RetrogeneDB ID: retro_ttru_1819

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_92717:170849..171634(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GALNTL5
• Ensembl ID: ENSTTRG00000017058
• Aliases: None
• Description: UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase-like 5 [Source:HGNC Symbol;Acc:21725]

Sequence

>retro_ttru_1819
TACCCATCCAACCTACCTAGTTCCAGGATTGTCATTTGTTTCCACAATGAAGAATTTAATGTCTTGTTTTAGACAGTGTC
CAGTGTCATGACTGTCACTCCACAGTATATCCTTGAAGAAATTATTTTGGTAGATGACATGAGGGAATTTGATGATTTGA
AAGAGAAACTAGACTACCATGTGGAAAATTTTCGGGGAAAGATTAAATTAGTAAGAAACAAAAAGAGAGAGGGACTGATT
CGAGCAAGGCTGATTGGAGCATCGCGTGCTTCAGGGGACGTTCTGATGCTCCTGGATAGCCACTGCAAGGTGACTAAAGT
ATGGCTGGAGCCCGTGCTGAATGCCATTGCTAAGGACCCCAAATGGGGGTGTGTCCTCTGATAGATGCCAGTGATTATGT
GACCCTGGAATACCAGTCCTCTCCTGTTGTCAGGGGAGCTTTCAACTGGTATCTGCAATTTAAACGGGATCGTGATTTCT
CTTATGAGATGGATGGACCAGAAGGACCCACTAGACCTATCTGGTCACCTGCAATGACTGGAGGAAGTTGTGCTATAAAT
AGGCATTATTTTAATGCAGTCGGAAAGTACAAGGGCATAAATCTCTGGGGAGGAGAACATTTGGAACTTTCATTAAGGAC
CTGGATGTATGGAGGCCAACTCTTTACACTCCCCTGCTCTCGAGTAGGACATATTGATAAGCAACACTTTGCAAACCACA
CTGGAATTGTAAAAGCCTTGGTATATAACAATCTCAGACTGGTGCACATTTGGCTAGATGAATAC

Alignment

ORF - retro_ttru_1819 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.71 %
• Parental protein coverage: 58.84 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  YPSNLPTASIVICFHNEEFNALFRTVSSVMTLTPQHILEEIILVDDMSEFDDLKEKLGYHLEIFRGKIKL
          YPSNLP...IVICFHNEEFN.LF.TVSSVMT.TPQ.ILEEIILVDDM.EFDDLKEKL.YH.E.FRGKIKL
Retrocopy YPSNLPSSRIVICFHNEEFNVLF*TVSSVMTVTPQYILEEIILVDDMREFDDLKEKLDYHVENFRGKIKL

Parental  IRNKKREGLIRARLIGASRASGDVLVFLDSHCEVNKVWLEPLLNAIAKDPR-MVVCPLIDVIDYVTLEYQ
          .RNKKREGLIRARLIGASRASGDVL..LDSHC.V.KVWLEP.LNAIAKDP..M.VCPLID..DYVTLEYQ
Retrocopy VRNKKREGLIRARLIGASRASGDVLMLLDSHCKVTKVWLEPVLNAIAKDPK<MGVCPLIDASDYVTLEYQ

Parental  PSPVVRGAFNWYLQFKWDHVFSYEMDGPEGPTRPIRSPAMAGGIFAINRHYFNEIGQYDKGMNLWGGENL
          .SPVVRGAFNWYLQFK.D..FSYEMDGPEGPTRPI.SPAM.GG..AINRHYFN..G.Y.KG.NLWGGE.L
Retrocopy SSPVVRGAFNWYLQFKRDRDFSYEMDGPEGPTRPIWSPAMTGGSCAINRHYFNAVGKY-KGINLWGGEHL

Parental  ELSLRIWMCGGQLFILPCSRVGHIDKQHVANHTGIAKALAYNNLRLVHVWLDEY
          ELSLR.WM.GGQLF.LPCSRVGHIDKQH.ANHTGI.KAL.YNNLRLVH.WLDEY
Retrocopy ELSLRTWMYGGQLFTLPCSRVGHIDKQHFANHTGIVKALVYNNLRLVHIWLDEY

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_1819 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1819 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 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Tursiops truncatus	ENSTTRG00000002506	2 retrocopies	retro_ttru_793, retro_ttru_854,
Tursiops truncatus	ENSTTRG00000010848	1 retrocopy	retro_ttru_212,
Tursiops truncatus	ENSTTRG00000017058	1 retrocopy	retro_ttru_1819 ,