RetrogeneDB ID: retro_ttru_124

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_1299:191459..192030(-)
• Located in intron of: ENSTTRG00000000486

Retrocopy information

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

Parental gene information

• Parental gene symbol: HIBADH
• Ensembl ID: ENSTTRG00000015276
• Aliases: None
• Description: 3-hydroxyisobutyrate dehydrogenase [Source:HGNC Symbol;Acc:4907]

Sequence

>retro_ttru_124
TGGAGCCGCCGGCAGCAACCAGCAGTGGCCAGCCTTGCAGCAGTGTGTTCTAGGTCAGTGGCTTCTAAGACTCAAGTTGG
ATTCACTGGAGTAGGCAACATGGGGAATCCAATGGCAAAAAATCTCATGAAAAATGGCTAACCACTCATTATTTATGATG
TGTTCCCTGATGCATGCAAAGAGTTTCTAGATGCACGTGAACAGGTAGTGTCTTCCCCAGCAGATGTAGCTGAAAAAGCT
GACAGAATTATCACAGTGTTGCCCACCAGCATCAATGCGATAGAAGCTTATTCTGGAGCAAATGGAATTCTAAAGAAAGT
GAAGCAAGGCTCACTGTTAATAGATTCCAGCACTATTGATCCTATGGTTTTGAAAGAATTGGCCAAAGAAGTTGAGAAAA
TGGGAGCAGTTTTCATGGATGCCCGTTTCTGGTGGTGTGGGAGCTGCTCGGTCTGCGAACCTCACGTTTATGGTGGGAGG
GGTCGCAGACGAATTTGCTGCTGCTGCCCAACAGCTGCTGGGATGTGTGGGCTCCAATGCGGCGTGTTGTGGAGCTGCTG
GGAGTGGGCAG

Alignment

ORF - retro_ttru_124 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.43 %
• Parental protein coverage: 56.42 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  WSRRQQPAVASLAAVCSRSMASKTPVGFIGVGNMGNPMAKNLMKHGYPLIIYDVFPDACKEFLDAGEQVV
          WSRRQQPAVASLAAVCSRS.ASKT.VGF.GVGNMGNPMAKNLMK.G.PLIIYDVFPDACKEFLDA.EQVV
Retrocopy WSRRQQPAVASLAAVCSRSVASKTQVGFTGVGNMGNPMAKNLMKNG*PLIIYDVFPDACKEFLDAREQVV

Parental  SSPADVAEKADRIITMLPTSINAIEAYSGANGILKKVKKGSLLIDSSTIDPMVSKELAKEVEKMGAVFMD
          SSPADVAEKADRIIT.LPTSINAIEAYSGANGILKKVK.GSLLIDSSTIDPMV.KELAKEVEKMGAVFMD
Retrocopy SSPADVAEKADRIITVLPTSINAIEAYSGANGILKKVKQGSLLIDSSTIDPMVLKELAKEVEKMGAVFMD

Parental  APV-SGVGAARSGNLTFMVGGVEEEF-AAAQELLGCMGSNVVHCGAVGTGQ
          A....GVGAARS.NLTFMVGGV..EF.AAAQ.LLGC.GSN...CGA.G.GQ
Retrocopy ARF>GGVGAARSANLTFMVGGVADEFAAAAQQLLGCVGSNAACCGAAGSGQ

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_124 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_124 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 5 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003153	1 retrocopy	retro_chof_1225,
Dasypus novemcinctus	ENSDNOG00000008640	2 retrocopies	retro_dnov_1465, retro_dnov_1997,
Microcebus murinus	ENSMICG00000000512	1 retrocopy	retro_mmur_1059,
Sus scrofa	ENSSSCG00000016695	1 retrocopy	retro_sscr_792,
Tursiops truncatus	ENSTTRG00000015276	4 retrocopies	retro_ttru_124 , retro_ttru_150, retro_ttru_589, retro_ttru_807,