RetrogeneDB ID: retro_ttru_1158

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_105840:15860..16529(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ETFB
• Ensembl ID: ENSTTRG00000003974
• Aliases: None
• Description: electron-transfer-flavoprotein, beta polypeptide [Source:HGNC Symbol;Acc:3482]

Sequence

>retro_ttru_1158
GTGCGGTCAGACTGTGTGAAGCGCTCCATGAACCCCTTCTGCTAGATCGCCGTGGAGGAGGCCGTGCAGCTCAAGGAGAA
AAAGCTGGTGAAGGAAATCATTGCCGTCAGCTGCGGGCCTTCCCAGTGCCAGGAGACCATCTGCACCACTCTGGCCATGA
GTGCAGGTCAAGGCATCCACGTGGAGGTGCGGGCTGCATAGGCAGATCTCCTGGGTCCCCTGCAGGTGGCCTGGGTCCTG
GCCAAACTGGCAGAGAAGGGGAAGGTAGACCTGAGCAAGCAGGCCATCGATGATAATTGTAACCAGGCAGGGCAGTTGAC
AGCTGGGTTTCTGGACTGGCCACAGGGCACATTCATCTCCCAGGTGAGGCTGGAAGGGGACAAGGTGAAAGGGGAGCAGG
AGATTGATGGAGGCCTGGAGACCCTGCTCCTGAAGCTGCCTGGTGTGGTGACTGCTGACCTGTAGCTCAATGAGCCCCAC
TGTGATACGTTGCCCAACATCACGAAAGCCAAGAAGAAGATCGAGGTGATCAAGGCTGGGGACATGGGCATGGACCTGAC
CTCCAAGTTCTCTGTGATTAGCTTGGAAGACCCACCTCAGCACACGGCCGGTGTCAAGGTGGAGACCACAGAGGACCTGG
TGGTCAAGCTGAGGGAGATTGGGTGCATT

Alignment

ORF - retro_ttru_1158 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.3 %
• Parental protein coverage: 67.56 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VVTDGVKHSMNPFCEIAVEEAVRLKEKKLVKEVIAVSCGPTQCQETIRTALAMGADRGIHVEVPAAEVDR
          V..D.VK.SMNPFC.IAVEEAV.LKEKKLVKE.IAVSCGP.QCQETI.T.LAM.A..GIHVEV.AA..D.
Retrocopy VRSDCVKRSMNPFC*IAVEEAVQLKEKKLVKEIIAVSCGPSQCQETICTTLAMSAGQGIHVEVRAA*ADL

Parental  LGPLQVARVLAKLAEKEKVDLVLLGKQAIDDDCNQTGQMTAGFLDWPQGTFASQVTLEGDKVKVEREVDG
          LGPLQVA.VLAKLAEK.KVD...L.KQAIDD.CNQ.GQ.TAGFLDWPQGTF.SQV.LEGDKVK.E.E.DG
Retrocopy LGPLQVAWVLAKLAEKGKVD---LSKQAIDDNCNQAGQLTAGFLDWPQGTFISQVRLEGDKVKGEQEIDG

Parental  GLETLRLKLPAVVTADLRLNEPRYATLPNIMKAKKKKIEVIKAGDLGVDLTSKLSVISVEDPPQRTAGVK
          GLETL.LKLP.VVTADL.LNEP...TLPNI.KA.KKKIEVIKAGD.G.DLTSK.SVIS.EDPPQ.TAGVK
Retrocopy GLETLLLKLPGVVTADL*LNEPHCDTLPNITKA-KKKIEVIKAGDMGMDLTSKFSVISLEDPPQHTAGVK

Parental  VETTEDLVAKLKEIGRI
          VETTEDLV.KL.EIG.I
Retrocopy VETTEDLVVKLREIGCI

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_1158 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1158 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014360	1 retrocopy	retro_amel_1039,
Tursiops truncatus	ENSTTRG00000003974	1 retrocopy	retro_ttru_1158 ,
Xenopus tropicalis	ENSXETG00000022222	1 retrocopy	retro_xtro_54,