RetrogeneDB ID: retro_ptro_2748

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 8:50014034..50014382(-)
• Located in intron of: ENSPTRG00000020245

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL34
• Ensembl ID: ENSPTRG00000016353
• Aliases: None
• Description: ribosomal protein L34 [Source:HGNC Symbol;Acc:10340]

Sequence

>retro_ptro_2748
ATGGCCCAGCATTGGACATACTGTTGTAAGCTTTCCTATAATACAGCCTCTAACAAAACTAGGCTGTCCCAAACCCTGGT
AATAGAGTTGTTTACTTTTATACCAAGACATTTGGGGAAACACCAAAATCTGCATGTGGTGTGTACCCAGACACATTTTG
AGGGCTTCTTGCTGTGAGACCTGAAGTTCTTATGAGGTTGTCTAGAAGGAAAAAAACATGCTAGCAGTGCTTGCGGTGGT
GCCATGTGTGCTGAGTGTGTTTGTGGCAGGATCAAGCATGTGTTCCTTATCAGGGAGCAGAAAATCATGAAAGAGTTCAA
GGTACAAGCACAGAGTCAGAATGCTAAA

Alignment

ORF - retro_ptro_2748 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.55 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MVQRLTYRRRLSYNTASNKTRLSRT-PGNRIVYLYTKKVGKAPKSACGVCPGRLRGVRAVRPKVLMRLSK
          M.Q..TY...LSYNTASNKTRLS.T.PGNR.VY.YTK..G..PKSACGV.P....G..AVRP.VLMRLS.
Retrocopy MAQHWTYCCKLSYNTASNKTRLSQT<PGNRVVYFYTKTFGETPKSACGVYPDTF*GLLAVRPEVLMRLSR

Parental  T-KKHVSRAYGGSMCAKCVRDRIKRAFLIEEQKIVVKVLKAQAQSQKAK
          ..KKH.S.A.GG.MCA.CV..RIK..FLI.EQKI..K..K.QAQSQ.AK
Retrocopy R>KKHASSACGGAMCAECVCGRIKHVFLIREQKI-MKEFKVQAQSQNAK

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	0.04 RPM	97.95 RPM
SRP007412_cerebellum	0.00 RPM	85.36 RPM
SRP007412_heart	0.00 RPM	66.98 RPM
SRP007412_kidney	0.00 RPM	223.00 RPM
SRP007412_liver	0.00 RPM	113.88 RPM
SRP007412_testis	0.00 RPM	50.79 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2748 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2748 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2748 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4055
Gorilla gorilla	retro_ggor_2723
Pongo abelii	retro_pabe_3330

