RetrogeneDB ID: retro_ttru_538

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_2625:387865..388134(+)
• Located in intron of: ENSTTRG00000012901

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBE2K
• Ensembl ID: ENSTTRG00000003174
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2K [Source:HGNC Symbol;Acc:4914]

Sequence

>retro_ttru_538
ACGAGCAAAAATCAAACTAAAGTAGATCTTGTAGATGAGAATTTTACAGAATTAAGAGGAGAAGTAGCAGGACCTCCAAA
CACACCATATGAAGGAGGAAGATATCAACTAGAGATTAAATACCAGAAACATATCTATTTAATCCCCCTAAGTCCGGTTT
ATCACTAAAATATGGCATCCTAATATTAGTTCCATCACAGGGGGCTATTTGTTTGAATATCCTGAAAGATCAATGGCAGC
AGCAATGACTCCTCCGCACAGTATTATTG

Alignment

ORF - retro_ttru_538 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.95 %
• Parental protein coverage: 50.28 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  TSKNQIKVDLVDENFTELRGEIAGPPDTPYEGGRYQLEIK-IPETYPFNPPK-VRFITKIWHPNISSVT-
          TSKNQ.KVDLVDENFTELRGE.AGPP.TPYEGGRYQLEIK.IPETY.FNPPK.VRFITKIWHPNISS.T.
Retrocopy TSKNQTKVDLVDENFTELRGEVAGPPNTPYEGGRYQLEIK<IPETYLFNPPK<VRFITKIWHPNISSIT>

Parental  GAICLDILKDQWAAAMTLRTVLL
          GAICL.ILKDQW.....LRTVLL
Retrocopy GAICLNILKDQWQQQ*LLRTVLL

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_538 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_538 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 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001252	1 retrocopy	retro_chof_2683,
Otolemur garnettii	ENSOGAG00000008264	1 retrocopy	retro_ogar_2194,
Sorex araneus	ENSSARG00000013725	1 retrocopy	retro_sara_739,
Tursiops truncatus	ENSTTRG00000003174	1 retrocopy	retro_ttru_538 ,