307,
Myotis lucifugus	ENSMLUG00000023711	1 retrocopy	retro_mluc_810,
Monodelphis domestica	ENSMODG00000009539	2 retrocopies	retro_mdom_380, retro_mdom_408,
Mustela putorius furo	ENSMPUG00000013271	3 retrocopies	retro_mputfur_1284, retro_mputfur_199, retro_mputfur_774,
Mus musculus	ENSMUSG00000060036	30 retrocopies	retro_mmus_1148, retro_mmus_1158, retro_mmus_1164, retro_mmus_1165, retro_mmus_1167, retro_mmus_1183, retro_mmus_1238, retro_mmus_1239, retro_mmus_1240, retro_mmus_1241, retro_mmus_1242, retro_mmus_1243, retro_mmus_1244, retro_mmus_1245, retro_mmus_1246, retro_mmus_1465, retro_mmus_1548, retro_mmus_2231, retro_mmus_2275, retro_mmus_2276, retro_mmus_2474, retro_mmus_2501, retro_mmus_2547, retro_mmus_2849, retro_mmus_3125, retro_mmus_3215, retro_mmus_3422, retro_mmus_3467, retro_mmus_361, retro_mmus_897,
Nomascus leucogenys	ENSNLEG00000015234	2 retrocopies	retro_nleu_1038, retro_nleu_1449,
Oryctolagus cuniculus	ENSOCUG00000027712	4 retrocopies	retro_ocun_105, retro_ocun_179, retro_ocun_1893, retro_ocun_558,
Otolemur garnettii	ENSOGAG00000000032	7 retrocopies	retro_ogar_1264, retro_ogar_1679, retro_ogar_2096, retro_ogar_2122, retro_ogar_2448, retro_ogar_3431, retro_ogar_960,
Ochotona princeps	ENSOPRG00000013088	3 retrocopies	retro_opri_1004, retro_opri_1014, retro_opri_432,
Procavia capensis	ENSPCAG00000010642	1 retrocopy	retro_pcap_115,
Pongo abelii	ENSPPYG00000006973	1 retrocopy	retro_pabe_2854,
Pongo abelii	ENSPPYG00000011837	10 retrocopies	retro_pabe_1113, retro_pabe_1861, retro_pabe_2167 , retro_pabe_2743, retro_pabe_2985, retro_pabe_3170, retro_pabe_3318, retro_pabe_3349, retro_pabe_3696, retro_pabe_3761,
Pteropus vampyrus	ENSPVAG00000003204	2 retrocopies	retro_pvam_1220, retro_pvam_1390,
Rattus norvegicus	ENSRNOG00000016896	2 retrocopies	retro_rnor_1333, retro_rnor_731,
Sarcophilus harrisii	ENSSHAG00000003212	2 retrocopies	retro_shar_154, retro_shar_662,
Tupaia belangeri	ENSTBEG00000005989	1 retrocopy	retro_tbel_939,
Tursiops truncatus	ENSTTRG00000010880	2 retrocopies	retro_ttru_1266, retro_ttru_1518,