RetrogeneDB ID: retro_ttru_1673

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_84855:7504..7855(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: APH1B
• Ensembl ID: ENSTTRG00000006865
• Aliases: None
• Description: APH1B gamma secretase subunit [Source:HGNC Symbol;Acc:24080]

Sequence

>retro_ttru_1673
TTCCTTTTGGTGTCTCTGCTGCTTTCCTTCCTTGTTTGGTCCATGGCAGCGATCACTGCTGACAACAAAGATGGACCAAT
ACAGAAATATCTGCTGATCTTTGACATGTTAGTCTCAGTCCTTATCCAAGAAATGTTCCAGTTTGCGTATTACGAACTTG
AAAAAAAAGCCAGTGAAGGTTTGAAGAGTATAAACCCGGATGACATAGCGCCCTCTATGCGATTGCCGGCTTATGTTTCT
GGCTTGGGCTTTGGAATCATGAGGGGAGCATTTTCCTTTGTAAATACCCTGTCTGACTCCTTGGGGCCGGGCACAGTGGG
CATTCATGGAAACTCTCCCCCGTTCTTCCTT

Alignment

ORF - retro_ttru_1673 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.5 %
• Parental protein coverage: 73.58 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FWLVSLLLSSFIWFMAATLTDNKDEPRQRDLLIFGVLISVLIQEVFRFAYYKLLKKSSEGLKSINPGEKA
          F.LVSLLLS...W.MAA...DNKD.P.Q..LLIF..L.SVLIQE.F.FAYY.L....SEGLKSINP...A
Retrocopy FLLVSLLLSFLVWSMAAITADNKDGPIQKYLLIFDMLVSVLIQEMFQFAYYELXXXASEGLKSINPDDIA

Parental  PSMRLLAYVSGLGFGIMSGVFSFVNTLSDSLGPGTVGIHGDPPQFFL
          PSMRL.AYVSGLGFGIM.G.FSFVNTLSDSLGPGTVGIHG..P.FFL
Retrocopy PSMRLPAYVSGLGFGIMRGAFSFVNTLSDSLGPGTVGIHGNSPPFFL

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_1673 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1673 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
Bos taurus	ENSBTAG00000010641	1 retrocopy	retro_btau_1423,
Sus scrofa	ENSSSCG00000004567	1 retrocopy	retro_sscr_325,
Tursiops truncatus	ENSTTRG00000006865	2 retrocopies	retro_ttru_1673 , retro_ttru_983,