RetrogeneDB ID: retro_ttru_297

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_1800:4381..4950(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL48
• Ensembl ID: ENSTTRG00000005403
• Aliases: None
• Description: mitochondrial ribosomal protein L48 [Source:HGNC Symbol;Acc:16653]

Sequence

>retro_ttru_297
CTCTTGAGGTTCAGAACTTCAAGAGAGAATCCCATCTGTTCTGCAGGTGGCATTCTGCTGAGCACCAGTCGGCACTACAG
GTCACAGCCCACGCGCGGCATTGGAAGATGCAAGCACCTAGTTAAAGCACAAGAGCCCAAGAAGAAGAGGGGAAAGTGGA
AGTGAGACCTATTAATTCGGGGACAGATGATGAATATGGGGTTTGAAACATTCACCTGACTGCATATGATATGGCCCTGG
CAGAGAGTTATGCCCAATATGTTCACAACCTCTGCAACCATCTCTCCATTAAAGTCGAGGAAAGTTATGTGAGGCCCACC
AAAACCATGGAGGTGTTGCAGTTGCAGAACCAAGGCAGCAAAATGCTCCTGGACTCAGTTCTTACCACCCATGCGTGAGT
GGTTCAGATCAGTGGTTTGAGCGCTACATTTGCAGAGATTTTCTTGGAAATAATCCAAAGCAATCGTCCTGAAGGAGTCA
AACTGTCAGTGAGGGAGCACACTGAAGAAGACTTCAAGGGAAGGTTCAAAGCCCAGCCAGAACAGGAAGAACTGTTAGCC
AAGTTGAAC

Alignment

ORF - retro_ttru_297 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.96 %
• Parental protein coverage: 99.48 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LIMFRTSGENPICSAAGILLSISRHYRSQPTHGIGRYKHLVKAQEPKKKRGK-VEVRPINLGTDYEYGVL
          L..FRTS.ENPICSA.GILLS.SRHYRSQPT.GIGR.KHLVKAQEPKKKRGK.VEVRPIN.GTD.EYGV.
Retrocopy LLRFRTSRENPICSAGGILLSTSRHYRSQPTRGIGRCKHLVKAQEPKKKRGK<VEVRPINSGTDDEYGV*

Parental  NIHLIAYDMALAESYAQYVHNLCNHLSIKVEESYAMPTKTVEVLQLQDQGRKMLLDSVLTTHERVVQISG
          NIHL.AYDMALAESYAQYVHNLCNHLSIKVEESY..PTKT.EVLQLQ.QG.KMLLDSVLTTH..VVQISG
Retrocopy NIHLTAYDMALAESYAQYVHNLCNHLSIKVEESYVRPTKTMEVLQLQNQGSKMLLDSVLTTHA*VVQISG

Parental  LSATFAEIFLEIIQSNLPEGVKLSVKEHTEEDFKGRFKARPELEELLAKLN
          LSATFAEIFLEIIQSN.PEGVKLSV.EHTEEDFKGRFKA.PE.EELLAKLN
Retrocopy LSATFAEIFLEIIQSNRPEGVKLSVREHTEEDFKGRFKAQPEQEELLAKLN

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_297 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_297 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
Canis familiaris	ENSCAFG00000005585	1 retrocopy	retro_cfam_1437,
Homo sapiens	ENSG00000175581	1 retrocopy	retro_hsap_3557,
Mustela putorius furo	ENSMPUG00000009716	1 retrocopy	retro_mputfur_38,
Mus musculus	ENSMUSG00000030706	2 retrocopies	retro_mmus_2478, retro_mmus_563,
Nomascus leucogenys	ENSNLEG00000017097	1 retrocopy	retro_nleu_1376,
Oryctolagus cuniculus	ENSOCUG00000009302	1 retrocopy	retro_ocun_39,
Otolemur garnettii	ENSOGAG00000004771	1 retrocopy	retro_ogar_234,
Pan troglodytes	ENSPTRG00000004049	1 retrocopy	retro_ptro_2417,
Tursiops truncatus	ENSTTRG00000005403	2 retrocopies	retro_ttru_1123, retro_ttru_297 ,
Vicugna pacos	ENSVPAG00000004657	1 retrocopy	retro_vpac_538,