RetrogeneDB ID: retro_ttru_55

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_1062:32166..32572(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RFXAP
• Ensembl ID: ENSTTRG00000007901
• Aliases: None
• Description: regulatory factor X-associated protein [Source:HGNC Symbol;Acc:9988]

Sequence

>retro_ttru_55
ATGAGCAAGACCTGCACCTACGAGGGCTGCAGCGAGACCACGAGCCAGGTGGCCAAACAGCGCAAGCCGTGGATGTGCAA
GAAACATCGCAACAAGATGTACAAGGATAAGCACAAGAAGAAGAAAAGTGACCAAGCCCTGAACTGCAGTGCGGCCGCCC
AGGCTGGCAGCGCGGGAAACGTCAAACTTGAGGAAAGTGCAGATAATATACTCTCTACTGTTAAACAGAGAACAGGATCT
TTTGGGGATCAACCTGCAAGACCTGCTCTTTCAGAACAAGTGTTAAATCAAAAAAGACTTCTTACTAAGAAGTCCAGAAG
TGGTGCAGTTTTTACAGAAACAGCAACAACTATTATATTAGCAAGTTTTGGAGCAAAGACAACAGCAGTTTCCAGGAACA
TCAGTG

Alignment

ORF - retro_ttru_55 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.48 %
• Parental protein coverage: 56.43 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSKTCTYEGCSETTSQVAKQRKPWMCKKHRNKMYKDKYKKKKSDQALNCGGAAQAGSAGNVKLEESADNI
          MSKTCTYEGCSETTSQVAKQRKPWMCKKHRNKMYKDK.KKKKSDQALNC..AAQAGSAGNVKLEESADNI
Retrocopy MSKTCTYEGCSETTSQVAKQRKPWMCKKHRNKMYKDKHKKKKSDQALNCSAAAQAGSAGNVKLEESADNI

Parental  LSIVKQRKGSFGDRPARPTLLEQVLNQKRLSLLRSPEVVQFLQ-KQQQLLNQQVLEQRQQQFPGTSV
          LS.VKQR.GSFGD.PARP.L.EQVLNQKRL....S.....F....QQ.LL..QVLEQRQQQFPGTSV
Retrocopy LSTVKQRTGSFGDQPARPALSEQVLNQKRLLTKKSRSGAVFTE>QQQ-LLY*QVLEQRQQQFPGTSV

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_55 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_55 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012518	1 retrocopy	retro_chof_1951,
Tursiops truncatus	ENSTTRG00000007901	2 retrocopies	retro_ttru_220, retro_ttru_55 ,