RetrogeneDB ID: retro_ttru_1370

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_111542:138756..139140(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UCHL1
• Ensembl ID: ENSTTRG00000012095
• Aliases: None
• Description: ubiquitin carboxyl-terminal esterase L1 (ubiquitin thiolesterase) [Source:HGNC Symbol;Acc:12513]

Sequence

>retro_ttru_1370
CTCATTCATGCAGTGGCCAATAATCAGGACAAACTGGAGTTCGAGGATGGGTCAGTTCCGAAATAGTTTCTTTCTGAAAC
AGAGAAGTTGTACCCTGAAGACAGAGCAAAATGCTTTGAAAAGAATGAGGCCCTCCAGGGAACCCATGATGCCGTGGCAC
AGGATGGCCAATGTCGGGTAGATGACAAAGTGAACGTTCATTTTATTCTGTTTGACAACGTGGATGGCCACCTCTATGAA
CTTGATGGATGGAGGCCTTTTCCGGTGAACCGTGGCGCCAGTTCAGAGGACTCACTGCTGCAGGACGCCGCCCAGGTCTG
CAGAGAAGTCACTGAGCGTGGGCAAGGGGAGGTCTGCTCCTCCGCCGTGGCCCTCTGCAAGGCA

Alignment

ORF - retro_ttru_1370 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.94 %
• Parental protein coverage: 57.66 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LIHAVANNQDKLEFEDGSVLKQFLSETEKLSPEDRAKCFEKNEAIQAAHDAVAQEGQCRVDDKVNFHFIL
          LIHAVANNQDKLEFEDGSV.K.FLSETEKL.PEDRAKCFEKNEA.Q..HDAVAQ.GQCRVDDKVN.HFIL
Retrocopy LIHAVANNQDKLEFEDGSVPK*FLSETEKLYPEDRAKCFEKNEALQGTHDAVAQDGQCRVDDKVNVHFIL

Parental  FNNVDGHLYELDGRMPFPVNHGASSEGSLLQDAAKVCREFTEREQGEVRFSAVALCKA
          F.NVDGHLYELDG..PFPVN.GASSE.SLLQDAA.VCRE.TER.QGEV..SAVALCKA
Retrocopy FDNVDGHLYELDGWRPFPVNRGASSEDSLLQDAAQVCREVTERGQGEVCSSAVALCKA

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_1370 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1370 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 9 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003295	1 retrocopy	retro_chof_1737,
Callithrix jacchus	ENSCJAG00000019346	1 retrocopy	retro_cjac_365,
Echinops telfairi	ENSETEG00000012347	1 retrocopy	retro_etel_44,
Felis catus	ENSFCAG00000025457	1 retrocopy	retro_fcat_1321,
Macropus eugenii	ENSMEUG00000013774	1 retrocopy	retro_meug_8,
Oryctolagus cuniculus	ENSOCUG00000001353	1 retrocopy	retro_ocun_309,
Ictidomys tridecemlineatus	ENSSTOG00000015507	1 retrocopy	retro_itri_288,
Tupaia belangeri	ENSTBEG00000011438	1 retrocopy	retro_tbel_306,
Tursiops truncatus	ENSTTRG00000012095	1 retrocopy	retro_ttru_1370 ,