RetrogeneDB ID: retro_ttru_1405

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_112545:26958..27518(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL1
• Ensembl ID: ENSTTRG00000011899
• Aliases: None
• Description: mitochondrial ribosomal protein L1 [Source:HGNC Symbol;Acc:14275]

Sequence

>retro_ttru_1405
TCATACCACTATATGAAAATAAATCCTGAGTGTATGCATTTAAAACACTTGTACACACAGCAAATATACAAGGTTAATAA
AGCTATTCACTTACTTAAGAAATTTCAAATTCTGGACTCTATTAATCCAAAACAAGGTGTTTATCTTGATTTGACACTGG
TTACAGTACATGAGGAAAAGAAAAAAGTGGAGTCATTTGCCAGTGTTCTTTGTTTTCCATATCCATTGGTTTCAGAAACC
AATAAAGTTGCTATATTTACAAGGAATGCATCAAAGATTAAAATAGCAGAAGAAAATGCAGCTGCATTTGCAGAAGGAAC
TAATCTGATTCAGAAGATTTTGAATTATAAAATTCATGCAGATTTTTAAGTGGCTGTTCCTGAAGGAATGCCTGAGATTA
TTCCATTAAAGAAGAAACTGAAAAAAAAGATTTTCCAAGCTTATTCAAAATTCCATTGGCCATTACATCCCCCAAATTTG
AGTTACTTAAAAATGGGCATAAAATTAAGGTAGATGAAGAAAGAGAGAACTTTCTGGAGACCATAATAGCAACATTGGAT

Alignment

ORF - retro_ttru_1405 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.49 %
• Parental protein coverage: 57.85 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SYPFMEGEPEDDVYLKRLYPRQIYEVEKAIHLLKKFQVLDFTNPKQGVYLDLTLDMTLXXXKKVEPFASV
          SY..M...PE....LK.LY..QIY.V.KAIHLLKKFQ.LD..NPKQGVYLDLTL.......KKVE.FASV
Retrocopy SYHYMKINPEC-MHLKHLYTQQIYKVNKAIHLLKKFQILDSINPKQGVYLDLTLVTVHEEKKKVESFASV

Parental  LSLPYPFVSETSKVAVFTGNASEIKIAEENGAAFAGGTNLIQKILDDEIQPDFYVAVPEIMPELNPLRKK
          L..PYP.VSET.KVA.FT.NAS.IKIAEEN.AAFA.GTNLIQKIL...I..DF.VAVPE.MPE..PL.KK
Retrocopy LCFPYPLVSETNKVAIFTRNASKIKIAEENAAAFAEGTNLIQKILNYKIHADF*VAVPEGMPEIIPLKKK

Parental  L-KNRFPKLTRNSIGRDIPKM-LELFKTG-HEIKVDEERENFLETKIGTLD
          L....F.KL..NSIG..IP...L...K.G.H.IKVDEERENFLET.I.TLD
Retrocopy L>XXXFSKLIQNSIGHYIPQI<LSYLKMG<HKIKVDEERENFLETIIATLD

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_1405 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1405 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 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000024511	1 retrocopy	retro_ecab_665,
Myotis lucifugus	ENSMLUG00000011011	2 retrocopies	retro_mluc_2466, retro_mluc_534,
Pteropus vampyrus	ENSPVAG00000002696	2 retrocopies	retro_pvam_67, retro_pvam_913,
Tursiops truncatus	ENSTTRG00000011899	1 retrocopy	retro_ttru_1405 ,