RetrogeneDB ID: retro_ttru_1583

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_28170:493..1538(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: E2F4
• Ensembl ID: ENSTTRG00000010268
• Aliases: None
• Description: E2F transcription factor 4, p107/p130-binding [Source:HGNC Symbol;Acc:3118]

Sequence

>retro_ttru_1583
ATGGTGGAGGCTGGGCCACAGGCACCACCACTCCCGGGCACCCCAAGCCGGCACGAGAAGAGTTTGGAACTTCTCACTAC
CAAGTTCGTGTCGCTTCTGCAGGAGGCAAAGGACAGCGTGCTTGACCTCGAGCTGGCAGCTGACACCCTAGCTGTTCGCC
GGAAGTGGCGGATTTATGACATTACTAATGTGCTGGAAGGTATCAGGCTGATGGAGAAAAAATCCAAGCATAGCATCCAG
TAGAAGGGCGTGGGGCCTGGCTGCAATACCCGAGAGACTGCGGACAAGTTGATTGAGCTCAAGGCAGAGATGGAGGAGCT
GCAGCAGCGAGAGCAAGAACTAGACCAGCACAAGGTGTGGGTGCGGCAGAGCATCCGGAACATCACAAAGGATGTGCAGA
ACAGCTGCTTGGCCTATGTGACTCATGAGGACATCTGCAGATGCTTTGCTGGAGATGCCATCCAGGCCCCGTCGGGCACC
AGCCTGGAGGTGCCCATCCCAGAGGGCCTCAATGGGCAGGAGAAGTACCAGATTCACCTGAAGAATGTAAGTGGCGCCAT
CGAGGTGCTGCTGGTGAACTAGGAGGCATGGAGCTCACCACTTGTGGCGGTGCCTATGCCACCACCCAAAGATCTGCTCC
AGAGCCCACCTGCTGCCTCTCCCCCTCCACCTCTGCCCAAGCCTGCTCTGGCCCAGCCCCAGGATGCCTCACGCCCAAGC
AGTCCCCAGGTGACCACCCCGAACCCTGTTCCCGGCAGCACCGAAGCCCAGGGGGTGGCCGGTCCAGCAGCTGAGACCAC
AGTGGGTGGTGGCCCTGGAACCGATAGCAAGGACAGTGGTGAGCGCAGCTCCCTCCCGCTGGGCCTGACAGCACTGTACA
CCCGGCTGCTGCAGTCCTCTGCCCTGTTGGACAGCAGTAGCAGCAATAGCAGTTCATCCGGACCCAACCCTTCTACCTCC
TTTGAGCCCATCAAGGCAGACCCCACAGTGTTCTGGAGCTCCCCAAAGACCTGTCAGAATCTTTGATCCCACTCGAGAGT
GCATG

Alignment

ORF - retro_ttru_1583 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.77 %
• Parental protein coverage: 87.44 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAEAGPQAPPPPGTPSRHEKSLGLLTTKFVSLLQEAKDGVLDLKLAADTLAVRQKRRIYDITNVWEGIGL
          M.EAGPQAPP.PGTPSRHEKSL.LLTTKFVSLLQEAKD.VLDL.LAADTLAVR.K.RIYDITNV.EGI.L
Retrocopy MVEAGPQAPPLPGTPSRHEKSLELLTTKFVSLLQEAKDSVLDLELAADTLAVRRKWRIYDITNVLEGIRL

Parental  IEKKSKNSIQWKGVGPGCNTREIADKLIELKAEIEELQQREQELDQHKVWVQQSIRNVTEDVQNSCLAYV
          .EKKSK.SIQ.KGVGPGCNTRE.ADKLIELKAE.EELQQREQELDQHKVWV.QSIRN.T.DVQNSCLAYV
Retrocopy MEKKSKHSIQ*KGVGPGCNTRETADKLIELKAEMEELQQREQELDQHKVWVRQSIRNITKDVQNSCLAYV

Parental  THEDICRCFAGDTLLAIRAPSGTSLEVPIPEGLNGQKKYQIHLKSISGPIEVLLVNKEAWSSPPVAVPVP
          THEDICRCFAGD...AI.APSGTSLEVPIPEGLNGQ.KYQIHLK..SG.IEVLLVN.EAWSSP.VAVP.P
Retrocopy THEDICRCFAGD---AIQAPSGTSLEVPIPEGLNGQEKYQIHLKNVSGAIEVLLVN*EAWSSPLVAVPMP

Parental  PPEDLLQSPPAVSTPPPLPKPALVPPQDASRPSSPQVTTPNPVPGSTEAQGVAGPAAELTVSAIPGIDNK
          PP.DLLQSPPA.S.PPPLPKPAL..PQDASRPSSPQVTTPNPVPGSTEAQGVAGPAAE.TV...PG.D.K
Retrocopy PPKDLLQSPPAASPPPPLPKPALAQPQDASRPSSPQVTTPNPVPGSTEAQGVAGPAAETTVGGGPGTDSK

Parental  DRGELSSLP--LTALTP--LQSSACDSSSSSSSNSSSSGPPSSFEPIKADPT-GVLELPKELSE-IFDPT
          D.GE.SSLP..LTAL....LQSSA...SSSS.S.SS...P..SFEPIKADPT..VLELPK.LSE.IFDPT
Retrocopy DSGERSSLPLGLTALYTRLLQSSALLDSSSSNSSSSGPNPSTSFEPIKADPT<SVLELPKDLSE<IFDPT

Parental  RECM
          RECM
Retrocopy RECM

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_1583 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1583 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
Loxodonta africana	ENSLAFG00000026216	1 retrocopy	retro_lafr_1248,
Tursiops truncatus	ENSTTRG00000010268	1 retrocopy	retro_ttru_1583 ,