RetrogeneDB ID: retro_ttru_1025

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_100368:8867..9383(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PDXK
• Ensembl ID: ENSTTRG00000011152
• Aliases: None
• Description: pyridoxal (pyridoxine, vitamin B6) kinase [Source:HGNC Symbol;Acc:8819]

Sequence

>retro_ttru_1025
GAGGAAGATTGTCAGGTGCTCTCCATTCAGAGCCATGTCATCTGTGGCTACATGGGCAATCAGGCGGTCACACTCCCACT
ACATGTTTTGGGGTTCAAGATTGATGTAGTGAACTCTGTCCAGTTTTTAAACCACACAGGCTACTAACACTGGAATGGCC
AAGTGCTGAACTCAGATGAGCTCCACGAGCTGTATGATCGGCTGGAGCTGAACAACATGAACAAATATAACTATGTGCTC
ACAGGTTACATGAAAGATAAGTTCTTCCTGGCCATGGTGGTGGACACCAGGAAGGAGCTGAAGCAGCAGAACTCCAGGCT
CTTGGTCATGTGCGTCCCCGTGATGGGAGACAAGTGGAACAGAGAAGTTTCCATCTACCTCCCTGAGGACCTTCTTCTGG
TTTACAGAGAGAAGGACATGCCAGTTGCAGACATCATAACCCCCAACCAATTTGAGACTGAGTTGCTGAGCAGCAGAAAG
ATTCACAGCCAAGAAGAAGACTTAGCAGTGAGTGAT

Alignment

ORF - retro_ttru_1025 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75. %
• Parental protein coverage: 55.13 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EEECRVLSIQSHVVRGYVGNRAATFPLQVLGFEVDAVNSVQFSNHTGYSHWKGQVLNSEELHELYDGLKL
          EE.C.VLSIQSHV..GY.GN.A.T.PL.VLGF..D.VNSVQF.NHTGY.HW.GQVLNS.ELHELYD.L.L
Retrocopy EEDCQVLSIQSHVICGYMGNQAVTLPLHVLGFKIDVVNSVQFLNHTGY*HWNGQVLNSDELHELYDRLEL

Parental  NDVNKYDYVLTGYTRDKSFLAMVVDIVRELKQQNSRLVYVCDPVMGDKWNGEGSMYVPEDLLPVYREKVV
          N..NKY.YVLTGY..DK.FLAMVVD...ELKQQNSRL...C.PVMGDKWN.E.S.Y.PEDLL.VYREK..
Retrocopy NNMNKYNYVLTGYMKDKFFLAMVVDTRKELKQQNSRLLVMCVPVMGDKWNREVSIYLPEDLLLVYREKDM

Parental  PVADIITPNQFEAELLSGRKIHSEEEALAVMD
          PVADIITPNQFE.ELLS.RKIHS.EE.LAV.D
Retrocopy PVADIITPNQFETELLSSRKIHSQEEDLAVSD

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_1025 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1025 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
Bos taurus	ENSBTAG00000018186	1 retrocopy	retro_btau_1725,
Myotis lucifugus	ENSMLUG00000004931	1 retrocopy	retro_mluc_1783,
Tursiops truncatus	ENSTTRG00000011152	1 retrocopy	retro_ttru_1025 ,