RetrogeneDB ID: retro_ptro_1878

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 3:41226898..41227695(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL5
• Ensembl ID: ENSPTRG00000000963
• Aliases: None
• Description: ribosomal protein L5 [Source:HGNC Symbol;Acc:10360]

Sequence

>retro_ptro_1878
AGATTATACTTGGTGATACTGTATAAAAATAAGTACAACACACCCAAATACAGGATGATAGTTTGGTGACAAACAGAGAT
ATCATTTGTCAGATTGCTTATGCCTGTATAGGAGGGGATATGATAGTCTGCACAGCTTAAGCATATGAACTGACAAAATA
TGGTGTGAAGGTTGGCCTGACACATTATGCTACAGCATATTGTACTGGCTTGCTGCTGGCCTGCAGGCTTCTCAGTAAGT
CTGGCATGGTCAAGATTTATGAAGGCCAAGTGGAGGTGACCAGAGATGAACACAACGTGGAAAACATTGATGGTCAGCTG
GGTGATTTTACCTGCTATTTGAAGGCAGGCCTTGCCAGAACCACCACTAGTAATAAAGTTATGGGGGCTCTGAAGGGGGC
TGTGAATGGAGGCCTCTCCATCTCTCACAGTACACAATAACAGATTCCCTGCTTATGATTCTGAAAGCAAGGCATTTAAT
GCAGAAGTACATAGGAAGCACATCATGGGTCAGAATGTTGCAGATTACATGCATTACCTAATGGAAGAAGCTGAAGATCT
TACAAGAAACAGTTTTCTCAATACATAAAGAACAGCATAACTCCATACATGATGGAGGAGATGTGTAAGAAAGCCCACGT
TGCTATATGAGAGAATCCAGGTTATGAAAAGAAGCCCAAGAAAGAAGCTAAAGAGAAAAGGTGGAATCGTCCCAAAACGT
CTCTTGCCCAGAAGAAACACTGGGTAGCTCAAAAGAAGGCAAGCTTCATCAGAGCTTGAGAACAGGCTGCTGAGAGC

Alignment

ORF - retro_ptro_1878 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.93 %
• Parental protein coverage: 89.23 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  RKRLVIQDKNKYNTPKYRMIV-RVTNRDIICQIAYARIEGDMIVCAAYAHELPKYGVKVGLTNYAAAYCT
          R..LVI..KNKYNTPKYRMIV..VTNRDIICQIAYA.I.GDMIVC.A.A.EL.KYGVKVGLT.YA.AYCT
Retrocopy RLYLVILYKNKYNTPKYRMIV<LVTNRDIICQIAYACIGGDMIVCTA*AYELTKYGVKVGLTHYATAYCT

Parental  GLLLARRLLNRFGMDKIYEGQVEVTGDEYNVESIDGQPGAFTCYLDAGLARTTTGNKVFGALKGAVDGGL
          GLLLA.RLL...GM.KIYEGQVEVT.DE.NVE.IDGQ.G.FTCYL.AGLARTTT.NKV.GALKGAV.GGL
Retrocopy GLLLACRLLSKSGMVKIYEGQVEVTRDEHNVENIDGQLGDFTCYLKAGLARTTTSNKVMGALKGAVNGGL

Parental  SIPHSTK-RFP-GYDSESKEFNAEVHRKHIMGQNVADYMRYLMEEDED-AYKKQFSQYIKNSVTPDMMEE
          SI.HST....P..YDSESK.FNAEVHRKHIMGQNVADYM.YLMEE.ED..YKKQFSQYIKNS.TP.MMEE
Retrocopy SISHSTQ*QIP>AYDSESKAFNAEVHRKHIMGQNVADYMHYLMEEAED<SYKKQFSQYIKNSITPYMMEE

Parental  MYKKAHAAIRENPVYEKKPKKEVKKKRWNRPKMSLAQKKDRVAQKKASFLRAQERAAES
          M.KKAH.AI.ENP.YEKKPKKE.K.KRWNRPK.SLAQKK..VAQKKASF.RA.E.AAES
Retrocopy MCKKAHVAI*ENPGYEKKPKKEAKEKRWNRPKTSLAQKKHWVAQKKASFIRA*EQAAES

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	0.02 RPM	144.07 RPM
SRP007412_cerebellum	0.11 RPM	175.59 RPM
SRP007412_heart	0.00 RPM	212.10 RPM
SRP007412_kidney	0.00 RPM	383.05 RPM
SRP007412_liver	0.00 RPM	204.59 RPM
SRP007412_testis	0.00 RPM	178.94 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1878 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1878 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1878 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2777
Gorilla gorilla	retro_ggor_1934
Pongo abelii	retro_pabe_2238

