RetrogeneDB ID: retro_ttru_983

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_887:116645..116996(+)
• 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_983
TTTTCACCATCGCCACCGCCATTGCGCATCATCTTCCCCGTCACTGGAGCTTCCTTCAGGTTGGTGTCTCTACTGCTCTA
CTCCCTAGTTTGGTTCATGGTAGCAACCATTGCTGACGACAAAGATGGACCAATACAGAAATATCTGCTGATCTTTGGAG
TGCTAGTCTCAGTCCTTATCCAAGAAATGTGCCGTTTTGCATATTATAAACTTTTTTTTTTTAAAGCCTGTGTGGGCTTG
ACGAGTATAAACCCAAGGGAGACAGCACCTTCTATGTGATTAATGGCTTATGTTTCTGGTTTGGGCTTTGGAATCATGAG
TGGAGTATTTCCCTTTGTAAATAGCCTGACT

Alignment

ORF - retro_ttru_983 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.67 %
• Parental protein coverage: 72.96 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FTIATEPLRIIFIIIGAFFWLVSLLLSSFIWFMAATLTDNKDEPRQRDLLIFGVLISVLIQEVFRFAYYK
          F.....PLRIIF...GA.F.LVSLLL.S..WFM.AT..D.KD.P.Q..LLIFGVL.SVLIQE..RFAYYK
Retrocopy FSPSPPPLRIIFPVTGASFRLVSLLLYSLVWFMVATIADDKDGPIQKYLLIFGVLVSVLIQEMCRFAYYK

Parental  -LLKKSSEGLKSINPGEKAPSMRLLAYVSGLGFGIMSGVFSFVNTLS
          ....K...GL.SINP.E.APSM.L.AYVSGLGFGIMSGVF.FVN.L.
Retrocopy XXXXKACVGLTSINPRETAPSM*LMAYVSGLGFGIMSGVFPFVNSLT

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_983 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_983 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 ,