RetrogeneDB ID: retro_ttru_1345

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_111058:53532..55801(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TNPO1
• Ensembl ID: ENSTTRG00000000209
• Aliases: None
• Description: transportin 1 [Source:HGNC Symbol;Acc:6401]

Sequence

>retro_ttru_1345
AAACTGGAACAACTCAATCAATATCCAGACTTGAACAACTACCTGATTTTTGTTCTTACAAAATTAAAATCTGAAGATGA
ACCCACAAGATCATCGAGTGGTCTCATATTGAAGAATAACGTGAAAGCACACTTTCAGTATTTCCCAAATGGTGTAACAG
ACTTTATTAAGAGTGAATGTTTAAACAATATTGGTGACTCCTCTCCTCTGATTAGAGCTACTGTAGGCATTTTGATTACA
ACTATAGCCTCCAAGGGAAAACTGCAGAATTGGCCTGACCTCCTACCAAAACTCTGTAGCCTGTTGGATTATGAAGATTA
CAACACTTGTGAGGGAGCATTTGGTGCCCTTCAGAAGATTTGTGAAGATTCTGCTGAGATTTTAGATAGTGATGTTTTAG
ATCTTCCTCTCAACATCATGATTCCTAAATTTTTACAGTTCTTCAAGCACAGTAGTCCAAAAATAAGGCCTCATGTTGTT
GCATGTGTCAATCAGTTTATCATCAGTGGAACTCAAGCTGTGATGTTGCACTTTGATTCCTTTATTGAGAATCTCTTTGC
ATTGGCTGGTGATGAAGAACCAGAGGTACAGAAAAATGTGTGCCAGGCACTTGTGATATTGCTTGAAGTTCGAATGGATC
GCCTGCCTCCTCACATGCATAATATAGTTGAGTACATGCTACAGAGGCCCCAAGATCAAGGTGAAAATGTGGCTTTAGAA
GCCTGCGAATTTTGGCTTACTTTGGCTGAGCAACCAATATGCAAAGATGTACTCATAAGCCATCTTCCTAAGTTGATTCC
TGTGTTAGTGAAGGGCATGAAGTACTCAGATATAGATATTATCCTACTTGAGGGTGATGTTGAAGAAGATGAAACAATTC
CTGATAGTGAACAGGATACAAGGCCACGTTTTCATCGATCAAGGACAGTGGCTCAGCAGCATGACAAAGATGGAATTGAA
GAGGAAGGTGATGATGACGATGAAATTGATGATGATGATACGATTTCTGACTGGAATCTAAGAAAATGTTCTGCGGTTGC
CCTAGATGTTCTTGCAAATGTGTATCGTGATGAGCTTTTGCCACATATTTTGCCCCTTTTGAAAGAATTACTTTTTCATC
ATGAATGGGTTGTTAAAGAATCAGGCATCTTGGTTTTAGGAGCATTTGCTGAAGGTTGCATGCTGGGCATGATTCCCTAC
CAATCTGAGCTCATTCCTCACCTTATTCAGTGCCTCTCTGATAAAAAGTCTCTTGTGCGTTTCATAACGTGCTGGACTCT
TAGCCGCTATGCACACGGGGTAGTCAGCCAGCCCTCAGACACATACCTGAAGCCATTAATGACAGAACTGCTAAAACGTA
TCCTGGATAGTAACAAGAGAGTACAAGAAGCTGCCTGCAGTGCCTTTGCTACTCTGGAAGAGGAGGCTTGTACAGAACTT
GTTCCTCACCTTGCTTATATACTTGATACCTTGGTCTTTGCATTTAGTAAATACCAGCATAAAAACCTGCTCATTCTTTA
TGATGCCACAGGAACGTTAGCGGATTCAGTAGGACATCACTTAAACAAACCTGAATATATTCAGATGCTAATGCCTCCAC
TGATCCAGAAATGGAACATGTTAAAGGATGAAGATAAAGATCTCTTCCTTTTACTTGAGTGCCTATCTTCAGTTGCCACA
GCCCTGCAGTCTGGCTTCTTCCATACTGTGAACCTGTGTATCAGCGTTGTGTAAATTAGTACAGAAGACTCTTGCACAAG
CAATGCTGAGCAGTGCTCAACGAGATCAGTATGAGGCTCCAGATAAAGATTTTATGATAGTGGCTCTTGATTTACTCAGT
GGCCTGGCTGAAGGACTTGGAGGCAACATTGAACAGCTAGTAGCCCGAAGTAACATTCTAACACTAATGTATCAGTGCAT
GCAGGATAAAATGCCAGAGGTTAGACAGAATTCCTTCGCCCTGTTAGGTGACCTGACAAAAGCTTGCTTCCAGCATGTTA
AGCCTTGTATAGCTGATTTCATGACAATATTGGGAACCTACCTAAATCCAGAGTTCATTTCAGTCTGCAATAATGCCACA
TGGGCAACTGGAGAAATCTCCATTCAAATGGGCATAGAGATGCAGCCTTATATTCCTATGGTGTTGCACCAGTTTTGCAC
CAGACCCAACACACCAAAGACGTTGTTAGAGAATACAGCAATAACAATTGGTCGTCTTGGTTACGTTTGTCCTCAAGAGG
TGGCTCCCATGCTACAGCAGTTTATTAAG

