RetrogeneDB ID: retro_ttru_468

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_2386:110187..110931(-)
• Located in intron of: ENSTTRG00000011559

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS6
• Ensembl ID: ENSTTRG00000001787
• Aliases: None
• Description: ribosomal protein S6 [Source:HGNC Symbol;Acc:10429]

Sequence

>retro_ttru_468
ATGAAGCTGAACATCTCTTTCCCAGCCACTGGCTGCCAGTAACTCATTGAAGTGGACGATGAATGAAAACTTCATACCTT
TTATCAGAAGCGTATGGCCACAGAAGTTGCTGCTGACGCTCCGGGAGAAGAATGGAAGGGTTACATGGTCCGAATCAGTG
GTGGAAACGACAAACAGGGTTTCCCCGTGAAACAGGGTGTTTTGACCCATGGCCAAGTCCACCTGCTACTGAGTAAGGGG
CATTCTTGTTACAGACCAAGGAGGACTGGAGAAAGAAAGGGCAAATCTGCATGGGGTTGCATTGTAGATGCCAATCTGAG
AGTTCTCAATTTGGTCATCGATAAAAAAGGGGAGAAGGATATTCCTGGACTCACTGATACTACTGTGCCTCATCGCCTGG
GGCTCCAAAGAGCTAGCAGAATCCGCAAACTTTTCAATCTCTCTAAAGAAGATGATGTCCACCAATATGTTGTGAGAAAG
CACCTAAACAAAGAAGGTAAGAAACCTAGGACCAAAGCACCCAAGATTCAGCATCTTGTTACTCCACGTGTTCTGCAAGA
CAAACATCAGTGTATTGCTCTGAAGAAACAGTGTACTATGAAAAATAAGGAAGAGGCTGCAGAATATGCTAAACTTTGGG
CCAGGAGGATGAAGGAGGCCAAAGAAAAACGCCAGGAACAGATTGCCAAGAGTTGGAGGCTGTCCTCTCTGAAAGCTTCT
ACTTCTAAGTCTGAGTCCAGTCAA

Alignment

ORF - retro_ttru_468 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.1 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKLNISFPATGCQKLIEVDDERKLRTFYEKRMATEVAADALGEEWKGYVVRISGGNDKQGFPMKQGVLTH
          MKLNISFPATGCQ.LIEVDDE.KL.TFY.KRMATEVAADA.GEEWKGY.VRISGGNDKQGFP.KQGVLTH
Retrocopy MKLNISFPATGCQ*LIEVDDE*KLHTFYQKRMATEVAADAPGEEWKGYMVRISGGNDKQGFPVKQGVLTH

Parental  GRVRLLLSKGHSCYRPRRTGERKRKSVRGCIVDANLSVLNLVIVKKGEKDIPGLTDTTVPRRLGPKRASR
          G.V.LLLSKGHSCYRPRRTGERK.KS..GCIVDANL.VLNLVI.KKGEKDIPGLTDTTVP.RLG..RASR
Retrocopy GQVHLLLSKGHSCYRPRRTGERKGKSAWGCIVDANLRVLNLVIDKKGEKDIPGLTDTTVPHRLGLQRASR

Parental  IRKLFNLSKEDDVRQYVVRKPLNKEGKKPRTKAPKIQRLVTPRVLQHKRRRIALKKQRTKKNKEEAAEYA
          IRKLFNLSKEDDV.QYVVRK.LNKEGKKPRTKAPKIQ.LVTPRVLQ.K...IALKKQ.T.KNKEEAAEYA
Retrocopy IRKLFNLSKEDDVHQYVVRKHLNKEGKKPRTKAPKIQHLVTPRVLQDKHQCIALKKQCTMKNKEEAAEYA

Parental  KLLAKRMKEAKEKRQEQIAKRRRLSSLRASTSKSESSK
          KL.A.RMKEAKEKRQEQIAK..RLSSL.ASTSKSESS.
Retrocopy KLWARRMKEAKEKRQEQIAKSWRLSSLKASTSKSESSQ

Legend:

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

Expression

RNA-Seq

Tursiops truncatus was not studied using RNA-Seq expression data.

ChIP-Seq

Tursiops truncatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ttru_468 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_468 was not experimentally validated.

Homology

Retrocopy orthology:

Tursiops truncatus 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 11 parental genes, and 105 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,
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,
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,