RetrogeneDB ID: retro_nleu_546

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397267.1:17655340..17656089(+)
• Located in intron of: ENSNLEG00000003836

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS6
• Ensembl ID: ENSNLEG00000017532
• Aliases: None
• Description: 40S ribosomal protein S6 [Source:UniProtKB/TrEMBL;Acc:G1S6Z0]

Sequence

>retro_nleu_546
ATGAAGCTGGACATCTCCTTCCAGCCACTGACTGCCAGAAACTCATTGAAGTGGACGATAAACACAAACTCTGCACTTTT
TATGAGAAGGATATGGCCACAGAAGTTGCTGCTGATGCTCTGGTTGAAGAATGTAAGGGTTATGTGGTCCTAATCAGTGG
TGGGAATGACAAACAATGGTTCCCCATGAAGCAGGTGTCTTGATTCATGGCTGTGTCTGCCTGCTAATGAGTAAGGGGCA
TTCCTGTTACAGACCAAGGAAAACTGGAGAAAGAAAGAGAAAATCAGTTCGTGGTTGCATTGTGGATGCCAATCGGAGCT
TTCTAACTTGGTTATTGTAAAAAAAAAAAGGAGATAAGTATATTCCTGGATTGACTGATAACTATGGTGCCTCGTCGCCT
GGGGCCCAAAAGAGCTAGCAGAATCCACAAACTTTTCAATCTCTCTAAAGAAGGTGATGTCCACCAGTATGTTGTAAGAA
AGCCTTTAAACAAAGAAGGTAAGAAACCTAGGACCAAAGCACCCAAAATTCAGCGTCTTATTACTCCATGTGTCCTGCAG
CACAAATGGCGGCATATTGCTCTGGAGAAGCAGCATACTAAGAAAAGTTAGGAAGAGGCTGCAGAATATGCTTAACTTTT
GGCCAAGAGAATGAAGGAGGCTAAACAGAAGCGTCAGGAACAAATTGCTAAGAAATGCAGACTTTCCTCTCTTCAAGCTT
CTACTTCTAAGTCTGAATCCAGTCAGAAA

Alignment

ORF - retro_nleu_546 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.82 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MKLNISF-PATGCQKLIEVDDERKLRTFYEKRMATEVAADALGEEWKGYVVRISGGNDKQGFPMKQ-GVL
          MKL.ISF.PAT.CQKLIEVDD..KL.TFYEK.MATEVAADAL.EE.KGYVV.ISGGNDKQ.FPMKQ.GVL
Retrocopy MKLDISF<PATDCQKLIEVDDKHKLCTFYEKDMATEVAADALVEECKGYVVLISGGNDKQWFPMKQ<GVL

Parental  THGRVRLLLSKGHSCYRPRRTGERKRKSVRGCIVDANLSVLN-LVIVKKGEKDIPGLTD-TTVPRRLGPK
          .HG.V.LL.SKGHSCYRPR.TGERKRKSVRGCIVDAN.S.L..L.....G.K.IPGLTD.T.VPRRLGPK
Retrocopy IHGCVCLLMSKGHSCYRPRKTGERKRKSVRGCIVDANRSFLTWLLXXXXGDKYIPGLTD>TMVPRRLGPK

Parental  RASRIRKLFNLSKEDDVRQYVVRKPLNKEGKKPRTKAPKIQRLVTPRVLQHKRRRIALKKQRTKKNKEEA
          RASRI.KLFNLSKE.DV.QYVVRKPLNKEGKKPRTKAPKIQRL.TP.VLQHK.R.IAL.KQ.TKK..EEA
Retrocopy RASRIHKLFNLSKEGDVHQYVVRKPLNKEGKKPRTKAPKIQRLITPCVLQHKWRHIALEKQHTKKS*EEA

Parental  AEYAKLLAKRMKEAKEKRQEQIAKRRRLSSLRASTSKSESSQK
          AEYA.LLAKRMKEAK.KRQEQIAK..RLSSL.ASTSKSESSQK
Retrocopy AEYA*LLAKRMKEAKQKRQEQIAKKCRLSSLQASTSKSESSQK

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Nomascus leucogenys was not studied using RNA-Seq expression data.

