RetrogeneDB ID: retro_ttru_454

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_2343:357337..357577(+)
• Located in intron of: ENSTTRG00000017338

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM254
• Ensembl ID: ENSTTRG00000006122
• Aliases: None
• Description: transmembrane protein 254 [Source:HGNC Symbol;Acc:25804]

Sequence

>retro_ttru_454
TGGATGATCTTCTAGCCTGAGACTATTCCTTATCAGAGCCTAGGGCCGCTGGGCCCCTTCACTCAGTACTTGCTGGAGCA
TCATCACACCCTCGTGCACAGTTGGTATTGGCTTGCCTGGCTGATTCACGTGGGAGAGTCCTTGTATGCCATTGGATTGT
TCAAGTCTAAAGGCATCACGCATAGTTGGATTCAACTACTCTGGTTCCTGCAAACATTCCTTTTTGGGATGGCATCTATT

Alignment

ORF - retro_ttru_454 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.5 %
• Parental protein coverage: 56.34 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  WVVFWPEAIPYQSLGPLGPFTQYLLEHHHTLLHSWYWLAWLIHVGESLYAIVLCKSKGITNSWTQLLWFL
          W..F.PE.IPYQSLGPLGPFTQYLLEHHHTL.HSWYWLAWLIHVGESLYAI.L.KSKGIT.SW.QLLWFL
Retrocopy WMIF*PETIPYQSLGPLGPFTQYLLEHHHTLVHSWYWLAWLIHVGESLYAIGLFKSKGITHSWIQLLWFL

Parental  QTFLFGMASL
          QTFLFGMAS.
Retrocopy QTFLFGMASI

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_454 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_454 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 11 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000015748	3 retrocopies	retro_cfam_602, retro_cfam_635, retro_cfam_637,
Callithrix jacchus	ENSCJAG00000007670	1 retrocopy	retro_cjac_3839,
Dasypus novemcinctus	ENSDNOG00000024625	1 retrocopy	retro_dnov_555,
Felis catus	ENSFCAG00000026147	1 retrocopy	retro_fcat_401,
Myotis lucifugus	ENSMLUG00000007585	16 retrocopies	retro_mluc_1178, retro_mluc_2482, retro_mluc_2491, retro_mluc_2492, retro_mluc_2528, retro_mluc_2532, retro_mluc_2550, retro_mluc_2551, retro_mluc_2552, retro_mluc_2572, retro_mluc_2573, retro_mluc_2583, retro_mluc_2586, retro_mluc_2603, retro_mluc_2623, retro_mluc_766,
Macaca mulatta	ENSMMUG00000003015	1 retrocopy	retro_mmul_1583,
Mus musculus	ENSMUSG00000072676	1 retrocopy	retro_mmus_2102,
Oryctolagus cuniculus	ENSOCUG00000013679	1 retrocopy	retro_ocun_453,
Otolemur garnettii	ENSOGAG00000028898	1 retrocopy	retro_ogar_59,
Tarsius syrichta	ENSTSYG00000006920	1 retrocopy	retro_tsyr_103,
Tursiops truncatus	ENSTTRG00000006122	1 retrocopy	retro_ttru_454 ,