---

Parental genes homology:

Parental genes homology involve 14 parental genes, and 141 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000002852	1 retrocopy	retro_eeur_620,
Echinops telfairi	ENSETEG00000009889	8 retrocopies	retro_etel_1044, retro_etel_1089, retro_etel_1103, retro_etel_1264, retro_etel_2028, retro_etel_64, retro_etel_785, retro_etel_814,
Homo sapiens	ENSG00000122406	30 retrocopies	retro_hsap_1266, retro_hsap_138, retro_hsap_1469, retro_hsap_1539, retro_hsap_1588, retro_hsap_1767, retro_hsap_183, retro_hsap_1989, retro_hsap_2143, retro_hsap_2385, retro_hsap_2594, retro_hsap_2600, retro_hsap_2777, retro_hsap_2962, retro_hsap_3105, retro_hsap_3178, retro_hsap_3181, retro_hsap_3209, retro_hsap_3430, retro_hsap_3520, retro_hsap_3941, retro_hsap_4048, retro_hsap_4104, retro_hsap_486, retro_hsap_590, retro_hsap_632, retro_hsap_646, retro_hsap_742, retro_hsap_780, retro_hsap_827,
Gorilla gorilla	ENSGGOG00000002699	24 retrocopies	retro_ggor_1129, retro_ggor_1172, retro_ggor_1206, retro_ggor_1342, retro_ggor_1343, retro_ggor_1656, retro_ggor_1934, retro_ggor_2052, retro_ggor_2130, retro_ggor_2178, retro_ggor_2243, retro_ggor_2318, retro_ggor_233, retro_ggor_2380, retro_ggor_264, retro_ggor_2649, retro_ggor_2715, retro_ggor_2755, retro_ggor_457, retro_ggor_521, retro_ggor_553, retro_ggor_622, retro_ggor_647, retro_ggor_996,
Macropus eugenii	ENSMEUG00000006361	3 retrocopies	retro_meug_1168, retro_meug_1537, retro_meug_2146,
Myotis lucifugus	ENSMLUG00000008956	1 retrocopy	retro_mluc_925,
Monodelphis domestica	ENSMODG00000011635	1 retrocopy	retro_mdom_748,
Nomascus leucogenys	ENSNLEG00000010500	2 retrocopies	retro_nleu_2102, retro_nleu_39,
Ornithorhynchus anatinus	ENSOANG00000004669	1 retrocopy	retro_oana_97,
Otolemur garnettii	ENSOGAG00000013246	6 retrocopies	retro_ogar_1164, retro_ogar_134, retro_ogar_1627, retro_ogar_2374, retro_ogar_2633, retro_ogar_707,
Petromyzon marinus	ENSPMAG00000002040	1 retrocopy	retro_pmar_23,
Pongo abelii	ENSPPYG00000001152	32 retrocopies	retro_pabe_1053, retro_pabe_1219, retro_pabe_1274, retro_pabe_1307, retro_pabe_1331, retro_pabe_1501, retro_pabe_1918, retro_pabe_1931, retro_pabe_2019, retro_pabe_2123, retro_pabe_2238, retro_pabe_2457, retro_pabe_246, retro_pabe_247, retro_pabe_2640, retro_pabe_2641, retro_pabe_2658, retro_pabe_2813, retro_pabe_2841, retro_pabe_2909, retro_pabe_3247, retro_pabe_3320, retro_pabe_3360, retro_pabe_3534, retro_pabe_446, retro_pabe_447, retro_pabe_480, retro_pabe_51, retro_pabe_562, retro_pabe_572, retro_pabe_637, retro_pabe_740,
Pan troglodytes	ENSPTRG00000000963	30 retrocopies	retro_ptro_1038, retro_ptro_1068, retro_ptro_1184, retro_ptro_1326, retro_ptro_139, retro_ptro_1519, retro_ptro_1524, retro_ptro_1568, retro_ptro_169, retro_ptro_1744, retro_ptro_1878 , retro_ptro_2005, retro_ptro_2241, retro_ptro_2262, retro_ptro_2264, retro_ptro_2329, retro_ptro_2391, retro_ptro_2674, retro_ptro_2742, retro_ptro_2785, retro_ptro_2941, retro_ptro_3027, retro_ptro_366, retro_ptro_433, retro_ptro_460, retro_ptro_470, retro_ptro_528, retro_ptro_577, retro_ptro_866, retro_ptro_997,
Sarcophilus harrisii	ENSSHAG00000006417	1 retrocopy	retro_shar_202,