ChIP-Seq

Nomascus leucogenys was not studied using ChIP-Seq data.

EST

Nomascus leucogenys was not studied using EST data.

TSS

Nomascus leucogenys was not studied using FANTOM5 data.

Lab

retro_nleu_546 was not experimentally validated.

Homology

Retrocopy orthology:

Nomascus leucogenys does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 107 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000017634	1 retrocopy	retro_acar_20,
Choloepus hoffmanni	ENSCHOG00000004622	15 retrocopies	retro_chof_1018, retro_chof_1101, retro_chof_1107, retro_chof_1590, retro_chof_193, retro_chof_2036, retro_chof_2037, retro_chof_2051, retro_chof_2188, retro_chof_2363, retro_chof_2455, retro_chof_2486, retro_chof_2608, retro_chof_849, retro_chof_941,
Cavia porcellus	ENSCPOG00000003750	4 retrocopies	retro_cpor_1244, retro_cpor_22, retro_cpor_317, retro_cpor_486,
Dipodomys ordii	ENSDORG00000012057	2 retrocopies	retro_dord_37, retro_dord_452,
Ficedula albicollis	ENSFALG00000003078	1 retrocopy	retro_falb_24,
Loxodonta africana	ENSLAFG00000010766	4 retrocopies	retro_lafr_1021, retro_lafr_1239, retro_lafr_59, retro_lafr_667,
Myotis lucifugus	ENSMLUG00000007588	27 retrocopies	retro_mluc_1041, retro_mluc_1146, retro_mluc_1169, retro_mluc_1393, retro_mluc_1411, retro_mluc_1448, retro_mluc_1472, retro_mluc_1532, retro_mluc_1566, retro_mluc_1593, retro_mluc_1629, retro_mluc_1635, retro_mluc_1723, retro_mluc_1799, retro_mluc_1909, retro_mluc_1928, retro_mluc_1933, retro_mluc_2110, retro_mluc_2129, retro_mluc_490, retro_mluc_493, retro_mluc_514, retro_mluc_557, retro_mluc_652, retro_mluc_678, retro_mluc_722, retro_mluc_830,
Monodelphis domestica	ENSMODG00000004095	1 retrocopy	retro_mdom_301,
Nomascus leucogenys	ENSNLEG00000017532	14 retrocopies	retro_nleu_1033, retro_nleu_1333, retro_nleu_1613, retro_nleu_226, retro_nleu_2471, retro_nleu_252, retro_nleu_2536, retro_nleu_2611, retro_nleu_2652, retro_nleu_2655, retro_nleu_2860, retro_nleu_313, retro_nleu_476, retro_nleu_546 ,
Otolemur garnettii	ENSOGAG00000016254	21 retrocopies	retro_ogar_1208, retro_ogar_1222, retro_ogar_1335, retro_ogar_1356, retro_ogar_1359, retro_ogar_1439, retro_ogar_1526, retro_ogar_1531, retro_ogar_1612, retro_ogar_1979, retro_ogar_2174, retro_ogar_2195, retro_ogar_2248, retro_ogar_2264, retro_ogar_2514, retro_ogar_2707, retro_ogar_2853, retro_ogar_3329, retro_ogar_462, retro_ogar_575, retro_ogar_782,
Ochotona princeps	ENSOPRG00000012290	5 retrocopies	retro_opri_123, retro_opri_642, retro_opri_78, retro_opri_862, retro_opri_895,
Sarcophilus harrisii	ENSSHAG00000005486	1 retrocopy	retro_shar_549,
Tursiops truncatus	ENSTTRG00000001787	11 retrocopies	retro_ttru_1024, retro_ttru_107, retro_ttru_1275, retro_ttru_370, retro_ttru_468, retro_ttru_587, retro_ttru_748, retro_ttru_786, retro_ttru_878, retro_ttru_905, retro_ttru_934,