RetrogeneDB ID: retro_ttru_1469

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_114143:9703..10388(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CYB5D1
• Ensembl ID: ENSTTRG00000010293
• Aliases: None
• Description: cytochrome b5 domain containing 1 [Source:HGNC Symbol;Acc:26516]

Sequence

>retro_ttru_1469
ATGCCACGCCGGGGCCTAGTGGCCGGGCCAGACTTTGACTATTTTCAGCGTCACTCTTTCACGCCAGCAGAGGTGGCCCA
ACATAACCAGCCGGAAGACCTCTGGGTTGTCTTACCTGGGAAACATGTACGACCTAACGCTGTTATTACAGGAGTACAAG
GGAGACCTGCTGCCGAAACCCATCGTGGAAGTTGCGGGCCAGGACATCAGCCACTGGTTTGATCCAGACACCAGAGACAT
CGGCAAAGCACACAGATCCGCTGACCGGTTCCCTGAGATACCGCATCCCCCGGGGCTGCTTTCTGCACGTGCCGCCTCAG
CTGCCCCTTTCAGACTGGGCCAATGATTTCGGGAAGCCTTGGTGGCAGGGGTCGCGTTACGAGGTGGGGCGGCTGTCTGC
CAAGACCCGGAATACCTGCATCATTAACACGCTCACATCGCAAGAGCACACACCGGAGGTGGGGGCCCGGGAATCAATGT
GGGAAATCCTACACAGCTATCTCCCCTATGCTGCACATGCTGCCAGCTACACATGGAAATATGAAGGGGAGAACCTGACA
TGGATTATACCCTGGAAGAGAATGGCATCTGGAATGAGGAGGAAGAATTTGATTATCTCAATATGGATAGTACACTCTAC
ACACCTGCAGTACTGCTGTACTTCAATGATGACCTCACAGAGCTA

Alignment

ORF - retro_ttru_1469 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.45 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MARRGLVAGPDFEYFQRRYFTPAEVAQHNQPEDLWV-SYLGNVYDLTPLAQEYKGDLLLKPIVEVAGQDI
          M.RRGLVAGPDF.YFQR..FTPAEVAQHNQPEDLWV.SYLGN.YDLT.L.QEYKGDLL.KPIVEVAGQDI
Retrocopy MPRRGLVAGPDFDYFQRHSFTPAEVAQHNQPEDLWV>SYLGNMYDLTLLLQEYKGDLLPKPIVEVAGQDI

Parental  SHWFDPDTRDI-RKHIDPLTGSLRYRTPWGRFLHVPPQLPRSDWANDFGKPWWQGSRYEVGRLSAKTRNI
          SHWFDPDTRDI..KH.DPLTGSLRYR.P.G.FLHVPPQLP.SDWANDFGKPWWQGSRYEVGRLSAKTRN.
Retrocopy SHWFDPDTRDI>AKHTDPLTGSLRYRIPRGCFLHVPPQLPLSDWANDFGKPWWQGSRYEVGRLSAKTRNT

Parental  RIINTLTSQEHTLEVGALESMWEILHRYLLYNAHAASYTWKYEGKNL-NMDYTLEENGIRDEEEEFDYLN
          .IINTLTSQEHT.EVGA.ESMWEILH.YL.Y.AHAASYTWKYEG.NL..MDYTLEENGI..EEEEFDYLN
Retrocopy CIINTLTSQEHTPEVGARESMWEILHSYLPYAAHAASYTWKYEGENL<DMDYTLEENGIWNEEEEFDYLN

Parental  MDSTLYTPAVLLYFSDDLTEL
          MDSTLYTPAVLLYF.DDLTEL
Retrocopy MDSTLYTPAVLLYFNDDLTEL

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_1469 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1469 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
Mus musculus	ENSMUSG00000044795	1 retrocopy	retro_mmus_7,
Rattus norvegicus	ENSRNOG00000045742	1 retrocopy	retro_rnor_2689,
Tursiops truncatus	ENSTTRG00000010293	1 retrocopy	retro_ttru_1469 ,