RetrogeneDB ID: retro_ttru_1335

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_110815:142698..143648(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MGME1
• Ensembl ID: ENSTTRG00000016431
• Aliases: None
• Description: mitochondrial genome maintenance exonuclease 1 [Source:HGNC Symbol;Acc:16205]

Sequence

>retro_ttru_1335
TCACCCAGTGTGGTCTTCTCCACTTCCTCTTATATGTGTGGCGGGAAGAAAAAAGTGAACCGTTATGAAGAAGAGGACCC
AAAAAAGTACTCTGATTTAGTAAGGTCTGTCTTGTCATTCAGAGGCCACGCTCAGACTCCACAGCCTTTGTTCGAGGAAG
ATGCTTTACTCTATGGACCTGTGAGGAAGTGTAAGGCCCCAAAGCAAGAAGAAGGGGCAGGAGGTCCACGAAACTGGGGT
CCTCTCTTCAATCCGGAGAAAAGCGGAAAACCAAATGATCCTACAGTTCCTCTGAAAATCCCTTTGCAAAGGAATATGAT
ACCAAGGGTGACCCGAGTCCTTTAGCAGACCATGAACTCAGAACAGATTTCCTGTTTGGAGAGGTGGAAACAGTGGATGA
TTCTGGAACTGGGAGAGGATGGTTTTGCAGAATATACTTCAAACATGTTTTTACAAGGGAAATGGTTTCATGAAGCCTTG
GAAAGCATACTTTCACCCCAGGGGAACTTAAGAGAGAGAGATGAAAATCTCCTCAAATCTGGCTACATCCAAAGGGTCCA
GCATGTTCTGAGAGATGTCAGTGGAGTGTGGGCTCTGGAAAATGCTGTTAGACGTGAGACCCTAAAGTATGTAGGTCTGC
TGCACTGTGTGGCTGATTATCAGGGAAAGCTGTGTGTGACTGATCGGAAGACATCTGAGAAACCAAAGCCTTTCATCCGA
AATACATTTGACAACCTGCTGCAAGTCGTGGTGTATGTCAGTGCCATAAACCATAAGGCCAACTACAGCTTTCAGGTTCA
GTGTGGCTTGATCGTGGTGGCCTACAAAGACAGGTCCCCCGCCCACCCACATTTCATGGATGCAGAGCTCTGCTCCCAGT
ACTAGGCAAAGTGACTTCGACTAGAAGAATATACAAAGAAGAAAAGAACCTGAATATTCAGAAACTAGAT

Alignment

ORF - retro_ttru_1335 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.78 %
• Parental protein coverage: 93.29 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  APRVVFSTSSYLCGRKKKVNPYEEVDQEKYSDLVRSVLSFRGHAQAPQSLFEEDALLYGPVRKCKAPKQE
          .P.VVFSTSSY.CG.KKKVN.YEE.D..KYSDLVRSVLSFRGHAQ.PQ.LFEEDALLYGPVRKCKAPKQE
Retrocopy SPSVVFSTSSYMCGGKKKVNRYEEEDPKKYSDLVRSVLSFRGHAQTPQPLFEEDALLYGPVRKCKAPKQE

Parental  E-AGVPRNWCPLFNPEKSGKPNATNDPTIPLKIPLQRNTIPSVTRILQQTMTSEQISCLERWKRRMILEL
          E.AG.PRNW.PLFNPEKSGKP...NDPT.PLKIPLQRN.IP.VTR.L.QTM.SEQISCLERWK..MILEL
Retrocopy EGAGGPRNWGPLFNPEKSGKP---NDPTVPLKIPLQRNMIPRVTRVL*QTMNSEQISCLERWKQWMILEL

Parental  GEDGFAEYTSNMFLQGKQFHEALESILSPQGNLKEPDENLLKSGYIQSIQHVLRDVSGVQALESAVRHET
          GEDGFAEYTSNMFLQGK.FHEALESILSPQGNL.E.DENLLKSGYIQ..QHVLRDVSGV.ALE.AVR.ET
Retrocopy GEDGFAEYTSNMFLQGKWFHEALESILSPQGNLRERDENLLKSGYIQRVQHVLRDVSGVWALENAVRRET

Parental  LKYVGLLDCVADYQGKLCVIDWKTSEKRKPFIQNTFDNPLQVVAYVGAINHDINYSFQVQCGLIVVAYKD
          LKYVGLL.CVADYQGKLCV.D.KTSEK.KPFI.NTFDN.LQVV.YV.AINH..NYSFQVQCGLIVVAYKD
Retrocopy LKYVGLLHCVADYQGKLCVTDRKTSEKPKPFIRNTFDNLLQVVVYVSAINHKANYSFQVQCGLIVVAYKD

Parental  GSPAHPHFMDAELCSQYWVKWLLRLEEYTKK-EKNQNIQKLD
          .SPAHPHFMDAELCSQY..K..LRLEEYTKK.EKN.NIQKLD
Retrocopy RSPAHPHFMDAELCSQY*AK-*LRLEEYTKK<EKNLNIQKLD

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_1335 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1335 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 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000002646	2 retrocopies	retro_dnov_1261, retro_dnov_1803,
Tursiops truncatus	ENSTTRG00000016431	1 retrocopy	retro_ttru_1335 ,