RetrogeneDB ID: retro_ttru_1161

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_105946:123438..124236(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FBXO27
• Ensembl ID: ENSTTRG00000009850
• Aliases: None
• Description: F-box protein 27 [Source:HGNC Symbol;Acc:18753]

Sequence

>retro_ttru_1161
CTAGAGCAAGAATCCGAGGAGGCGCTGGGCACGAACGAACTGCCAGCCGAGCTGCTCCTGATGGTGCTGAGCCACGTGCC
CCATCACATGCTGCTCGACACCGCCACCAGGTGTGCAAGCGCTGGCTCGACCTAGTGGACTGCCATGTCCTGTTGAGCAT
CTTGCCCCGGAAACAATCCGTCCTGCGGCCATCGTCAGCCCTGCCTGCCGCCGCCGCCGACTCAGTCCTGCGTCTGGGCC
CGCTCTGCGAGCGCAGACCCATAGGGCGCAACCTCCTCTGAACCCCAGGGGCGTAGATGGCTTCCCAGAACAGCTATGCT
GAGTGGTGGGGACGGCTGGACAAAGGAGAGAAAATGTAAGGGCATGCCTGCAGCTCCTTGTGATGTCCACTTCCTACCTG
CCTACCACCTACCTGGTTACAGGTGGTTTCGAAGAAAGGAAGTTTTGGACCTGGAGAAGGAGGGTTTCTGGCCAGAACTC
CTGGATAATGGAAAGATTGGGATTTGTGTCTCTGACTGCTGGATGGAACGAAGAGGCACTAACCGTATATGTATATATCG
GCTAATTGTCCAAACTCTAGACGTCAACCAGGCTGTCCTGCGTCATTTCTCTTCGAATCCTTTTTGCATCCGGCGGTGGA
GGAGAGTCCCCTTTGAGGCCAGCCATGTGTCCTCCAACCTCAAGAACGGTGTTCACTTTGTGTCTTTTGAACAATGGGTG
TCAAACCTGGAGTTAGGGAATGAGCAATATGGAGTCCCTTTTACCAACTCCAGTGTGTTTGCATGGGTCTGTCTGTCC

Alignment

ORF - retro_ttru_1161 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.73 %
• Parental protein coverage: 96.09 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LEQEPEEPLGLGQLPTELLEMVLSHVPPHVLLGRCRR-VCRRWRDLVDCQALWLSILARKHAALWPIVST
          LEQE.EE.LG...LP.ELL.MVLSHVP.H.LL....R.VC.RW.DLVDC..L.LSIL.RK...L.P..S.
Retrocopy LEQESEEALGTNELPAELLLMVLSHVPHHMLLDTATR<VCKRWLDLVDCHVL-LSILPRKQSVLRP--SS

Parental  CLPAADDPRPCVLGRFCERRPIGRNLL-RNPRGLDGSQKQ-PMLSGGDGWTKEGKCKGMPAPPCDVHFLP
          .LPAA.......LG..CERRPIGRNLL..NPRG.DG...Q..MLSGGDGWTKE.KCKGMPA.PCDVHFLP
Retrocopy ALPAAAADSVLRLGPLCERRPIGRNLL<LNPRGVDGFPEQ<AMLSGGDGWTKERKCKGMPAAPCDVHFLP

Parental  AYYLPGYRWFQKKEVLDLEEEGFWPELLDSGKIEICVSACWMEQRGTNRIRIYQLIVQILDVNQAVLHHF
          AY.LPGYRWF..KEVLDLE.EGFWPELLD.GKI.ICVS.CWME.RGTNRI.IY.LIVQ.LDVNQAVL.HF
Retrocopy AYHLPGYRWFRRKEVLDLEKEGFWPELLDNGKIGICVSDCWMERRGTNRICIYRLIVQTLDVNQAVLRHF

Parental  SSNPFPIRRWRRVPFEGSHVFSNLKKGVRFVSFEQWVSNLEFGNEQYGVLFTNSSVIVRVCLS
          SSNPF.IRRWRRVPFE.SHV.SNLK.GV.FVSFEQWVSNLE.GNEQYGV.FTNSSV...VCLS
Retrocopy SSNPFCIRRWRRVPFEASHVSSNLKNGVHFVSFEQWVSNLELGNEQYGVPFTNSSVFAWVCLS

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_1161 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1161 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 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000004611	1 retrocopy	retro_cpor_1475,
Mustela putorius furo	ENSMPUG00000017748	3 retrocopies	retro_mputfur_1473, retro_mputfur_465, retro_mputfur_965,
Ictidomys tridecemlineatus	ENSSTOG00000027765	1 retrocopy	retro_itri_401,
Tupaia belangeri	ENSTBEG00000010522	1 retrocopy	retro_tbel_1067,
Tursiops truncatus	ENSTTRG00000009850	1 retrocopy	retro_ttru_1161 ,
Vicugna pacos	ENSVPAG00000004974	1 retrocopy	retro_vpac_470,