RetrogeneDB ID: retro_ttru_1774

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_91214:1130..1828(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTTRG00000013662
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TBP
• Ensembl ID: ENSTTRG00000014825
• Aliases: None
• Description: TATA box binding protein [Source:HGNC Symbol;Acc:11588]

Sequence

>retro_ttru_1774
ACGTCCCAGCAGGCAACCCAGGGAGCCTCGGGTCAGACACCACAGCTTTTCCACTCACAAACTCTTAACGACCGCACCCT
TGCCGGGCACCACTCCCCTGTATCCCTCCCCCATGACCCCCATTACCTACCCCTGCCACGCCAGCCTCAGAGAGCTCTGG
GATTGTGCCGCAGCTGCAAAATATTGTATCCACAGTGAATCTTGGTTGTAAACTTGACCTAAAGACCACTGTACTTCATG
CAGGGAATGCTGAATATAATCCCAAACGGTTTGCTGCTGTAATTATGAGAATAAGAGAGCCCCAGGCCACTGCACTGATA
TTCAGTTCTGGGAAGATGGCGTGCACAGGAGCCAAGAGTGAAGAACAGTCCAGACTAGCAGCAAGAAAATATGCCAGGGT
TGTACAGAAGTTGGGTGTTCTAGCTAAGTTCTTGGACTTCAAGATTCAGGACATGGTGGGGAGCAGTGATGTGAAATTCC
CTATAAGGTTAGAAGACTTTGTGCTTACCCACCAACAGTTCAGTAGTTATGAGCCAGAGTTATTTCCTGGTTTAATCTAC
AGAATGATCAAACCGAGAATTGTTCTCCTTATTTTTGTTTCTGGACAAGTTATATTAACAGGTGCTAAAGTCAGAGCAGA
AATTTATGAAGCCTTTGAGAACATCTACCCTATTCTAAAGGGTTTCAGGAAGACAACG

Alignment

ORF - retro_ttru_1774 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.72 %
• Parental protein coverage: 73.35 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TSQQATQGASGQTPQLFHSQTL-TTAPLPGTTPLYPSPMTPMT-PI-TPATPASESSGIVPQLQNIVSTV
          TSQQATQGASGQTPQLFHSQTL.TTAPLPGTTPLYPS...PMT.P..TPATPASESSGIVPQLQNIVSTV
Retrocopy TSQQATQGASGQTPQLFHSQTL>TTAPLPGTTPLYPS---PMT>PLPTPATPASESSGIVPQLQNIVSTV

Parental  NLGCKLDLKTIALRARNAEYNPKRFAAVIMRIREPRTTALIFSSGKMVCTGAKSEEQSRLAARKYARVVQ
          NLGCKLDLKT..L.A.NAEYNPKRFAAVIMRIREP..TALIFSSGKM.CTGAKSEEQSRLAARKYARVVQ
Retrocopy NLGCKLDLKTTVLHAGNAEYNPKRFAAVIMRIREPQATALIFSSGKMACTGAKSEEQSRLAARKYARVVQ

Parental  KLGFPAKFLDFKIQNMVGSCDVKFPIRLEGLVLTHQQFSSYEPELFPGLIYRMIKPRIVLLIFVSGKVVL
          KLG..AKFLDFKIQ.MVGS.DVKFPIRLE..VLTHQQFSSYEPELFPGLIYRMIKPRIVLLIFVSG.V.L
Retrocopy KLGVLAKFLDFKIQDMVGSSDVKFPIRLEDFVLTHQQFSSYEPELFPGLIYRMIKPRIVLLIFVSGQVIL

Parental  TGAKVRAEIYEAFENIYPILKGFRKTT
          TGAKVRAEIYEAFENIYPILKGFRKTT
Retrocopy TGAKVRAEIYEAFENIYPILKGFRKTT

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_1774 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1774 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Myotis lucifugus	ENSMLUG00000014582	1 retrocopy	retro_mluc_1040,
Tursiops truncatus	ENSTTRG00000014825	1 retrocopy	retro_ttru_1774 ,