RetrogeneDB ID: retro_ttru_1844

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_94212:7463..8384(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PHYH
• Ensembl ID: ENSTTRG00000011113
• Aliases: None
• Description: phytanoyl-CoA 2-hydroxylase [Source:HGNC Symbol;Acc:8940]

Sequence

>retro_ttru_1844
ATAGCTCACCCCACTTCAGGGGCTGTTTTTCCTGCCAGTTTCCATAGTCAACAATTCCAGTATACTCGTGAAAATAAAGT
TCTAAGCCTAGAACAGAGAAATTTATGAAGAAAATGGGTTTCTTGTCATTAAAAATTTGGTGACTGATGCTGATATTCAA
CTCTTGAGGGATGAGTTTGACAGAATCTGCAAAAAGGTGAAACCACTGGGATTGATGGTGATGAAAGATGAGACCATTGC
AAAATCACAATATATGCCAAGTGAGAAAGTGACTACCAAGGTCCAAGATTTCCAAGAAGATAAGGAACTCTTCAGGTATT
GCACCCTCCCTGAAATTCTGAAATATGTGGAGTGCTTCACTGGACCCAATGTTATGGCCATGCATGCAATGCTGATAAAC
AAACCTCCAGACTCAGGCAGAAGACATCCCGTCCGTCACCTTTTGCACAAGGATCTGCACTATTTCCCCTAAGACCCAGC
AATAGCATCTTTTGTGCCTGGAAGGCCATGGAGAACATTGACCAGAGCAATGGCTGCCTGGTTGTGCTCCCAGGGACACA
CAAAGGTCCCTTGAAACCACACGATTATTCCCACTGAGAGGGAGGGTTTAACATCATATTCCACGGGGTCCAAGACTATG
ACAGAAATAATACCCAGGTGCACATCATGAAGGAGAAGAGAGACACCATTTTCTTTCATCCTTTGCTTGTCCCTGAATCT
GGTTCGGAACAAAAGTCAAGGATTCCAGAAGGCAATTTCCCACCATTTCGCGGATGCCAACCACCACTACATCAATGTTA
ATGGCACCAATCAAGAAAACATTGGAAAGGAAGTCTTAGGGTTAGTCAGTAAATCTATGGAGTGAAAGACGTCAGCCTGA
AGGATGTTTGGGAATTTCGAGCGCACATCGTGATAGGAGAA

Alignment

ORF - retro_ttru_1844 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.19 %
• Parental protein coverage: 98.73 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  IAHHTSGTVSPAGFHPQQFQYTRDNNILSLEQR-KF-YEENGFLVIKNLVSDADIQYFRDEFERICRMEV
          IAH.TSG.V.PA.FH.QQFQYTR.N..LSLEQR.KF.YEENGFLVIKNLV.DADIQ..RDEF.RIC...V
Retrocopy IAHPTSGAVFPASFHSQQFQYTRENKVLSLEQR<KF<YEENGFLVIKNLVTDADIQLLRDEFDRICK-KV

Parental  KPLGLMVMRDVTIAKSEYVPSEKVITKVQDFQEDKELFRYCTLPEILKYVECFTGPNIMAMHTMLINKPP
          KPLGLMVM.D.TIAKS.Y.PSEKV.TKVQDFQEDKELFRYCTLPEILKYVECFTGPN.MAMH.MLINKPP
Retrocopy KPLGLMVMKDETIAKSQYMPSEKVTTKVQDFQEDKELFRYCTLPEILKYVECFTGPNVMAMHAMLINKPP

Parental  DSGNCKKTSRHPLHQDLHYFP-FRPSNSIVCAWTAMEHIDRDNGCLVVLPGTHRGPLKTHDYPQWEGGVN
          DSG......RH.LH.DLHYFP..RPSNSI.CAW.AME.ID..NGCLVVLPGTH.GPLK.HDY...EGG.N
Retrocopy DSGR-RHPVRHLLHKDLHYFP<LRPSNSIFCAWKAMENIDQSNGCLVVLPGTHKGPLKPHDYSH*EGGFN

Parental  IMFHGIQDYDKNNDRVHLLMEKGDTVFFHPLLIHGSG-RNKSQGFRKAISCHFADANCHYIDVKGTSQEN
          I.FHG.QDYD.NN..VH...EK.DT.FFHPLL...SG.RNKSQGF.KAIS.HFADAN.HYI.V.GT.QEN
Retrocopy IIFHGVQDYDRNNTQVHIMKEKRDTIFFHPLLVPESG>RNKSQGFQKAISHHFADANHHYINVNGTNQEN

Parental  IGEEVLEIASK-IHGVKDVSLKDVWRFRARVVKGE
          IG.EVL...SK.I.GVKDVSLKDVW.FRA..V.GE
Retrocopy IGKEVLGLVSK<IYGVKDVSLKDVWEFRAHIVIGE

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_1844 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1844 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
Choloepus hoffmanni	ENSCHOG00000002160	1 retrocopy	retro_chof_334,
Cavia porcellus	ENSCPOG00000007582	1 retrocopy	retro_cpor_161,
Rattus norvegicus	ENSRNOG00000018044	1 retrocopy	retro_rnor_542,
Tursiops truncatus	ENSTTRG00000011113	1 retrocopy	retro_ttru_1844 ,