RetrogeneDB ID: retro_pabe_3139

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 7:49442221..49442934(-)
• Located in intron of: ENSPPYG00000017645

Retrocopy information

• Ensembl ID: ENSPPYG00000017647
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPL7
• Ensembl ID: ENSPPYG00000018671
• Aliases: None
• Description: 60S ribosomal protein L7 [Source:UniProtKB/Swiss-Prot;Acc:Q5R9R4]

Sequence

>retro_pabe_3139
ATTGAAGAGAAGAAACAAGTTTCCTGCTGTGCCAGAAACCCTTAAGAAAAAGCAAAGGAATTTCACAGAGCTGAAGATCA
AGCACCTGAGAAACAAGTTTGCCTCAAGAGATACTTCCAAAGGCAAGTTGGAAGCTTATTGATGAAAAAGCGAAACACTA
TCACAAGGAGTACAGGCAGATGGGACAGAACTGAAATTCAAATGGCTAGGATGGCAAGAAAAGCTGACCACTTCTATGTA
CCTGCAGAATGCAAATTGGCATTTGTCATCAGGATCAGAGATATCAATGATGTGAGCCCAAAGGTCCAAAAGATGTTGTA
GCTTCTTCGCCTTTGTCAGATCTTCAGTGGAAGCTTTGTTAAGCTCAACAAGCTTAGCATGCTGAGGATTGTAGAACCAT
ATATTGCACGAGGGTACCCAAACCTGAAGTCATTAAATGAACTAATCTACAAGCATTGTTATGGCAAGATCAATAAGAAG
AGAACTGCCCTGATAGATACCAATTTGATTGTTTGATCTGGCTTCATCTGCGTGGAGGATCTGATTCGTGAAATTTGTAC
TGCTGGAAAACACTTCAAAGAAGCAAATAACTTCCTGTACCCCTTCAAATTATCCTCTCTATGAGATGGAATGAAGAGAA
AAACCACTCATTTTATAGAGGTGGAGATGTTGGCAACAGGGAAGACCAGATTAATGGGCTCATTAGAAGGATA

Alignment

ORF - retro_pabe_3139 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.9 %
• Parental protein coverage: 98.38 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  VEEKKKV-PAVPETLKKKRRNFAELKIKRLRKKFA-QKMLRKARRKLIYEKAKHYHKEYRQMY-RTEIRM
          .EEKK.V.PAVPETLKKK.RNF.ELKIK.LR.KFA.Q..L.KA..KLI.EKAKHYHKEYRQM..RTEI.M
Retrocopy IEEKKQV>PAVPETLKKKQRNFTELKIKHLRNKFA>QEILPKASWKLIDEKAKHYHKEYRQMG>RTEIQM

Parental  ARMARKAGNFYVPAEPKLAFVIRIRGINGVSPKVRKVLQLLRLRQIFNGTFVKLNKASINMLRIVEPYIA
          ARMARKA..FYVPAE.KLAFVIRIR.IN.VSPKV.K.L.LLRL.QIF.G.FVKLNK....MLRIVEPYIA
Retrocopy ARMARKADHFYVPAECKLAFVIRIRDINDVSPKVQKML*LLRLCQIFSGSFVKLNK--LSMLRIVEPYIA

Parental  WGYPNLKSVNELIYKRGYGKINKKRIALTDNALIARSLGKYGIICMEDLIHEIYTVGKRFKEANNFLWPF
          .GYPNLKS.NELIYK..YGKINKKR.AL.D..LI..S....G.IC.EDLI.EI.T.GK.FKEANNFL.PF
Retrocopy RGYPNLKSLNELIYKHCYGKINKKRTALIDTNLIV*S----GFICVEDLIREICTAGKHFKEANNFLYPF

Parental  KLSSPRGGMKKKTTHFVE-GGDAGNREDQINRLIRRM
          KLSS...GMK.KTTHF.E.GGD.GNREDQIN.LIRR.
Retrocopy KLSSL*DGMKRKTTHFIE<GGDVGNREDQINGLIRRI

