RetrogeneDB ID: retro_ttru_531

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_2607:826447..827537(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TUBA4A
• Ensembl ID: ENSTTRG00000010042
• Aliases: None
• Description: tubulin, alpha 4a [Source:HGNC Symbol;Acc:12407]

Sequence

>retro_ttru_531
ATGTGTGAGTGCATTTCCATTCATGTTGGCAGGCCCGGTGTCCCCATCAGCAATGCCTTCTGAGAGTTCTACTGACTGGA
ACACGACATCCAGCCCAATGGCCAGATGTCAGGTGACAAGACTATTGGGGGAAGGGATGACTCCTTCAACACCTTCTTCA
GCGAGACAGGCACTGGCAGGCATGTGCCCACAACAGTGTTTGTAGACCTGGAACCCACGGTCATTGATGCATTTTGCACT
AGCACCTACTGCCAGCTCTTCCACCCTGAGCAGTTCCTCACAGGCAAGGAAGATGCTGCCAATAACTATGCCCGCAGTCA
CTACCCCATTGGCAAGGAGATCATTGACTTTGTCTTGGACCGGATTTGGAAATAGTATACAGGTCTTCAGGGTTTCTTGG
TTTTCCACAGCTTTGTTGGGGGAACTGGTTCTAGGTTTACCTCCCTGCTGATGGAACGTCTCTCTGTTGATTATGGCAAG
AAGTCCAAGCTGGAGTTCTCCATTTGCCCAGCACCCCAGGTTTCCTCAGCTGTAATTGAGCCCTACAACTCCATCCTCAC
CACACACACCATGCTGGAGCACTCATTGTGCCTTCATGGTAGACAATGAGGCCATCTATTACTTCTGTTGTAGAAACCTC
GATATTGAGCACCCAACCTACACTAATCTTAATCACCTCATGAGCCAAATAGTGTCCTCCATCACTGCTTCCCTGAGATT
GGATGGAGCCCAAATATTGATCTGACAGAATTCCAGACAAGCTTGGTGCCCTTATCCCCACATCCACTTCCCTCTATCTA
CATATGCCCCTGTCATCTCTGCTGAGAAAGCCTACCATGAACAGCTTACTGTAGCAGAGATCACCAATGCTTGCTTTGAA
ACAGCCAACCAGATGATGAAATACAACCCTCACCATGGTAAATGCATGTCTTACTGCCTGTTGTACCATGGTGATGTGGT
TCCCAAAGATGTCAATGCTGCCATTGCTACCATCAAGACCAAGCATACCATCCAGTTTGTGGACTAGACAGGCTTCAAAG
TTGGCAATAATTACCAGCCTCCCACTGTGGTACCTGGTGGAAACCTGGCC

Alignment

ORF - retro_ttru_531 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.39 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MRECISVHVGQAGVQMGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFTTFFCETGAGKHVPRAVFVDL
          M.ECIS.HVG..GV...NA..E.Y.LEH.IQP.GQM..DKTIGG.DDSF.TFF.ETG.G.HVP..VFVDL
Retrocopy MCECISIHVGRPGVPISNAF*EFY*LEHDIQPNGQMSGDKTIGGRDDSFNTFFSETGTGRHVPTTVFVDL

Parental  EPTVIDEIRNGPYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDPVLDRIRKLSDQCTGLQGFLVFHS
          EPTVID......Y.QLFHPEQ..TGKEDAANNYAR.HY.IGKEIID.VLDRI.K......G...F..F..
Retrocopy EPTVIDAFCTSTYCQLFHPEQFLTGKEDAANNYARSHYPIGKEIIDFVLDRIWK*YTGLQGFLVFHSF--

Parental  FGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCA-FMVDNEAI
          .GG.TGS.FTSLLMERLSVDYGKKSKLEFSI.PAPQVS.AV.EPYNSILTTHT.LEHS.C..........
Retrocopy VGG-TGSRFTSLLMERLSVDYGKKSKLEFSICPAPQVSSAVIEPYNSILTTHTMLEHSLCL>MVDNEAIY

Parental  YDICRRNLDIERPTYTNLNRLISQIVSSITASLRFDGAL-NVDLTEFQTNLV-PYPRIHFPLATYAPVIS
          Y..CR.NLDIE.PTYTNLN.L.SQIVSSITASLR.DGA..N.DLTEFQT.LV.PYP.IHFPL.TYAPVIS
Retrocopy YFCCR-NLDIEHPTYTNLNHLMSQIVSSITASLRLDGAQ<NIDLTEFQTSLV>PYPHIHFPLSTYAPVIS

Parental  AEKAYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPTDVNAAIAAIKTKRSIQFVDWC
          AEKAYHEQL.VAEITNACFE.ANQM.K..P.HGK.M..CLLY.GDVVP.DVNAAIA.IKTK..IQFVD..
Retrocopy AEKAYHEQLTVAEITNACFETANQMMKYNPHHGKCMSYCLLYHGDVVPKDVNAAIATIKTKHTIQFVD--

Parental  PTGFKVGINYQPPTVVPGGDLA
          .TGFKVG.NYQPPTVVPGG.LA
Retrocopy *TGFKVGNNYQPPTVVPGGNLA

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_531 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_531 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 13 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008444	2 retrocopies	retro_chof_179, retro_chof_360,
Dipodomys ordii	ENSDORG00000000154	3 retrocopies	retro_dord_460, retro_dord_564, retro_dord_786,
Echinops telfairi	ENSETEG00000010296	2 retrocopies	retro_etel_1816, retro_etel_1993,
Felis catus	ENSFCAG00000027277	1 retrocopy	retro_fcat_596,
Felis catus	ENSFCAG00000028689	3 retrocopies	retro_fcat_1802, retro_fcat_254, retro_fcat_798,
Macropus eugenii	ENSMEUG00000010779	2 retrocopies	retro_meug_1648, retro_meug_2174,
Microcebus murinus	ENSMICG00000000804	1 retrocopy	retro_mmur_103,
Otolemur garnettii	ENSOGAG00000009435	1 retrocopy	retro_ogar_240,
Pteropus vampyrus	ENSPVAG00000010798	1 retrocopy	retro_pvam_1019,
Rattus norvegicus	ENSRNOG00000003597	1 retrocopy	retro_rnor_2819,
Ictidomys tridecemlineatus	ENSSTOG00000019497	1 retrocopy	retro_itri_203,
Tursiops truncatus	ENSTTRG00000004794	1 retrocopy	retro_ttru_407,
Tursiops truncatus	ENSTTRG00000010042	1 retrocopy	retro_ttru_531 ,