RetrogeneDB ID: retro_ttru_475

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_2406:63836..65066(-)
• Located in intron of: ENSTTRG00000011908

Retrocopy information

• Ensembl ID: ENSTTRG00000011910
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PAPOLG
• Ensembl ID: ENSTTRG00000006237
• Aliases: None
• Description: poly(A) polymerase gamma [Source:HGNC Symbol;Acc:14982]

Sequence

>retro_ttru_475
AAGCACTATGGCGTCTCCTCCCCCATCAGTTTAGCACCCCCCAGGGAGACTGACTGCATACTTACCCAGAAATTAATTGA
AACCCTGAAGCCCTTTGGGGTTTTTGAAGAGGAAGAGGAACTACAGCGCAGGATTTTAATTTTGGAGAAATTAAATAACC
TGGTAAAGGAATGGATACGAGAAATCAGTGAAAGCAAGAGTCTTCCACAAGCTGTAATAGAAAACGTTGGAGGGAAAATC
TTTACATTCGGTTCTTATAGATTAGGGGTGCATACGAAAGGTGCCGATATCGACGCGTTGTGCGTGGCACCAAGACATGT
TGATCGAAGCGACTTTTTCACCTCCTTCTATGGTAAATTGAAACTACATGAAGAAGTAAAGGATTTAAGGGCTGTTGAAG
AGGCATTTGTACCAGTTATCAAACTGTGTTTTGATGGGATAGAGATTGATATTTTGTTCGCAAGATTAGCACTGCAGACT
ATTCCGGAAGATTTGGACCTAAGAGATGACAGTCTGCTTAAAAACTTAGATATTAGGTGCATAAGAAGTCTTAATGGTTG
CCGGGTAACTGATGAGATTTTACATCTGGTACCAAACATTGACAACTTCAGATTAACTCTGAGAGCCATCAAGTTGTGGG
CCAAATGCCACAATATCTATTCCAATATATTAGGTTTCCTAGGAGGTGTTTCCTGGGCGATGCTAGTAGCAAGAACTTGC
CAGCTTTATCCAAATGCGATAGCATCAACTCTTGTACGTAAATTTTTCTTGGTGTTTTCTGAATGGGAATGGCCAAATCC
AGTGCTACTGAAAGAGCCTGAAGAACGGAATCTTAATTTGCCTGTCTGGGACCCAAGAGTAAATCCCAGCGATAGGTACC
ATCTCATGCCTATAATTACACCAGCATACCCACAGCAGAACTCCACGTACAACGTGTCTGTTTCAACAAGGATGGTCATG
ATTGAGGAGTTTAAGCAAGGGCTTGCTATTACACATGAGATTTTGCTGAGTAAGGCAGAGTGGTCCAAACTTTTTGAAGC
TCCCAGCTTCTTTCAAAAGTACAAGCATTATATTGTACTTCTAGCAAGTGCGCCAACAGAAAAACAACATCTAGAATGGG
TGGGCTTGGTGGAATCAAAAATCCGAATCCTGGTTGGAAGCTTGGAGAAGAATGAATTTATTACACTGGCACATGTGAAT
CCTCAGTCGTTTCCAGCACCCAAGGAAAAT

Alignment

ORF - retro_ttru_475 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.27 %
• Parental protein coverage: 55.33 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KHYGITSPISLACPKEIDHIYTQKLIDAMKPFGVFEDEEELNHRLVVLGKLNNLVKEWISEVSESKNLPP
          KHYG..SPISLA.P.E.D.I.TQKLI...KPFGVFE.EEEL..R...L.KLNNLVKEWI.E.SESK.LP.
Retrocopy KHYGVSSPISLAPPRETDCILTQKLIETLKPFGVFEEEEELQRRILILEKLNNLVKEWIREISESKSLPQ

Parental  SVVATVGGKIFTFGSYRLGVHTKGADIDALCVAPRHVERSDFFQSFFEKLKHQDGIRNLRAVEDAFVPVI
          .V...VGGKIFTFGSYRLGVHTKGADIDALCVAPRHV.RSDFF.SF..KLK.......LRAVE.AFVPVI
Retrocopy AVIENVGGKIFTFGSYRLGVHTKGADIDALCVAPRHVDRSDFFTSFYGKLKLHEEVKDLRAVEEAFVPVI

Parental  KFEFDGIEIDLVFARLSIQTISDNLDLRDDSRLRSLDIRCIRSLNGCRVTDEILHLVPNKETFRLTLRAV
          K..FDGIEID..FARL..QTI...LDLRDDS.L..LDIRCIRSLNGCRVTDEILHLVPN...FRLTLRA.
Retrocopy KLCFDGIEIDILFARLALQTIPEDLDLRDDSLLKNLDIRCIRSLNGCRVTDEILHLVPNIDNFRLTLRAI

Parental  KLWAKRRGIYSNMLGFLGGVSWAMLVARTCQLYPNAAASTLVHKFFLVFSKWEWPNPVLLKQPEESNLNL
          KLWAK...IYSN.LGFLGGVSWAMLVARTCQLYPNA.ASTLV.KFFLVFS.WEWPNPVLLK.PEE.NLNL
Retrocopy KLWAKCHNIYSNILGFLGGVSWAMLVARTCQLYPNAIASTLVRKFFLVFSEWEWPNPVLLKEPEERNLNL

Parental  PVWDPRVNPSDRYHLMPIITPAYPQQNSTYNVSTSTRTVMVEEFKQGLAVTDEILQGKSDWSKLLEPPNF
          PVWDPRVNPSDRYHLMPIITPAYPQQNSTYNVS.STR.VM.EEFKQGLA.T.EIL..K..WSKL.E.P.F
Retrocopy PVWDPRVNPSDRYHLMPIITPAYPQQNSTYNVSVSTRMVMIEEFKQGLAITHEILLSKAEWSKLFEAPSF

Parental  FQKYRHYIVLTASASTEENHLEWVGLVESKIRVLVGNLERNEFITLAHVNPQSFPGNKEH
          FQKY.HYIVL.ASA.TE..HLEWVGLVESKIR.LVG.LE.NEFITLAHVNPQSFP..KE.
Retrocopy FQKYKHYIVLLASAPTEKQHLEWVGLVESKIRILVGSLEKNEFITLAHVNPQSFPAPKEN

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_475 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_475 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 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000014028	4 retrocopies	retro_chof_2125, retro_chof_2361, retro_chof_2456, retro_chof_2571,
Ochotona princeps	ENSOPRG00000009630	4 retrocopies	retro_opri_208, retro_opri_395, retro_opri_827, retro_opri_861,
Ictidomys tridecemlineatus	ENSSTOG00000010861	1 retrocopy	retro_itri_1616,
Tursiops truncatus	ENSTTRG00000006237	1 retrocopy	retro_ttru_475 ,