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	195.23 RPM
SRP007412_cerebellum	0.00 RPM	236.51 RPM
SRP007412_heart	0.00 RPM	246.64 RPM
SRP007412_kidney	0.00 RPM	458.95 RPM
SRP007412_liver	0.00 RPM	335.15 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3139 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3139 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3139 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3717

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 256 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020139	22 retrocopies	retro_btau_1088, retro_btau_1231, retro_btau_1367, retro_btau_1381, retro_btau_1422, retro_btau_1434, retro_btau_1468, retro_btau_1548, retro_btau_1559, retro_btau_1616, retro_btau_1627, retro_btau_1784, retro_btau_1814, retro_btau_304, retro_btau_426, retro_btau_622, retro_btau_668, retro_btau_730, retro_btau_750, retro_btau_758, retro_btau_863, retro_btau_879,
Callithrix jacchus	ENSCJAG00000007686	1 retrocopy	retro_cjac_105,
Equus caballus	ENSECAG00000009188	1 retrocopy	retro_ecab_35,
Homo sapiens	ENSG00000147604	49 retrocopies	retro_hsap_1001, retro_hsap_1023, retro_hsap_1033, retro_hsap_1034, retro_hsap_1128, retro_hsap_113, retro_hsap_1232, retro_hsap_1281, retro_hsap_1614, retro_hsap_1626, retro_hsap_1844, retro_hsap_1862, retro_hsap_1957, retro_hsap_2008, retro_hsap_203, retro_hsap_2093, retro_hsap_2101, retro_hsap_2588, retro_hsap_2837, retro_hsap_3197, retro_hsap_3204, retro_hsap_3244, retro_hsap_3254, retro_hsap_3356, retro_hsap_3399, retro_hsap_344, retro_hsap_3453, retro_hsap_3493, retro_hsap_3560, retro_hsap_3573, retro_hsap_3625, retro_hsap_3717, retro_hsap_3775, retro_hsap_3883, retro_hsap_3918, retro_hsap_4137, retro_hsap_415, retro_hsap_426, retro_hsap_4306, retro_hsap_4662, retro_hsap_4704, retro_hsap_4718, retro_hsap_4761, retro_hsap_558, retro_hsap_616, retro_hsap_708, retro_hsap_729, retro_hsap_973, retro_hsap_976,
Latimeria chalumnae	ENSLACG00000003571	1 retrocopy	retro_lcha_63,
Macropus eugenii	ENSMEUG00000016319	9 retrocopies	retro_meug_1002, retro_meug_1449, retro_meug_1942, retro_meug_1947, retro_meug_60, retro_meug_760, retro_meug_84, retro_meug_968, retro_meug_99,
Microcebus murinus	ENSMICG00000002880	8 retrocopies	retro_mmur_1170, retro_mmur_1379, retro_mmur_139, retro_mmur_158, retro_mmur_52, retro_mmur_596, retro_mmur_646, retro_mmur_903,
Macaca mulatta	ENSMMUG00000005141	1 retrocopy	retro_mmul_129,
Monodelphis domestica	ENSMODG00000007136	4 retrocopies	retro_mdom_1341, retro_mdom_1998, retro_mdom_371, retro_mdom_66,
Otolemur garnettii	ENSOGAG00000003903	2 retrocopies	retro_ogar_15, retro_ogar_225,