Alignment

ORF - retro_ttru_1345 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.86 %
• Parental protein coverage: 84.63 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KLEQLNQYPDFNNYLIFVLTKLKSEDEPTRSLSGLILKNNVKAHFQNFPNGVTDFIKSECLNNIGDSSPL
          KLEQLNQYPD.NNYLIFVLTKLKSEDEPTRS.SGLILKNNVKAHFQ.FPNGVTDFIKSECLNNIGDSSPL
Retrocopy KLEQLNQYPDLNNYLIFVLTKLKSEDEPTRSSSGLILKNNVKAHFQYFPNGVTDFIKSECLNNIGDSSPL

Parental  IRATVGILITTIASKGELQNWPDLLPKLCSLLDSEDYNTCEGAFGALQKICEDSAEILDSDVLDRPLNIM
          IRATVGILITTIASKG.LQNWPDLLPKLCSLLD.EDYNTCEGAFGALQKICEDSAEILDSDVLD.PLNIM
Retrocopy IRATVGILITTIASKGKLQNWPDLLPKLCSLLDYEDYNTCEGAFGALQKICEDSAEILDSDVLDLPLNIM

Parental  IPKFLQFFKHSSPKIRSHAVACVNQFIISRTQALMLHIDSFIENLFALAGDEEPEVRKNVCRALVMLLEV
          IPKFLQFFKHSSPKIR.H.VACVNQFIIS.TQA.MLH.DSFIENLFALAGDEEPEV.KNVC.ALV.LLEV
Retrocopy IPKFLQFFKHSSPKIRPHVVACVNQFIISGTQAVMLHFDSFIENLFALAGDEEPEVQKNVCQALVILLEV

Parental  RMDRLLPHMHNIVEYMLQRTQDQDENVALEACEFWLTLAEQPICKDVLMRHLPKLIPVLVNGMKYSDIDI
          RMDRL.PHMHNIVEYMLQR.QDQ.ENVALEACEFWLTLAEQPICKDVL..HLPKLIPVLV.GMKYSDIDI
Retrocopy RMDRLPPHMHNIVEYMLQRPQDQGENVALEACEFWLTLAEQPICKDVLISHLPKLIPVLVKGMKYSDIDI

