RetrogeneDB ID: retro_ttru_358

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_198:7855..8593(-)
• 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_358
CTACAGGCTCAGCTCGGCCTGCACCGCACTTTCACCTCCCGGCTCCGCTTGCGGTTCGGCACCTGGAACTGGACCTGGCG
GAGCTACTGCTGCGCCGCCTCCGCCGCGGTCCTAGCGCCGCTCGGCTTCGCGCTCCGCCAGCCCCCGGCTGTCGGCGGGA
ACAGCCTTGACCACAGGCATCCGCGCGGGGAGCCCGCCCCGCTCGCCGCCCACCCGTGGCTGCAATGGCGCGAGGACGCC
AGCTCCTTGAAGAGGCTGCCTGTGCACGTAGACCTAGGGATCTCCGAAGAGCCGGAGCCCGGCTTCTCCGACATCGCAAG
CCTCTTGGTGTGATGTATGGCAGTGGGCACCTCTTACATCAGCGTCTACGACCACAAAGGAATTTTCAAAAGAAATAACT
CCAGATTGACGGATGAAATCTTAAAACAACAGCAGGAACTTCTGGACATAGAGGGTTCCAAATACTCACCAGAATTTGCA
AATCGTAATGACGAAGATTGCCATTCGGCAGTCAAGGTGCTGTCCCCAGAAGATGCAAAAGCAGATATGGTGAGAGCTGC
TCAAGACTTTTGCCAGTCAGTAGCCCAGCAGCAAAAGAAATCCACAGATTTGGATGTAGATATATCAGACCGTTTATTTA
GTTCGAATGGTGCCCGTGGTCCTGATTTAGTACTGAAGTTTAGTCCTGAGGACAGCGCACTAGGCTTTCTGCCCTGGCAC
ATCAGCCTGACAGAGATT

Alignment

ORF - retro_ttru_358 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.37 %
• Parental protein coverage: 95.86 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LHALLCLHRTLTSWLRVRFGTWNWIWRRCCRAASAAVLAPLGFTLPKLLAVGRNGRNRRHHRHPRGGPTP
          L.A.L.LHRT.TS.LR.RFGTWNW.WR..C.AASAAVLAPLGF.L....AVG.N......HRHPRG.P.P
Retrocopy LQAQLGLHRTFTSRLRLRFGTWNWTWRSYCCAASAAVLAPLGFALRQPPAVGGNSLD---HRHPRGEPAP

Parental  VAAHPRLRWRADGRSLEKLPVHMGLVITEEEQEPSFSDIASLVVWCMAVGISYISVYDHQGIFKRNNSRL
          .AAHP.L.WR.D..SL..LPVH..L.I.EE..EP.FSDIASL.V.CMAVG.SYISVYDH.GIFKRNNSRL
Retrocopy LAAHPWLQWREDASSLKRLPVHVDLGISEEP-EPGFSDIASLLV*CMAVGTSYISVYDHKGIFKRNNSRL

Parental  MDEILKQQQELLGLDCSKYSPEFANSNDKDDQVLNCQSAVKVLSPEDGKADIVRAAQDFCQLVAQQQKKC
          .DEILKQQQELL....SKYSPEFA..N..D.....C.SAVKVLSPED.KAD.VRAAQDFCQ.VAQQQKK.
Retrocopy TDEILKQQQELLDIEGSKYSPEFA--NRNDE---DCHSAVKVLSPEDAKADMVRAAQDFCQSVAQQQKKS

Parental  TDLDVDMLDSLLSSNGFPDPDLVLKFGPVDSTLGFLPWHIRLTEI
          TDLDVD..D.L.SSNG...PDLVLKF.P.DS.LGFLPWHI.LTEI
Retrocopy TDLDVDISDRLFSSNGARGPDLVLKFSPEDSALGFLPWHISLTEI

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_358 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_358 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,