RetrogeneDB ID: retro_ttru_761

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_332:356894..357434(-)
• Located in intron of: ENSTTRG00000016304

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBLCP1
• Ensembl ID: ENSTTRG00000005876
• Aliases: None
• Description: ubiquitin-like domain containing CTD phosphatase 1 [Source:HGNC Symbol;Acc:28110]

Sequence

>retro_ttru_761
ATGGCTCTTCCTATCATTGTAAAATGGGGCAGACAGGAATATTCAGTGACCACACTTTCAGAAGATGATACTGCGCTAGA
TCTCAATTTCTCAAGACCCTTACGGGAGTGTTACCAAAACGTCAGAAGTTACCTGGACTCAAAGTTAAAGGCAAACCTAC
AGAAAATTATGTTAAGCTTGGAGCTCTCAAACTGAAACCAAATACTAAAATCATGATGATGCGAACTCATGAGGAGAGCT
TGGAAGATGCCTTAGGTCCACCTCCTGACAATGATGATGTTGTTAACGACTCTGATATTGAAGATGAAGTAGTTGAAGCA
GAAAATAGGGAGGAAAACCTACTGAAAATTTCCCACAGAGTAAAAGAGTACAAAGTGGAAATTTTGAATCCTCCCAGGGA
AGGGAAAAAACCTTTGGTACTAGGTGTTGATTATATATTATTTGACCATAGTCTCTTGTGCAGATACTGGGATAGAATTA
ATGTGGCCATATCTTCATGAATACCTAACATCTGCATATGAGGATTATGACATTGTTATC

Alignment

ORF - retro_ttru_761 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.15 %
• Parental protein coverage: 56.78 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MALPIIVKWGGQEYSVTTLSEDDTVLDLKQFLKTL-TGVLPERQKLLGLKVKGKPAENDVKLGALKLKPN
          MALPIIVKWG.QEYSVTTLSEDDT.LDL..F...L.TGVLP.RQKL.GLKVKGKP.EN.VKLGALKLKPN
Retrocopy MALPIIVKWGRQEYSVTTLSEDDTALDL-NFSRPL<TGVLPKRQKLPGLKVKGKPTENYVKLGALKLKPN

Parental  TKIMMMGTREESLEDVLGPPPDNDDVINDFDIEDEVVEVENREENLLKISRRVKEYKVEVLNPPREGKKL
          TKIMMM.T.EESLED.LGPPPDNDDV.ND.DIEDEVVE.ENREENLLKIS.RVKEYKVE.LNPPREGKK.
Retrocopy TKIMMMRTHEESLEDALGPPPDNDDVVNDSDIEDEVVEAENREENLLKISHRVKEYKVEILNPPREGKKP

Parental  LVLDVDYTLFDHR-SCAETGVELMRPYLHE-LTSAYEDYDIVI
          LVL.VDY.LFDH..SCA.TG.ELM.PYLHE.LTSAYEDYDIVI
Retrocopy LVLGVDYILFDHS>SCADTGIELMWPYLHEYLTSAYEDYDIVI

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_761 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_761 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 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007691	1 retrocopy	retro_chof_51,
Echinops telfairi	ENSETEG00000000170	1 retrocopy	retro_etel_1142,
Microcebus murinus	ENSMICG00000010060	2 retrocopies	retro_mmur_1083, retro_mmur_1319,
Myotis lucifugus	ENSMLUG00000006359	1 retrocopy	retro_mluc_1367,
Monodelphis domestica	ENSMODG00000008063	2 retrocopies	retro_mdom_1251, retro_mdom_1351,
Mustela putorius furo	ENSMPUG00000013396	1 retrocopy	retro_mputfur_1098,
Mus musculus	ENSMUSG00000041231	1 retrocopy	retro_mmus_762,
Oryctolagus cuniculus	ENSOCUG00000002224	1 retrocopy	retro_ocun_1036,
Tupaia belangeri	ENSTBEG00000008983	1 retrocopy	retro_tbel_41,
Tursiops truncatus	ENSTTRG00000005876	1 retrocopy	retro_ttru_761 ,