RetrogeneDB ID: retro_ttru_1533

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_115502:315400..315939(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTTRG00000016223
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: B4GALT5
• Ensembl ID: ENSTTRG00000004300
• Aliases: None
• Description: UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 5 [Source:HGNC Symbol;Acc:928]

Sequence

>retro_ttru_1533
CGAGCCATGCTTTTTAATGTGGGTTTTCAAGAAGCAATGAAGGACTTGGACTGGGACTGTCTTATTTTTCGTGATGTGGA
TCATATACCAGAAAGCGATTGTAACTACTATGGATGTGGAACAGATGCCAAGGCACTTTGCAACTAAACTGGGTAAGTAT
ATGTATCTGCTTCCTTATACTGAGTTCTTTGGCGGAGTGAGCGGCTTAACAGTGGAACAGTTTCAGAAAATCAACGGCTT
TCCTAATGCTTTCTGGGGTTGGGGTGGAGAAGATGACGACCTGTGGAACCGAGTACAGAATGCAGGCTGTTCTGTGAGTC
GGCCCGGAAGATGACACAGGGAAGTACAAGTCCATTCTTCCTCACCACCGAGGAGAAGTCCAGTTTCTTGGAAGGTACGC
GTTGCTGAGGAAGTCCAAAGAACGGCAAGGGCTAGATGGTCTCAACAACTTGAACTACTTTGCAAACGTCACATACGATG
CCTTGTATAAAAACATTACTGTCAATTTGACACCCGAGTTGGCTCAGGTGACCGAGTAC

Alignment

ORF - retro_ttru_1533 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.37 %
• Parental protein coverage: 51.29 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RAMLFNVGFQEAMKDLDWDCLIFHDVDHIPESDRNYYGCG-QMPRHFATKLDKYMYLLPYTEFFGGVSGL
          RAMLFNVGFQEAMKDLDWDCLIF.DVDHIPESD.NYYGCG.QMPRHFATKL.KYMYLLPYTEFFGGVSGL
Retrocopy RAMLFNVGFQEAMKDLDWDCLIFRDVDHIPESDCNYYGCG>QMPRHFATKLGKYMYLLPYTEFFGGVSGL

Parental  TVEQFRKINGFPNAFWGWGGEDDDLWNRVQNAGYSVSR-PEGDAGKYKSIPHHHRGEVQFLGRYALLRKS
          TVEQF.KINGFPNAFWGWGGEDDDLWNRVQNAG.SVSR.PE.D.GKYKSI..HHRGEVQFLGRYALLRKS
Retrocopy TVEQFQKINGFPNAFWGWGGEDDDLWNRVQNAGCSVSR>PEDDTGKYKSILPHHRGEVQFLGRYALLRKS

Parental  KERQGLDGLNNLNYFANITYDALYKNITVNLTPELAQVTEY
          KERQGLDGLNNLNYFAN.TYDALYKNITVNLTPELAQVTEY
Retrocopy KERQGLDGLNNLNYFANVTYDALYKNITVNLTPELAQVTEY

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_1533 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1533 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000016301	1 retrocopy	retro_mdom_1782,
Tetraodon nigroviridis	ENSTNIG00000010472	1 retrocopy	retro_tnig_6,
Takifugu rubripes	ENSTRUG00000005726	1 retrocopy	retro_trub_9,
Tursiops truncatus	ENSTTRG00000004300	1 retrocopy	retro_ttru_1533 ,