RetrogeneDB ID: retro_ttru_1249

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_108703:22109..22445(-)
• Located in intron of: ENSTTRG00000009581

Retrocopy information

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

Parental gene information

• Parental gene symbol: ORAOV1
• Ensembl ID: ENSTTRG00000017307
• Aliases: None
• Description: oral cancer overexpressed 1 [Source:HGNC Symbol;Acc:17589]

Sequence

>retro_ttru_1249
AGTCAGGACGCATTCGACGCCATCGTGATGGCGGATGAGAGGTTTCACGGGGAAGGGTATCAGGAAGGCTATGAAAAAGG
AAGTAGTTTGGGTATGATTGAAGGAAGGCAGCATGGCACGTTTCATGGAGCTAAAATCGGATCTGAGATCAGGTGCTACC
AAGGTTTCGCTTTTGCTTGGAGATGTCTCCTGCACGGTTGCTCCACTGAGAAAGACAGCAAATAGATGAAGGTCTTAGAA
TCGTTGATTGCAATGATTCAGAAATTCCCTTATGATGACCCTTCTTATGATAAACTTCACGAAGACTTAGACAAAACTAG
AGGGAAATTTAAGCAG

Alignment

ORF - retro_ttru_1249 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.82 %
• Parental protein coverage: 97.39 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SQDMFDAVVMADDRFHGEGYQEGYEEGSSLGMIEGRRYGTLHGAKIGSELGCYQGFALAWRCLLHGCTTE
          SQD.FDA.VMAD.RFHGEGYQEGYE.GSSLGMIEGR..GT.HGAKIGSE..CYQGFA.AWRCLLHGC.TE
Retrocopy SQDAFDAIVMADERFHGEGYQEGYEKGSSLGMIEGRQHGTFHGAKIGSEIRCYQGFAFAWRCLLHGCSTE

Parental  KDSKKMKVLESLLGMIQKFPYDDPTYDKLHEDLDRIRGKFKQ
          KDSK.MKVLESL..MIQKFPYDDP.YDKLHEDLD..RGKFKQ
Retrocopy KDSK*MKVLESLIAMIQKFPYDDPSYDKLHEDLDKTRGKFKQ

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_1249 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1249 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 5 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001983	1 retrocopy	retro_amel_309,
Felis catus	ENSFCAG00000026606	1 retrocopy	retro_fcat_1023,
Homo sapiens	ENSG00000149716	1 retrocopy	retro_hsap_3131,
Microcebus murinus	ENSMICG00000003061	1 retrocopy	retro_mmur_410,
Tursiops truncatus	ENSTTRG00000017307	6 retrocopies	retro_ttru_1122, retro_ttru_1249 , retro_ttru_1408, retro_ttru_1785, retro_ttru_272, retro_ttru_860,