RetrogeneDB ID: retro_ttru_1076

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_102162:29672..30802(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PUS3
• Ensembl ID: ENSTTRG00000012167
• Aliases: None
• Description: pseudouridylate synthase 3 [Source:HGNC Symbol;Acc:25461]

Sequence

>retro_ttru_1076
AGACTAGGAGAAAACAGGCAGACCTCCAACCCTCACTGATGTGGGTGAACAAACAAAGACATTAAATGACTTTGGACAGG
TGATTTCTCTTGACCTTTGTTTTTACTTTCCAAGGGGCAGGGATTCAGAGGATTTTAATTTGAAAGGGGTCAACGATGCT
GCTAAAGAGATTCATTATGCCCACATTTCCAATCAGGTGCTCCCTCCAGACTTCTCTCTACTGGCCTGGGCCCCTGTAGA
ACCCAGCTTCAGTGCTAGGTTCAGCTATCATGAGCAGACTTACTGCCATTTTCCCTTTGTGCTGATTTAGATATTGTAAC
CATGAATTATACAGCTCAGAAATATGACGACACATAAGATTTTAGGAACTTGTGTAAAATACATGTAGCCAACAGAGTGA
TTAATTTTCAGTGGACTACTCTCTCTGCTCAAGTACAGCTAGGAGTCCAGAGCCTGGGTGAGGGGAAAGGACAAGAACCT
TTCTAGTTATGTCAATGTGAAGTGAGTGGCCAGGTGTTCCTTTATCGTCAAGTCTCCTGTACGATGGCTGTCTTTTTCTG
ATTGCCAAAGGAATGGAGAAGCCAGAGATTATTGATAAATCTGCTGAACATAGAGAAATATCCCCAGAAACCTCACTATG
GTATGGCTGTAGAATTTTCTCTTGTCTTATATGACTTTAAGTTTGAAAATATCAACTGGCTCTAGGATTGGGAGGTTCAG
GAGTTCAGTGCTACCCACCACCGACAGCTATAGGCTAAATACACTGTTAAAACTTACATGTTGTATAGTATACTAGAAGG
ACTGGACTCTGTTGCCATACCCTGTGGGAAAGGACCAAAAATGGATGGAGTGATAGAATAAAGAAAAGTTAATAACTCTG
TCATAAGGCAGACCATTGCATTTGTAGTAGGAGTGGAAATGTACATTATAAGCCCCTAATAGATCATCCTAAATGTCAAG
TATAGGAATCCTGATCCAGCATCTTGTAAGTAGGGGATGCATCGAGCATCCACGTTTATTTCATGAAGAGTAAACAAAAG
CCTAAAGGGACTGTAATGACACACAGAGGAAGAAAATATTATATATAGAAGACAACAAACAGGCTCTGTGTTTATACAGA
AACTAAAACA

Alignment

ORF - retro_ttru_1076 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.27 %
• Parental protein coverage: 78.91 %
• Number of stop codons detected: 11
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  RLVENRQTSNYHRCGRTDKGV-SAFGQVISLDLRSHFPKGKDSEDFNLKDEVNDAAIEIRYTHILNRVLP
          RL.ENRQTSN.H.CG.T.K.....FGQVISLDL...FP.G.DSEDFNLK..VNDAA.EI.Y.HI.N.VLP
Retrocopy RLGENRQTSNPH*CG*TNKDI>NDFGQVISLDLCFYFPRGRDSEDFNLKG-VNDAAKEIHYAHISNQVLP

Parental  PDIRVLAWAPVEPSFSARFSCLERTYRYF-FPCADLDIVTMNNAAQKYVGTHDFRNLCKMDVANGVINFQ
          PD...LAWAPVEPSFSARFS..E.TY..F...CADLDIVTMN..AQKY..T.DFRNLCK..VAN.VINFQ
Retrocopy PDFSLLAWAPVEPSFSARFSYHEQTYCHF<SLCADLDIVTMNYTAQKYDDT*DFRNLCKIHVANRVINFQ

Parental  RTILSAQVQLVGQSLAEERWQEPFQLCQFEVIGQAFLYHQVRCMMAI-LFLIGQGMEKPEVIDE-LLNIE
          .T.LSAQVQL..QSL.E...QEPF.LCQ.EV.GQ.FLY.QV.C.MA..LFLI..GMEKPE.ID..LLNIE
Retrocopy WTTLSAQVQLGVQSLGEGKGQEPF*LCQCEVSGQVFLYRQVSCTMAV<LFLIAKGMEKPEIIDK>LLNIE

Parental  KNPQKPQYSMAVEFPLVLYDCKFENIEWIYDREVQEFNVTHLQQLWANHAVKTQMLYSMLQGLDSVAVPC
          K.PQKP.Y.MAVEF.LVLYD.KFENI.W..D.EVQEF..TH..QL.A...VKT.MLYS.L.GLDSVA.PC
Retrocopy KYPQKPHYGMAVEFSLVLYDFKFENINWL*DWEVQEFSATHHRQL*AKYTVKTYMLYSILEGLDSVAIPC

Parental  RIGPKMDGVTEWRNVKPSVIKQTSAFVEGVKMRT-YKPLMDRPKCQGLES-RIQHFVRRGRIEHPHLFHD
          ..GPKMDGV.E.R.V..SVI.QT.AFV.GV.M...YKPL.D.PKCQ..ES..IQH.V.RG.IEHP.LFH.
Retrocopy GKGPKMDGVIE*RKVNNSVIRQTIAFVVGVEMYI<YKPLIDHPKCQV*ES<LIQHLVSRGCIEHPRLFHE

Parental  EETKAKRDCNDTLEENTI-LEKPTKRVCVDTEIKS
          E.TKA.RDCNDT.........K.T.R.CV.TE.K.
Retrocopy E*TKA*RDCNDTQRKKIL>I*KTTNRLCVYTETKT

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_1076 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1076 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Tursiops truncatus	ENSTTRG00000012167	1 retrocopy	retro_ttru_1076 ,