RetrogeneDB ID: retro_ttru_1704

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_86814:52221..52845(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDT1
• Ensembl ID: ENSTTRG00000004567
• Aliases: None
• Description: chromatin licensing and DNA replication factor 1 [Source:HGNC Symbol;Acc:24576]

Sequence

>retro_ttru_1704
GTCACCCTTTCTGAGCTCAAGTCTTGCCTGCAGTGGGCGCAGGAGCTGGGGGCACGGGTCCAGGAGCTGAAGGCAAGTGC
ACAGAAGAATGCTGGGGAACCCAGAGCACCGGAGGACAAGGGGCACCCAGCGGGGCTACGTGGTGAGCAGATGCCTGCCT
ATCAGCGCTTCCTCGCCCTGGCCCAGCAGGGGCCCCTGGGCCTTGTGCTGCCCTACAAGTACCAGGTGCTGGCCGAGATG
TTCTGCTGCATGGACACCATCGTGGGCATGCTTTACAACCGCTCTGTGACTGTGACCTTTGCCAGGGTCAAGCAGGGAGT
CCAGGACATGATGCACAAGCGCTTTGAGGAGCGCAGTGTGGGCCGGATCAAAACCGTGTACCCTGGCTCCTACTGCTTCC
ACCAGGAGCGCTACGCCACCACATTCAAGGACGATGGCAGGAGGTCTGATTACCAGCTCACCATCGAGCCGCTGCTGGAC
CAGCAGGCTGGCAGTGTGGCTCCCCAGCTCACGGCATCGCGCCTGCTGCGGTGGTGCCAGATCTTCAGCCAGAATCTGGT
AGCCCGTGTCCGGTAGTATCACAGGGCCTTCCTGGCCTCCCTGAAACCCCCCCACCCCCCGCCG

Alignment

ORF - retro_ttru_1704 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.85 %
• Parental protein coverage: 55.91 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VSLSELTSCLQRTQELGARVQELKASAQKNAGEPSAPEDEGHPAGLCGEQMPAYQRFHALAQPGPPGLGL
          V.LSEL.SCLQ..QELGARVQELKASAQKNAGEP.APED.GHPAGL.GEQMPAYQRF.ALAQ.GP.GL.L
Retrocopy VTLSELKSCLQWAQELGARVQELKASAQKNAGEPRAPEDKGHPAGLRGEQMPAYQRFLALAQQGPLGLVL

Parental  PYKYQVLAEMFRSMDTIVSMLYNRSETVTFTKVKQGVQDMMHKRFEERNVGQIKTVYPGSYRFRQEHHIP
          PYKYQVLAEMF..MDTIV.MLYNRS.TVTF..VKQGVQDMMHKRFEER.VG.IKTVYPGSY.F.QE....
Retrocopy PYKYQVLAEMFCCMDTIVGMLYNRSVTVTFARVKQGVQDMMHKRFEERSVGRIKTVYPGSYCFHQERYAT

Parental  TFKDGVRRSDYQLTIEPLLDQQAGSAAPRLTASHLLQRRQVFTQKLVARVREHHRAFLASLNPPMEVP
          TFKD..RRSDYQLTIEPLLDQQAGS.AP.LTAS.LL...Q.F.Q.LVARVR..HRAFLASL......P
Retrocopy TFKDDGRRSDYQLTIEPLLDQQAGSVAPQLTASRLLRWCQIFSQNLVARVR*YHRAFLASLKXXXXXP

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_1704 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1704 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Myotis lucifugus	ENSMLUG00000003204	1 retrocopy	retro_mluc_774,
Tursiops truncatus	ENSTTRG00000004567	1 retrocopy	retro_ttru_1704 ,