RetrogeneDB ID: retro_ttru_1557

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_116289:36360..36892(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTTRG00000008219
• Aliases: None
• Description: None

Sequence

>retro_ttru_1557
AAGCTTTCTAGCCAGAAAACTGGAGGGCATCTTCATAAGCACGACCCCAAACCAACAACACTCCTGTAGCCGGAACTCTG
CCGCCAGGGGCAACAGCAATTACTGCCTTCACCTTCGAAGCCTGCCCCTGAGTGAGGGACTTCTTTCCTACCGATCCTCC
TGCTAGAAAAGTGACAAAAGTGAGTTGGACGGGATACAAGTCACAGGGCAGAGCTTCGGTGGCCCTGCTTACTGGGAGAA
GGTGGAGCTGGGGCGGCTCCTGTGGCGGCGGCGGCCCGGGGAGCAGGATCGCCGGCGCACGGGGGACCTGCGCGGAGGGG
AACACGACCTGCTCCTCCTCCATGGGGGTGACCTGCGCCACATGGGAGGTGGTGGCAGCATTCTCCTGGGAGGGGTAAAT
CGCCTGGGGGGTGGCCGAGGCCAGGGGGCCAGCACAGCAGTGGCAGTGATCTCCTGGTCATCCATTTGTCCTCCGTCCGT
ATGCTTCAGCGCCTTCTCGGCCTCATCTGGATTTTCAAACTCCACATATGCG

Alignment

ORF - retro_ttru_1557 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.42 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  KLSSQKTGGHHYKHDPKPTTLLQPELCRQ-GNTAF---LRSLP--EGI-FPTDPPSARKVTKVSWMVYKS
          KLSSQKTGGH..KHDPKPTTLL.PELCRQ.GN......LRSLP..EG..FPTDPP.ARKVTKVSW..YKS
Retrocopy KLSSQKTGGHLHKHDPKPTTLL*PELCRQ>GNSNYCLHLRSLPLSEGL>FPTDPP-ARKVTKVSWTGYKS

Parental  QG-ELRWP-AYREELELERLLWRRRPGERDRRRTGDLRRGERDLLLIRGGDLRHMGGGGSILLGGLNRLG
          QG.ELRWP.AY.E..EL.RLLWRRRPGE.DRRRTGDLR.GE.DLLL..GGDLRHMGGGGSILLGG.NRLG
Retrocopy QG>ELRWP>AYWEKVELGRLLWRRRPGEQDRRRTGDLRGGEHDLLLLHGGDLRHMGGGGSILLGGVNRLG

Parental  GGRGQGASTAVAVISWPSICPPPSMCFSAFSASSGFSNSTYA
          GGRGQGASTAVAVISW.SIC.PPS.CFSAFSASSGFSNSTYA
Retrocopy GGRGQGASTAVAVISWSSIC-PPSVCFSAFSASSGFSNSTYA

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_1557 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1557 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 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004876	3 retrocopies	retro_chof_1586, retro_chof_1986, retro_chof_2273,
Homo sapiens	ENSG00000167970	1 retrocopy	retro_hsap_3023,
Tursiops truncatus	ENSTTRG00000008219	1 retrocopy	retro_ttru_1557 ,
Vicugna pacos	ENSVPAG00000009975	1 retrocopy	retro_vpac_116,