RetrogeneDB ID: retro_ttru_306

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_1818:615435..616281(+)
• Located in intron of: ENSTTRG00000009981

Retrocopy information

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

Parental gene information

• Parental gene symbol: CPNE4
• Ensembl ID: ENSTTRG00000010418
• Aliases: None
• Description: copine IV [Source:HGNC Symbol;Acc:2317]

Sequence

>retro_ttru_306
ATTGGAGAATTCACCTCAACATTCAAGTAGATGAGAAGAGTGATGGAAGGAAAACAGGTGCAGTAGGAGTGCATCAACCC
CAAGTACAAAGCCAAGAAGAAGAATTATAAGAACTCAGGCATTGTGATTTTGAATCAGTGCAAGACCCACAAGATGCATT
CTTTCTTGGACTACATCATGGGTGGCTGCCTAATCCAGTTTACAGTAGCTATAGATTTCACAGCCTCGAATGGGTACCCC
AGGAACAGCTGTTCCCTGCCCTACATCCACCCCTGCCAGCCCAATGAGTACCTGAAGGCCTTGGAGGCTGTGGGAGAGAT
TTGCCAAGACTATGATAGCAACAAAATGTTCCCAGCCTTTGGGTTTGGTGCCAGGATACTGCCAGAGTACAGGGTATCTC
ATGACTTCGCAATCAACTTTAATGAAGACAACCCAGAATGGGCAGGGATTCAAGGAGTTGTGGAAGCCTACCAGAGCTGC
CTTCCCAAACTCTAGCTCTAGGGCCCCACCAACAGTGCTCCCATCATGCAGAAGGTCGCCAAGTCAGCATCAGAGGAGAC
CAGCACCAAGGAGGCATCACAATACTTCATCCTGCTGATCCCGACCGACGGGGTCATCACAGACATGGCCGACACGCGGG
AGGACATTGTCCACGCCTCCCACCTCTCCATGTCGGTCATCATCGTGGGAGTGGGCAATGCAGACTTCAGCGACATGCAG
ATGCTGGACAGAGACGACGGGATTCTGAGGTCACCCAAGGGAGAGCCCGTCCTTCGTGACATCGTCCAGTTCGTGCCCTT
CAGGAACTTCAAACACACATCTCCAGCTGCCCTGGCAGAGCGTGTT

Alignment

ORF - retro_ttru_306 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.65 %
• Parental protein coverage: 50.63 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IGEFTSTFKEMRGVMEGKQVQWECINPKYKAKKKNYKNSGIVILNQCKIHKMHSFLDYIMGGCQIQFTVA
          IGEFTSTFK.MR.VMEGKQVQ.ECINPKYKAKKKNYKNSGIVILNQCK.HKMHSFLDYIMGGC.IQFTVA
Retrocopy IGEFTSTFK*MRRVMEGKQVQ*ECINPKYKAKKKNYKNSGIVILNQCKTHKMHSFLDYIMGGCLIQFTVA

Parental  IDFTASNGDPRNSCSLHYIHPYQPNEYLKALVAVGEICQDYDSDKMFPAFGFGARIPPEYTVSHDFAINF
          IDFTASNG.PRNSCSL.YIHP.QPNEYLKAL.AVGEICQDYDS.KMFPAFGFGARI.PEY.VSHDFAINF
Retrocopy IDFTASNGYPRNSCSLPYIHPCQPNEYLKALEAVGEICQDYDSNKMFPAFGFGARILPEYRVSHDFAINF

Parental  NEDNPECAGIQGVVEAYQSCLPKLQLYGPTNIAPIIQKVAKSASEETNTKEASQYFILLILTDGVITGMA
          NEDNPE.AGIQGVVEAYQSCLPKL.L.GPTN.API.QKVAKSASEET.TKEASQYFILLI.TDGVIT.MA
Retrocopy NEDNPEWAGIQGVVEAYQSCLPKL*L*GPTNSAPIMQKVAKSASEETSTKEASQYFILLIPTDGVITDMA

Parental  GRRGALVHASHLPMSVIIVGVGNADFSDMQGLDGDDGILRSPKGEPVLGDIVQFVPFRNFKHASPAALAK
          ..R...VHASHL.MSVIIVGVGNADFSDMQ.LD.DDGILRSPKGEPVL.DIVQFVPFRNFKH.SPAALA.
Retrocopy DTREDIVHASHLSMSVIIVGVGNADFSDMQMLDRDDGILRSPKGEPVLRDIVQFVPFRNFKHTSPAALAE

Parental  SV
          .V
Retrocopy RV

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_306 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_306 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	ENSTTRG00000010418	1 retrocopy	retro_ttru_306 ,