RetrogeneDB ID: retro_ttru_569

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_2706:206305..206737(-)
• Located in intron of: ENSTTRG00000005065

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSME1
• Ensembl ID: ENSTTRG00000008620
• Aliases: None
• Description: proteasome (prosome, macropain) activator subunit 1 (PA28 alpha) [Source:HGNC Symbol;Acc:9568]

Sequence

>retro_ttru_569
CCCAGGGCCCAACCCCAGGTGGATATGTTTCACAAAGACCAGGGCAAAAGACAGAACCTACCTAGGAGCTATTTCCCCAG
GAAGATTTCTGAGTCAGATGAATTTTTGAAGGAAACAGCTCTCAAGAAGCCAACCGGAGCTATCTGAAGGCTCTGTTGGA
CATCTTGGTGCCTATCCAGTCCAGAAGACGGAGAATGAGGAATGGAAGAAACAGCAGGAGAAGGAGGATAGGGATGAAAA
GACAAAAGGGGAAGATGAAGGCAAAGGTCCTCCCAGTGGCCCAGTGAATGGCAAGGAGAGGCTTGAAGTCCTCTGCAAGG
GCCTGAAGCTGGGGACCACGGATGTCACTGAGCAGTCCACAGGGTCACCACCTGGTTGCAGCTGCAGATACCTCAGACTG
AAGATGGGAAAAGTTTTGAAGAAGGTGTCCGA

Alignment

ORF - retro_ttru_569 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.73 %
• Parental protein coverage: 58.87 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  PEAQAKVDVFREDLCAKTENLLGSYFPKKISELDAFLKEPALN-EANLSNLKAPLDIPVPD-PVKEKEKE
          P.AQ..VD.F..D...K..NL..SYFP.KISE.D.FLKE.AL..EAN.S.LKA.LDI.VP..PV...E.E
Retrocopy PRAQPQVDMFHKDQ-GKRQNLPRSYFPRKISESDEFLKETALK<EANRSYLKALLDILVPI<PVQKTENE

Parental  ERKKQQEKEDKDEKKKGEDEDKGPPCGPVNCNEKIVVLLQRLKPEIKDVIEK-LNLVTTWLQLQIPRIED
          E.KKQQEKED.DEK.KGEDE.KGPP.GPVN..E...VL...LK....DV.E.....VTTWLQLQIP..ED
Retrocopy EWKKQQEKEDRDEKTKGEDEGKGPPSGPVNGKERLEVLCKGLKLGTTDVTEQ<VHRVTTWLQLQIPQTED

Parental  GNNFGVAVQ
          G..F...V.
Retrocopy GKSFEEGVR

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_569 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_569 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
Ailuropoda melanoleuca	ENSAMEG00000016433	1 retrocopy	retro_amel_637,
Bos taurus	ENSBTAG00000021395	1 retrocopy	retro_btau_1189,
Canis familiaris	ENSCAFG00000011924	1 retrocopy	retro_cfam_246,
Equus caballus	ENSECAG00000016855	1 retrocopy	retro_ecab_1001,
Felis catus	ENSFCAG00000005583	1 retrocopy	retro_fcat_1567,
Macropus eugenii	ENSMEUG00000014712	1 retrocopy	retro_meug_1052,
Mus musculus	ENSMUSG00000022216	1 retrocopy	retro_mmus_466,
Rattus norvegicus	ENSRNOG00000019041	1 retrocopy	retro_rnor_50,
Tursiops truncatus	ENSTTRG00000008620	1 retrocopy	retro_ttru_569 ,