Pongo abelii	ENSPPYG00000016619	21 retrocopies	retro_pabe_1064, retro_pabe_1069, retro_pabe_1315, retro_pabe_1341, retro_pabe_1370, retro_pabe_1379, retro_pabe_1457, retro_pabe_2078, retro_pabe_2154, retro_pabe_2354, retro_pabe_2527, retro_pabe_2543, retro_pabe_2598, retro_pabe_2609, retro_pabe_2644, retro_pabe_2988, retro_pabe_3053, retro_pabe_3259, retro_pabe_3410, retro_pabe_3714, retro_pabe_3753,
Pongo abelii	ENSPPYG00000018671	50 retrocopies	retro_pabe_1025, retro_pabe_1061, retro_pabe_1087, retro_pabe_1326, retro_pabe_1454, retro_pabe_1520, retro_pabe_1642, retro_pabe_1677, retro_pabe_1908, retro_pabe_1998, retro_pabe_2004, retro_pabe_2118, retro_pabe_2197, retro_pabe_2348, retro_pabe_2656, retro_pabe_2690, retro_pabe_2762, retro_pabe_2796, retro_pabe_2807, retro_pabe_2808, retro_pabe_2856, retro_pabe_2886, retro_pabe_2936, retro_pabe_2946, retro_pabe_307, retro_pabe_3085, retro_pabe_3117, retro_pabe_3139 , retro_pabe_3191, retro_pabe_3414, retro_pabe_3468, retro_pabe_3506, retro_pabe_352, retro_pabe_3622, retro_pabe_3651, retro_pabe_3662, retro_pabe_3669, retro_pabe_3675, retro_pabe_436, retro_pabe_497, retro_pabe_514, retro_pabe_551, retro_pabe_628, retro_pabe_655, retro_pabe_826, retro_pabe_844, retro_pabe_859, retro_pabe_865, retro_pabe_867, retro_pabe_933,
Rattus norvegicus	ENSRNOG00000006992	27 retrocopies	retro_rnor_1018, retro_rnor_1174, retro_rnor_1222, retro_rnor_1233, retro_rnor_1307, retro_rnor_1388, retro_rnor_1466, retro_rnor_1580, retro_rnor_1745, retro_rnor_1916, retro_rnor_1944, retro_rnor_2025, retro_rnor_2028, retro_rnor_2100, retro_rnor_2247, retro_rnor_2304, retro_rnor_2347, retro_rnor_2531, retro_rnor_2715, retro_rnor_2765, retro_rnor_2814, retro_rnor_2824, retro_rnor_530, retro_rnor_666, retro_rnor_911, retro_rnor_929, retro_rnor_977,
Ictidomys tridecemlineatus	ENSSTOG00000004586	18 retrocopies	retro_itri_1025, retro_itri_1080, retro_itri_1358, retro_itri_1375, retro_itri_1412, retro_itri_1430, retro_itri_1464, retro_itri_1593, retro_itri_1776, retro_itri_271, retro_itri_346, retro_itri_349, retro_itri_351, retro_itri_390, retro_itri_534, retro_itri_542, retro_itri_827, retro_itri_917,
Tupaia belangeri	ENSTBEG00000002301	1 retrocopy	retro_tbel_2042,
Tarsius syrichta	ENSTSYG00000006100	25 retrocopies	retro_tsyr_1149, retro_tsyr_1200, retro_tsyr_1293, retro_tsyr_1297, retro_tsyr_1403, retro_tsyr_1598, retro_tsyr_1633, retro_tsyr_1850, retro_tsyr_1891, retro_tsyr_191, retro_tsyr_2109, retro_tsyr_2130, retro_tsyr_344, retro_tsyr_421, retro_tsyr_433, retro_tsyr_521, retro_tsyr_589, retro_tsyr_601, retro_tsyr_651, retro_tsyr_724, retro_tsyr_779, retro_tsyr_877, retro_tsyr_930, retro_tsyr_953, retro_tsyr_992,
Tursiops truncatus	ENSTTRG00000009074	16 retrocopies	retro_ttru_1241, retro_ttru_1546, retro_ttru_1690, retro_ttru_174, retro_ttru_1776, retro_ttru_1918, retro_ttru_210, retro_ttru_290, retro_ttru_367, retro_ttru_402, retro_ttru_534, retro_ttru_604, retro_ttru_726, retro_ttru_852, retro_ttru_933, retro_ttru_952,