RetrogeneDB ID: retro_ttru_220

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_1588:160464..161110(+)
• Located in intron of: ENSTTRG00000008786

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_220
GGCGCCCTGCGGCAGGCTCCGGCCCTGGGGGGCAGCGCCCGGGCTGCCCGATCGGTACCTGTGCCAAGTGGCGGGGGGGA
TGGCGAGGGGGAGGCGGGAGAAGATGAGGCAGACCTGCTGGACACTTCGAACCCCCCCGGGGGGAGGCGAGAGCACGGCT
AGTCTGGAGGATCTGGAGGACAAGGGGACCCACTCTGGGGGAGAGGGCGGCAGCGGTGGAGCCCGGAGACGGGGCAGCGT
GAGCAAGACCTGCACCTACGAGGGCTGCAGCCAGATCCCCAGCCAGGTGGCCAAGCAGCACAAGCCATGGATGTGCAAGA
AGCACTGCAACCAGATGGACGAGGATAAGTACAAGAAGCAGAAAAGCCACCAGGCCCCGAACCGCGGTGGGGCCGCCCAG
CCTGGTGGCGCAGGAAACGTCAAACTCGAGGAAAGTGCAGGTAATACACTCTCCACTGTTAAACAGAGAACAGGATCTTT
GGGGGATCGACCTGCAAGACCTACTCTTTTAGAACAAGTGTTAAATCAGAAAAGACGGTCATTACTAAGAAGTCCAGAAG
TGGTGCAGTTTTCACAGAAACGGCAGCAACTCCTAATTCAGCAAGTTTTGGAGCAAAGACAACAGCGGTTTCCAGGAACA
TCAGTG

Alignment

ORF - retro_ttru_220 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.92 %
• Parental protein coverage: 91.29 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GGPDEAAALGGSAGAGKPVRYLCEVAGDGEEEAGEDETDLLDTSDPPGG-GESTASLEDLEDEETHSGGE
          G....A.ALGGSA.A...V.......GDGE.EAGEDE.DLLDTS.PPGG.GESTASLEDLED..THSGGE
Retrocopy GALRQAPALGGSARAARSVP-VPSGGGDGEGEAGEDEADLLDTSNPPGG>GESTASLEDLEDKGTHSGGE

Parental  GGSGGARRRGSGGGSMSKTCTYEGCSETTSQVAKQRKPWMCKKHRNKMYKDKYKKKKSDQALNCGGAAQA
          GGSGGARRR....GS.SKTCTYEGCS...SQVAKQ.KPWMCKKH.N.M..DKYKK.KS.QA.N.GGAAQ.
Retrocopy GGSGGARRR----GSVSKTCTYEGCSQIPSQVAKQHKPWMCKKHCNQMDEDKYKKQKSHQAPNRGGAAQP

Parental  GSAGNVKLEESADNILSIVKQRKGSFGDRPARPTLLEQVLNQKRLSLLRSPEVVQFLQKQQQLLNQQVLE
          G.AGNVKLEESA.N.LS.VKQR.GS.GDRPARPTLLEQVLNQKR.SLLRSPEVVQF.QK.QQLL.QQVLE
Retrocopy GGAGNVKLEESAGNTLSTVKQRTGSLGDRPARPTLLEQVLNQKRRSLLRSPEVVQFSQKRQQLLIQQVLE

Parental  QRQQQFPGTSV
          QRQQ.FPGTSV
Retrocopy QRQQRFPGTSV

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_220 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_220 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,