RetrogeneDB ID: retro_ttru_1013

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_998:75068..76058(-)
• Located in intron of: ENSTTRG00000007778

Retrocopy information

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

Parental gene information

• Parental gene symbol: LAP3
• Ensembl ID: ENSTTRG00000006175
• Aliases: None
• Description: leucine aminopeptidase 3 [Source:HGNC Symbol;Acc:18449]

Sequence

>retro_ttru_1013
GCATATCTTGGTCTATACGAATGTGCGGAGCTGAAGCAGAAAGACAAAACTCTTGTCTTTGCTTAGCTACGTGGAAGTGG
GGAATCGCAGGCCTGGTAGAAAGGAGTCCTATTTGCTTCTGGGCAGAACTTGGCCTCCTATTTGATGGGGACACCAGCCT
ATGAGATGATACCTACCATATTTGCAGAAATAATGGAGAAGAATCTTAAAGTTCTAAGAGTAAAAGCTCAGGTCTAGATC
GCACCTAAGTCTTGGACTGAAGACCCAGAAATTGGATCTTTTTAAAGTGTGGCCAAATGACGTAATGAACATCTGGTCTT
CTTGCAGATTCACTACAGAGGCAGCCTCAATGCAAGTAAAGTGCCGCTCGTATTTTTAGGAAGGGGATGTACTTTGACCC
TGGTGGTAATCTTATCAAGGTGTCTGCAAACATCAACTTCCTGAGGGCTGACATGGGAGGAGCTGCCGTGTGTTCAGCCA
TCGTGACTGCCACAAGCTCAGCTTGCCACTTAATGTAATAGGTCTGGCCCTCTTGGTGAACGTAACCTCAAGCCTAAGCC
TTCAAGCCAGGAGATGTCATCAGAGCCAAGAATGGGGAGACCATACAAGTCAGTAACATTAATGCTGAGCCAAGGGTATT
AGCTGGCGTTCTCTGTTATGTGTACATCTTCAATCCAAAGTTCATCAGCAATGTTTCCACCGACCTTAACAGGTGCCACA
GACATAGCTTGGGGGTCGGGAGGAGGGACAGTTATCACTGGAATTTTTACCAGTTCATACTGGTGGCATACCAGAATACT
TGAGGCCAGCATTGAAATGGAGGACCATGTCTGGGGGATGTCTCTATTTGAACGTTGTATAAGGCAGATTACAGATTGTC
AGCTCATTGCTGTTAATAACAGTGGGCAATATAGGTCTGCAGGGTCATGTCCAGCCACAGCATACCTGAATGGGACACAT
TCTCCATGGGCTCATTTAGACATAGCAGGT

Alignment

ORF - retro_ttru_1013 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.92 %
• Parental protein coverage: 64.13 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  AMLGLYEYDDLKQKKKVAVSVKLHGSGDQEAWQRGVLFASGQNLARHLMETPANEMTPTKFAEIIEKNLR
          A.LGLYE...LKQK.K..V...L.GSG...AW..GVLFASGQNLA..LM.TPA.EM.PT.FAEI.EKNL.
Retrocopy AYLGLYECAELKQKDKTLVFA*LRGSGESQAW*KGVLFASGQNLASYLMGTPAYEMIPTIFAEIMEKNLK

Parental  SASSKTEVHIRPKPWIEEQEMGSFLSVAKGSEEPPVFLEIHYKGSPNASEPPLVFVGKGIT-FDXXXXXX
          ....K..V.I.PK.W.E..E.GSF.SVAK...E..VFL.IHY.GS.NAS..PLVF.G.G.T.FD......
Retrocopy VLRVKAQV*IAPKSWTEDPEIGSF*SVAK*RNEHLVFLQIHYRGSLNASKVPLVFLGRGCT<FDPGGNLI

Parental  XAAANMDLMRADMGGAATISAIVSAA-KLDLPINVVGLA-PLCENM-PSGKANKPGDVVRAKNGKTIQVD
          ...AN....RADMGGAA..SAIV.A..KL.LP.NV.GLA.PL.E...P...A.KPGDV.RAKNG.TIQV.
Retrocopy KVSANINFLRADMGGAAVCSAIVTAT<KLSLPLNVIGLA<PLGERN<PQA*AFKPGDVIRAKNGETIQVS

Parental  NTDAEGRLI-LADALCYAHTFNPKVIINAATLTGAMDIALGSGA----TGVFTNSSWLWNKLFEASIETG
          N..AE.R...LA..................TLTGA.DIA.GSG.....TG.FT.S.W......EASIE..
Retrocopy NINAEPRVL>LAFSVMCTSSIQSSSAMFPPTLTGATDIAWGSGGGTVITGIFTSSYWWHTRILEASIEME

Parental  DRVWRMPLFEHYTRQVVDCQLADVNNIGKYRSAGACTAAAFLKEFVTHPKWAHLDIAG
          D.VW.M.LFE...RQ..DCQL..VNN.G.YRSAG.C.A.A.L....TH..WAHLDIAG
Retrocopy DHVWGMSLFERCIRQITDCQLIAVNNSGQYRSAGSCPATAYLNG--THSPWAHLDIAG

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_1013 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1013 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 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Ciona intestinalis	ENSCING00000004383	1 retrocopy	retro_cint_4,
Homo sapiens	ENSG00000002549	1 retrocopy	retro_hsap_3457,
Gorilla gorilla	ENSGGOG00000001110	1 retrocopy	retro_ggor_2333,
Nomascus leucogenys	ENSNLEG00000016606	1 retrocopy	retro_nleu_2711,
Pongo abelii	ENSPPYG00000014626	1 retrocopy	retro_pabe_2858,
Pan troglodytes	ENSPTRG00000015938	1 retrocopy	retro_ptro_2344,
Rattus norvegicus	ENSRNOG00000003289	1 retrocopy	retro_rnor_1332,
Tursiops truncatus	ENSTTRG00000006175	1 retrocopy	retro_ttru_1013 ,