Parental  ILLKGDVEEDETIPDSEQDIRPRFHRSRTVAQQHDEDGIEEEDDDDDEIDDDDTISDWNLRKCSAAALDV
          ILL.GDVEEDETIPDSEQD.RPRFHRSRTVAQQHD.DGIEEE...........TISDWNLRKCSA.ALDV
Retrocopy ILLEGDVEEDETIPDSEQDTRPRFHRSRTVAQQHDKDGIEEEXXXXXXXXXXXTISDWNLRKCSAVALDV

Parental  LANVYRDELLPHILPLLKELLFHHEWVVKESGILVLGAIAEGCMQGMIPYLPELIPHLIQCLSDKKALVR
          LANVYRDELLPHILPLLKELLFHHEWVVKESGILVLGA.AEGCM.GMIPY..ELIPHLIQCLSDKK.LVR
Retrocopy LANVYRDELLPHILPLLKELLFHHEWVVKESGILVLGAFAEGCMLGMIPYQSELIPHLIQCLSDKKSLVR

Parental  SITCWTLSRYAHWVVSQPPDTYLKPLMTELLKRILDSNKRVQEAACSAFATLEEEACTELVPYLAYILDT
          .ITCWTLSRYAH.VVSQP.DTYLKPLMTELLKRILDSNKRVQEAACSAFATLEEEACTELVP.LAYILDT
Retrocopy FITCWTLSRYAHGVVSQPSDTYLKPLMTELLKRILDSNKRVQEAACSAFATLEEEACTELVPHLAYILDT

Parental  LVFAFSKYQHKNLLILYDAIGTLADSVGHHLNKPEYIQMLMPPLIQKWNMLKDEDKDLFPLLECLSSVAT
          LVFAFSKYQHKNLLILYDA.GTLADSVGHHLNKPEYIQMLMPPLIQKWNMLKDEDKDLF.LLECLSSVAT
Retrocopy LVFAFSKYQHKNLLILYDATGTLADSVGHHLNKPEYIQMLMPPLIQKWNMLKDEDKDLFLLLECLSSVAT

Parental  ALQSGF-LPYCEPVYQRCVN-LVQKTLAQAMLNNAQPDQYEAPDKDFMIVALDLLSGLAEGLGGNIEQLV
          ALQSGF.LPYCEPVYQRCVN.LVQKTLAQAML..AQ.DQYEAPDKDFMIVALDLLSGLAEGLGGNIEQLV
Retrocopy ALQSGF<LPYCEPVYQRCVN<LVQKTLAQAMLSSAQRDQYEAPDKDFMIVALDLLSGLAEGLGGNIEQLV

Parental  ARSNILTLMYQCMQDKMPEVRQSSFALLGDLTKACFQHVKPCIADFMPILGTNLNPEFISVCNNATWAIG
          ARSNILTLMYQCMQDKMPEVRQ.SFALLGDLTKACFQHVKPCIADFM.ILGT.LNPEFISVCNNATWA.G
Retrocopy ARSNILTLMYQCMQDKMPEVRQNSFALLGDLTKACFQHVKPCIADFMTILGTYLNPEFISVCNNATWATG

Parental  EISIQMGIEMQPYIPMVLHQLVEIINRPNTPKTLLENTAITIGRLGYVCPQEVAPMLQQFIR
          EISIQMGIEMQPYIPMVLHQ......RPNTPKTLLENTAITIGRLGYVCPQEVAPMLQQFI.
Retrocopy EISIQMGIEMQPYIPMVLHQ---FCTRPNTPKTLLENTAITIGRLGYVCPQEVAPMLQQFIK

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_1345 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1345 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 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000083312	2 retrocopies	retro_hsap_1724, retro_hsap_1813,
Mus musculus	ENSMUSG00000009470	1 retrocopy	retro_mmus_1501,
Pongo abelii	ENSPPYG00000015545	1 retrocopy	retro_pabe_1528,
Pan troglodytes	ENSPTRG00000016972	2 retrocopies	retro_ptro_1176, retro_ptro_3060,
Tursiops truncatus	ENSTTRG00000000209	1 retrocopy	retro_ttru_1345 ,