RetrogeneDB ID: retro_ttru_1068

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_101912:43595..44273(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TRAPPC13
• Ensembl ID: ENSTTRG00000006537
• Aliases: None
• Description: trafficking protein particle complex 13 [Source:HGNC Symbol;Acc:25828]

Sequence

>retro_ttru_1068
GACTTGTTTCTTGAAATCCAGATTCAGAATATTTCATCTTCAACTGTCTTTATACAAAAGGTTTCCTTAAAGCCGTCTGA
AATGTACACTGGGGCAGAATTAAATACTGTCTATCAGGCTGGAGAAGATGAGTGTACCTTTGGAATGAGAACTTTTTGTA
GTCAATGGAAGGACGCCAGTATTTATACCAGCTTCAGCTCAAGCAGGAATTTTCAGAAAAAGCTGCTACCATTAGAGGAC
TAGCAAAATGGGAAAATTGGATATAGTGTGGAAAAGAAATCTAGGTGAAATGGCAATGCTACAGACAATTAAAATTGAAC
GAGAGGCTCCAGGTTATGGAAACATGAGCTGTCTTTGGAGACAGTCCCAGATACCGTAATTCTAGAAGTGCCTTTTCATA
TTACCTGTAAGATAACAAACCACAGTGATTGGAAATGAAATTCGTTTTGAAGATGTGTGATACAGATTCTATTTGCTGGT
GTGGTGATTTAGGAAGATATCTTGGAAAGCTACCTCCCAAGTTCAATGCTCAATTTTACCCTGACACTACTCTCCTTACA
ACTGGGCTTACAAAGTGTCTCTGGCATACAAATAACAGACAAATTATTAAAGAAAATATACATCTGTGATGATGTGGCAA
AAGTTTTTGTAATACTTTCCATGGTTAAAATGAGAAGC

Alignment

ORF - retro_ttru_1068 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.19 %
• Parental protein coverage: 63.94 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  EVFLEAQIQNITTSPMFMEKVSLEPSIMYNVAELNSVNQAGECVTTFGSRA-YLQPMDTRQYLYCLKPKK
          ..FLE.QIQNI..S..F..KVSL.PS.MY..AELN.V.QAGE...TFG.R...L..M..RQYLY.L..K.
Retrocopy DLFLEIQIQNISSSTVFIQKVSLKPSEMYTGAELNTVYQAGEDECTFGMRT<FL*SMEGRQYLYQLQLKQ

Parental  EFAEKAGIIKGV-TVIGKLDIVWKTNLGERGRLQTSQLQRMAPGYGDV-RLSLEAIPDTVNLEEPFHITC
          EF.EKA..I.G.....GKLDIVWK.NLGE...LQT....R.APGYG....LSLE..PDTV.LE.PFHITC
Retrocopy EFSEKAATIRGL<SKMGKLDIVWKRNLGEMAMLQTIKIEREAPGYGNM<ELSLETVPDTVILEVPFHITC

Parental  KITNCSE-RTMDLVLEMCNTSSIHWCGISGRQLGKLH-PSSSLCLALTLLSSVQGLQSVSGLRLTDTFLK
          KITN.S....M..VL.MC.T.SI.WCG..GR.LGKL..PSS.L...LTLLS...GLQSVSG...TD..LK
Retrocopy KITNHSD<LEMKFVLKMCDTDSICWCGDLGRYLGKLP>PSSMLNFTLTLLSLQLGLQSVSGIQITDKLLK

Parental  RTYEYDDIAQVCVVSSAIKVES
          ..Y..DD.A.V.V..S..K..S
Retrocopy KIYICDDVAKVFVILSMVKMRS

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_1068 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1068 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
Choloepus hoffmanni	ENSCHOG00000006026	1 retrocopy	retro_chof_1834,
Dasypus novemcinctus	ENSDNOG00000006386	1 retrocopy	retro_dnov_1288,
Equus caballus	ENSECAG00000011983	1 retrocopy	retro_ecab_1074,
Pteropus vampyrus	ENSPVAG00000008275	1 retrocopy	retro_pvam_980,
Sorex araneus	ENSSARG00000000639	1 retrocopy	retro_sara_394,
Ictidomys tridecemlineatus	ENSSTOG00000021318	1 retrocopy	retro_itri_1455,
Tarsius syrichta	ENSTSYG00000004582	1 retrocopy	retro_tsyr_18,
Tursiops truncatus	ENSTTRG00000006537	1 retrocopy	retro_ttru_1068 ,