RetrogeneDB ID: retro_ttru_1074

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_102137:55370..55947(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LIN37
• Ensembl ID: ENSTTRG00000003834
• Aliases: None
• Description: lin-37 homolog (C. elegans) [Source:HGNC Symbol;Acc:33234]

Sequence

>retro_ttru_1074
TTCCCGGTGAAGGTGAAAGTAGAGAAATAAGAATTGAAGATGTCCCAGACCAGGAACAAACTGGATGCCCTTCCGCAGTG
TCTGTTGGAGAAGAGTTACAAGGACAGGGAGCATCTGGCTGAGGAAGCCTGGAAGACCCACTCAGATACCCACAGCATGG
ATTGCTCCATCATTGTGGCCACCGGCAAAAGGCCATCTGCCCACTTCTGCCACCAGCGAATGAGGAAGAAGAGGAAGATG
GATGGGCTGGCAGAGGGAGACTGCAGAAAGCCAATAAGTGTGTGATCAAGCTGTTTGACTGGAGTGGTGATTTAGCTCGG
TTTAGGGAGAACACACTGCTGTAGTCAATCTGTAGTGCTGGATGTGCAGGAGCCTCTCATAGCCAACGTGTCAACACTCG
TCCAGCTCACTGCTACTCACAGTGTTTGAGGATGCAGAGGTTTCAGAGGTCACCAACAGCAAGAGTCGTTAGGTGTACAA
GCTGCTTTCGCCCATAGCCCCTGGGCCACCTGGAGATGCCTGCAGATTCTGCATACCTTCCCCTCTGCAACCAGAGACAC
AGGATACCCCCAATGAT

Alignment

ORF - retro_ttru_1074 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.82 %
• Parental protein coverage: 78.46 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FPVKVKVEKSELEMAKARNQLDAVLQCLLEKSHMDRERLDEEAGKTPSDTHNKDCS-ITASGKRPSARFP
          FPVKVKVEK.EL.M...RN.LDA..QCLLEKS..DRE.L.EEA.KT.SDTH..DCS.I.A.GKRPSA.F.
Retrocopy FPVKVKVEK*ELKMSQTRNKLDALPQCLLEKSYKDREHLAEEAWKTHSDTHSMDCSIIVATGKRPSAHFC

Parental  HQRRKKRREMDEGLAEGG-PQRSNSYVIKLFDRSVDLAQFSENTPLYPICRA-WMRNSPTVREREHSPSS
          HQR..K.R.MD.GLAEG...Q..N..VIKLFD.S.DLA.F.ENT.L..IC.A.WM..S.......HS.SS
Retrocopy HQRMRKKRKMD-GLAEGD<LQKANKCVIKLFDWSGDLARFRENTLL*SICSA<WMCRSLS*PTCQHSSSS

Parental  PLPPLPEDEEGSEVTNSKSRDVYKLPPPTAPGPPGDACRSRIPSPLQPETQGTPDD
          .L....ED.E.SEVTNSKSR.VYKL..P.APGPPGDACR..IPSPLQPETQ.TP.D
Retrocopy LLLTVFEDAEVSEVTNSKSR*VYKLLSPIAPGPPGDACRFCIPSPLQPETQDTPND

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_1074 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1074 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 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000010100	1 retrocopy	retro_cjac_2736,
Echinops telfairi	ENSETEG00000004801	1 retrocopy	retro_etel_199,
Mus musculus	ENSMUSG00000036845	1 retrocopy	retro_mmus_2542,
Tursiops truncatus	ENSTTRG00000003834	1 retrocopy	retro_ttru_1074 ,