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 183 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000011179	26 retrocopies	retro_dnov_1172, retro_dnov_1775, retro_dnov_2020, retro_dnov_2025, retro_dnov_2079, retro_dnov_2127, retro_dnov_2137, retro_dnov_2275, retro_dnov_2385, retro_dnov_2501, retro_dnov_252, retro_dnov_262, retro_dnov_2627, retro_dnov_2651, retro_dnov_325, retro_dnov_339, retro_dnov_430, retro_dnov_553, retro_dnov_565, retro_dnov_59, retro_dnov_606, retro_dnov_635, retro_dnov_658, retro_dnov_862, retro_dnov_88, retro_dnov_978,
Gadus morhua	ENSGMOG00000009982	1 retrocopy	retro_gmor_31,
Loxodonta africana	ENSLAFG00000032615	6 retrocopies	retro_lafr_1039, retro_lafr_1232, retro_lafr_182, retro_lafr_298, retro_lafr_306, retro_lafr_733,
Macropus eugenii	ENSMEUG00000009361	3 retrocopies	retro_meug_1012, retro_meug_1754, retro_meug_1775,
Microcebus murinus	ENSMICG00000002180	32 retrocopies	retro_mmur_1029, retro_mmur_1274, retro_mmur_1302, retro_mmur_1328, retro_mmur_134, retro_mmur_1366, retro_mmur_1412, retro_mmur_1424, retro_mmur_147, retro_mmur_1495, retro_mmur_1541, retro_mmur_187, retro_mmur_221, retro_mmur_286, retro_mmur_309, retro_mmur_336, retro_mmur_417, retro_mmur_494, retro_mmur_57, retro_mmur_643, retro_mmur_67, retro_mmur_677, retro_mmur_686, retro_mmur_737, retro_mmur_745, retro_mmur_76, retro_mmur_763, retro_mmur_789, retro_mmur_823, retro_mmur_864, retro_mmur_879, retro_mmur_980,
Macaca mulatta	ENSMMUG00000011901	1 retrocopy	retro_mmul_162,
Monodelphis domestica	ENSMODG00000020601	3 retrocopies	retro_mdom_1690, retro_mdom_774, retro_mdom_836,
Mustela putorius furo	ENSMPUG00000008873	17 retrocopies	retro_mputfur_1028, retro_mputfur_1095, retro_mputfur_1130, retro_mputfur_1170, retro_mputfur_12, retro_mputfur_1242, retro_mputfur_1305, retro_mputfur_1480, retro_mputfur_1501, retro_mputfur_360, retro_mputfur_378, retro_mputfur_475, retro_mputfur_517, retro_mputfur_557, retro_mputfur_562, retro_mputfur_852, retro_mputfur_923,
Otolemur garnettii	ENSOGAG00000006774	1 retrocopy	retro_ogar_44,
Pongo abelii	ENSPPYG00000014988	18 retrocopies	retro_pabe_1171, retro_pabe_1351, retro_pabe_1609, retro_pabe_1630, retro_pabe_1859, retro_pabe_2338, retro_pabe_2560, retro_pabe_2784, retro_pabe_2931, retro_pabe_3330, retro_pabe_3352, retro_pabe_3375, retro_pabe_3788, retro_pabe_385, retro_pabe_420, retro_pabe_566, retro_pabe_77, retro_pabe_827,
Pelodiscus sinensis	ENSPSIG00000003295	1 retrocopy	retro_psin_60,
Pan troglodytes	ENSPTRG00000016353	31 retrocopies	retro_ptro_1105, retro_ptro_1210, retro_ptro_1224, retro_ptro_1285, retro_ptro_133, retro_ptro_1358, retro_ptro_1500, retro_ptro_1570, retro_ptro_1819, retro_ptro_201, retro_ptro_2087, retro_ptro_218, retro_ptro_2302, retro_ptro_2347, retro_ptro_237, retro_ptro_2502, retro_ptro_2748 , retro_ptro_2775, retro_ptro_2922, retro_ptro_3244, retro_ptro_388, retro_ptro_468, retro_ptro_513, retro_ptro_538, retro_ptro_580, retro_ptro_592, retro_ptro_643, retro_ptro_651, retro_ptro_674, retro_ptro_856, retro_ptro_865,
Sarcophilus harrisii	ENSSHAG00000001357	1 retrocopy	retro_shar_799,
Sarcophilus harrisii	ENSSHAG00000002052	3 retrocopies	retro_shar_131, retro_shar_324, retro_shar_419,
Ictidomys tridecemlineatus	ENSSTOG00000025964	14 retrocopies	retro_itri_1144, retro_itri_1207, retro_itri_1234, retro_itri_1249, retro_itri_1406, retro_itri_1508, retro_itri_1521, retro_itri_1542, retro_itri_209, retro_itri_267, retro_itri_344, retro_itri_766, retro_itri_898, retro_itri_967,
Tupaia belangeri	ENSTBEG00000003574	24 retrocopies	retro_tbel_1109, retro_tbel_1298, retro_tbel_1337, retro_tbel_1532, retro_tbel_1781, retro_tbel_1857, retro_tbel_1941, retro_tbel_213, retro_tbel_2162, retro_tbel_2165, retro_tbel_2372, retro_tbel_2391, retro_tbel_2601, retro_tbel_279, retro_tbel_335, retro_tbel_3606, retro_tbel_3984, retro_tbel_4059, retro_tbel_4398, retro_tbel_657, retro_tbel_74, retro_tbel_901, retro_tbel_974, retro_tbel_983,
Xenopus tropicalis	ENSXETG00000021095	1 retrocopy	retro_xtro_5,