RetrogeneDB ID: retro_ttru_1605

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_57780:51..752(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CSNK2A3
• Ensembl ID: ENSTTRG00000007064
• Aliases: None
• Description: casein kinase 2, alpha 3 polypeptide [Source:HGNC Symbol;Acc:2458]

Sequence

>retro_ttru_1605
CTGGATTATTGTCACAGCATGGGGATTATGCACAGAGATGTAAAGCCCCATAATGTCATCATTAATCATGAGCACAGAAG
CTACGGCTAATAGACTGGGGTTTGGCTGAGTTTTACCATCCTGGCCAAGAACATAACGTCCGAGTTGCTTCCCAATATTT
TAAAGGTCCTGAGCTACTTGTGGACTATCAGATGTATGATTATAGTTTGGATATGTGGAGCTTGGGTTGTATGCTGGCAA
GTGTGATCTTCCGGAAGGAGCCATTTTTCCATGAACATGACAATTATGATCAGTTGGTGAGGACAGCCAAGGTTCTGGGG
ACAGAGATTTATATGACTATATTGACAAATACAACATTCAATTAGATCCACGTTTTAACGATATCTTGGGCAGACATTCC
CATAAGCGATGGGAATGCTTTGTCCACAGTGAAAACCAGTACCTTGTCAGTCCTGAGGCCTTGGATTTCCTGGACAAGCT
GCTGCGGTACGACCAACAGTCATGGCTCACCACAAGAGAGGCCGTGGAGCACCCCTATTTCTACACTGTTGTGAAGGACC
AGACTCGAATGGGCTCATCTAGCATGCCAGGGGGGCAGTATGCCTGTCAGCAGCACCAATATGATGTCAGGGATTTCTTC
AGTGCCAACCCCTTCAGCCCTTAGACCTCAGGCAGGCTCACCAGTGATTGCTGCTGCCAAC

Alignment

ORF - retro_ttru_1605 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.87 %
• Parental protein coverage: 59.39 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LDYCHSMGIMHRDVKPHNVMIDHEHR-KLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYS
          LDYCHSMGIMHRDVKPHNV.I.HEHR.KLRLIDWGLAEFYHPGQE.NVRVAS.YFKGPELLVDYQMYDYS
Retrocopy LDYCHSMGIMHRDVKPHNVIINHEHR<KLRLIDWGLAEFYHPGQEHNVRVASQYFKGPELLVDYQMYDYS

Parental  LDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTE-DLYDYIDKYNIELDPRFNDILGRHSRKRW
          LDMWSLGCMLAS.IFRKEPFFH.HDNYDQLVR.AKVLGTE.DLYDYIDKYNI.LDPRFNDILGRHS.KRW
Retrocopy LDMWSLGCMLASVIFRKEPFFHEHDNYDQLVRTAKVLGTE<DLYDYIDKYNIQLDPRFNDILGRHSHKRW

Parental  ERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVKDQARMGSSSMP-GGSTPVSSAN
          E.FVHSENQ.LVSPEALDFLDKLLRYD.QS.LT.REA.EHPYFYTVVKDQ.RMGSSSMP.GGS.PVSS.N
Retrocopy ECFVHSENQYLVSPEALDFLDKLLRYDQQSWLTTREAVEHPYFYTVVKDQTRMGSSSMP>GGSMPVSSTN

Parental  MMSGISSVPTPSPLGPLAGSPVIAAAN
          MMSGISSVPTPS.L.P.AGSPVIAAAN
Retrocopy MMSGISSVPTPSALRPQAGSPVIAAAN

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_1605 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1605 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 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014039	2 retrocopies	retro_amel_138, retro_amel_1888,
Homo sapiens	ENSG00000101266	1 retrocopy	retro_hsap_53,
Sorex araneus	ENSSARG00000002896	10 retrocopies	retro_sara_188, retro_sara_189, retro_sara_240, retro_sara_357, retro_sara_468, retro_sara_508, retro_sara_534, retro_sara_572, retro_sara_738, retro_sara_755,
Tursiops truncatus	ENSTTRG00000007064	1 retrocopy	retro_ttru_1605 ,