RetrogeneDB ID: retro_ttru_56

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_1066:438963..439965(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UGP2
• Ensembl ID: ENSTTRG00000000694
• Aliases: None
• Description: UDP-glucose pyrophosphorylase 2 [Source:HGNC Symbol;Acc:12527]

Sequence

>retro_ttru_56
CTACAGAAGTAGAATCACTGTCGTGTGAAAATCTACACTTTTAATCAAACCAGGTACCTGAGGATTAATAAAGAATCTTT
ACTACCTGTAGCAAAGAATGTTTCATTCTCAGGGGCAAATACAGAAGCCTGGTACCCTCCGGGTTATGGAAATATTTATG
CCGGTTTCTACAACTCTGGTTTGCTTTATACCTTTATAGGAGAAGGCAAAGGGTATATTTTTGAGTCCAACATAGATAAT
CTGGGTACCACAGTGGATCTTTATATTCTTAATCATCTAACAAACCCACCCAATGGAAAACCTTGTCAATTTGTCATGGA
AGTCACAAATAAAACACATGCAGATGTAAAGGGTGGGACACTCACTCAGTATGAAGGCAAATTGAGACTGATGGAAATTG
CTCAAGTGCCAAAAGCATATGCTGATGAGTATAAATCTGTATCAAAATTCAAAATATTTAATACAAACAACCTATGGATC
TCTCTTACAGCAGTTAAAAGACTGCAGGAGCAGAATGCTATTGACATGGAAATCATTGTAAATCCAAAGACTTTGGATGG
AGGCCTGAATGTCATTCAGTTGGAAACTGCAGTAGGGGCTGCCATTAAAAACTTTGAGAACTCTCTAGGTATTAATGTTC
CTAGGAGCCGTTTTCTGCCTGTCAAAACCACATCAGATCTCTTGCTTTTGATGTCAAACCTTTATAGTCTTAATGCAGGA
TCTCTGACAATGAGTGAAAAGCGGGAATTTCCTACAGTGCCCTTGGTTAAATTAGGCGGTCCTTTTACGAAGGTTCAGGA
TTATCTAAGGAGATTTGAAAGCATACCAGATATGCTTGAATTGGATCACCTCACAGTTTCAGGAGATATAACATTTGACA
AGAATGTTTTATTACAGGGAACGGTTATCATCATCGCAAATCATGGTGACTGAATTGACATCCCACCTGGAGCAGTATTA
GAGAACAAGATTGTATCTGGGAACCTTCATACCTTGGACCAC

Alignment

ORF - retro_ttru_56 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.02 %
• Parental protein coverage: 66.27 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LQKYNHCRVKIYTFNQSRYPRINKESLLPVAKNVSFSGENTEAWYPPGHGDIYASFYNSGLLDTFIGEGK
          LQK.NHCRVKIYTFNQ.RY.RINKESLLPVAKNVSFSG.NTEAWYPPG.G.IYA.FYNSGLL.TFIGEGK
Retrocopy LQK*NHCRVKIYTFNQTRYLRINKESLLPVAKNVSFSGANTEAWYPPGYGNIYAGFYNSGLLYTFIGEGK

Parental  EYIFVSNIDNLGATVDLYILNHLMNPPNGKPCEFVMEVTNKTRADVKGGTLTQYEGKLRLVEIAQVPKAH
          .YIF.SNIDNLG.TVDLYILNHL.NPPNGKPC.FVMEVTNKT.ADVKGGTLTQYEGKLRL.EIAQVPKA.
Retrocopy GYIFESNIDNLGTTVDLYILNHLTNPPNGKPCQFVMEVTNKTHADVKGGTLTQYEGKLRLMEIAQVPKAY

Parental  VDEFKSVSKFKIFNTNNLWISLAAVKRLQEQNAIDMEIIVNPKTLDGGLNVIQLETAVGAAIKSFENSLG
          .DE.KSVSKFKIFNTNNLWISL.AVKRLQEQNAIDMEIIVNPKTLDGGLNVIQLETAVGAAIK.FENSLG
Retrocopy ADEYKSVSKFKIFNTNNLWISLTAVKRLQEQNAIDMEIIVNPKTLDGGLNVIQLETAVGAAIKNFENSLG

Parental  INVPRSRFLPVKTTSDLLLVMSNLYSLNAGSLTMSEKREFPTVPLVKLGSSFTKVQDYLRRFESIPDMLE
          INVPRSRFLPVKTTSDLLL.MSNLYSLNAGSLTMSEKREFPTVPLVKLG..FTKVQDYLRRFESIPDMLE
Retrocopy INVPRSRFLPVKTTSDLLLLMSNLYSLNAGSLTMSEKREFPTVPLVKLGGPFTKVQDYLRRFESIPDMLE

Parental  LDHLTVSGDVTFGKNVSLKGTVIIIANHGDRIDIPPGAVLENKIVSGNLRILDH
          LDHLTVSGD.TF.KNV.L.GTVIIIANHGD.IDIPPGAVLENKIVSGNL..LDH
Retrocopy LDHLTVSGDITFDKNVLLQGTVIIIANHGD*IDIPPGAVLENKIVSGNLHTLDH

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_56 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_56 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 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006960	1 retrocopy	retro_cjac_1709,
Cavia porcellus	ENSCPOG00000008459	1 retrocopy	retro_cpor_811,
Microcebus murinus	ENSMICG00000006509	1 retrocopy	retro_mmur_1277,
Oryctolagus cuniculus	ENSOCUG00000002137	1 retrocopy	retro_ocun_815,
Tursiops truncatus	ENSTTRG00000000694	1 retrocopy	retro_ttru_56 ,