RetrogeneDB ID: retro_ttru_684

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_3070:382211..383015(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NUS1
• Ensembl ID: ENSTTRG00000007352
• Aliases: None
• Description: nuclear undecaprenyl pyrophosphate synthase 1 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:21042]

Sequence

>retro_ttru_684
ATGACGAGGGTGTACAAGCTGGTGTGGCGGGTGCTGCACGCTCTGCTCTGCCTGCACCGCATGCTCACCTCCTGGCTCCG
TGTTTGGTCCGGCACCTGGAACTGGATCTGGTGGCGCTGCCGTCGGGCCGCCTCCGCCGCTGTCCTAGCGCCGCTCGGCT
TCACGCTCCCCAAGCTCCTGGCTGTCGGCAGGAAAGGTAGGAACCGCCGTCACCACCGGCATCCACGCGGGGGGCCCGAC
CCCGGCCGCCGACCACCCGCGGCTACGCTGGCGCGCGGACGGCAGTTCCCTGGAGAAGCTGCCTGTGCACATGGGCCTGG
TGATCACCGAGGAGGAGCAGGAGCCCAGCTTCTCTTCTGGGACATCGCAAGCCTCGTGGTGTGGTGTATGGCCGTGGGCG
TTTCTTACATTAGCTTCTACGACCACCAAGGTATTCTCAAAAGAAATAATTCCAGATTGATGGATGAAATTTTAAAACAA
CAGCAGGAACTCCTGGGCTTAGATTGGTCCAAATACTCACCAGAGTTTGCAAATAGTAATGACAAAGATGATCAAGTTTT
AAATTGCCAATCGTTAGTGAAGGTGCTGTCCCCAGAAGATGGAATAGTAGATATTGTGAGAGCTGCTCAAGACTTCTGCC
AGTTAGTAGCTCAGCAGCAAAAGAAATGCACAGATTTGGATGTAGATATGTTAGACAGTTTACTTAGTTCAAATGGTTTC
CCTGATCCTGATTTACTATTGAAGTTTGGTCCTGTGGACAGCACACTAGGCTTTCTTCCCTGGCACATCAGGTTGACTGA
GATT

Alignment

ORF - retro_ttru_684 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.26 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MTGLYELVWRVLHALLCLHRTLTSWLRVRFGTWNWIWRRCCRAASAAVLAPLGFTLPKLLAVGRNGRNRR
          MT..Y.LVWRVLHALLCLHR.LTSWLRV..GTWNWIW.RC.RAASAAVLAPLGFTLPKLLAVGR.GRNRR
Retrocopy MTRVYKLVWRVLHALLCLHRMLTSWLRVWSGTWNWIWWRCRRAASAAVLAPLGFTLPKLLAVGRKGRNRR

Parental  HHRHPRGGP-TPVAAHPRLRWRADGRSLEKLPVHMGLVIT--EEEQEPS-FSDIASLVVWCMAVGISYIS
          HHRHPRGGP.TP.A.HPRLRWRADG.SLEKLPVHMGLVIT..E.E...S.F.DIASLVVWCMAVG.SYIS
Retrocopy HHRHPRGGP>TPAADHPRLRWRADGSSLEKLPVHMGLVITEEEQEPSFS<FWDIASLVVWCMAVGVSYIS

Parental  VYDHQGIFKRNNSRLMDEILKQQQELLGLDCSKYSPEFANSNDKDDQVLNCQSAVKVLSPEDGKADIVRA
          .YDHQGI.KRNNSRLMDEILKQQQELLGLD.SKYSPEFANSNDKDDQVLNCQS.VKVLSPEDG..DIVRA
Retrocopy FYDHQGILKRNNSRLMDEILKQQQELLGLDWSKYSPEFANSNDKDDQVLNCQSLVKVLSPEDGIVDIVRA

Parental  AQDFCQLVAQQQKKCTDLDVDMLDSLLSSNGFPDPDLVLKFGPVDSTLGFLPWHIRLTEI
          AQDFCQLVAQQQKKCTDLDVDMLDSLLSSNGFPDPDL.LKFGPVDSTLGFLPWHIRLTEI
Retrocopy AQDFCQLVAQQQKKCTDLDVDMLDSLLSSNGFPDPDLLLKFGPVDSTLGFLPWHIRLTEI

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_684 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_684 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 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000001780	1 retrocopy	retro_dnov_1639,
Erinaceus europaeus	ENSEEUG00000008948	1 retrocopy	retro_eeur_443,
Homo sapiens	ENSG00000153989	4 retrocopies	retro_hsap_1174, retro_hsap_1176, retro_hsap_1289, retro_hsap_4825,
Gorilla gorilla	ENSGGOG00000022321	4 retrocopies	retro_ggor_1012, retro_ggor_914, retro_ggor_915, retro_ggor_993,
Microcebus murinus	ENSMICG00000007831	1 retrocopy	retro_mmur_423,
Nomascus leucogenys	ENSNLEG00000013457	1 retrocopy	retro_nleu_2411,
Oryctolagus cuniculus	ENSOCUG00000011553	1 retrocopy	retro_ocun_1713,
Pongo abelii	ENSPPYG00000025886	1 retrocopy	retro_pabe_81,
Pan troglodytes	ENSPTRG00000018547	1 retrocopy	retro_ptro_808,
Tarsius syrichta	ENSTSYG00000003212	1 retrocopy	retro_tsyr_633,
Tursiops truncatus	ENSTTRG00000007352	2 retrocopies	retro_ttru_358, retro_ttru_684 ,