RetrogeneDB ID: retro_ttru_1314

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_110270:27391..28230(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPIE
• Ensembl ID: ENSTTRG00000014385
• Aliases: None
• Description: peptidylprolyl isomerase E (cyclophilin E) [Source:HGNC Symbol;Acc:9258]

Sequence

>retro_ttru_1314
GGACTTGCAGAGGAGGTGGATGACAAAGTTCTTCATGCTGCTTTTATCCCTTTTGGAGACAGCACAGATATCCAGATTCC
CCTGGATTAGGAAACAGAAAAGCACCGAGGATTTGCTTTTGTTGCATTTGAGTTGGCAGAGGATGCTGCAGCAGCTGTAG
ACAGCATGAATGAACCTGAGCTGTTTATATGGACAATTCGTGTCAATTTGGCAAAACCCATAAGGATTAAGGAAGGCTCT
TCCAGACCAGTTTGGTCCGAGGATGGCTGGTTGAAGAAGTTTTCTGGGAAGACTCTTGAGGAGAATAAAGAAGAAGGGAC
AGAGCCTCCCAAAGTGGAAACCCAGGAGGGAGAGCCCGCTGTAAAAAAAGCCCAGTCAAACCCTCAGGTGTACATGGACA
TCAAGACTGAGAACAAGCCAGCAGGCTGAATCCAGATGCTCCTGGGTTCAGGCGTCGTTCCCATGACAGCAGAGAATTTC
CACTGCCCGTGCACCCACGAGAAGGGCTTTGGCTTCAAGGGCAGCAGCTTCCACCATATCATCCCCCAGTTCATGTGCCA
GGGCTGCGATTTCACCAACCACAAGGGCACTGGGGCAAGTCCACCTACGGGAGGAAGTTTGACGATGAAAACTTTATTCT
CAAACACACGGGACCAGGCCTGCTCTCCATGGCCAACTCAGGCCCAAACACCAACGGTTCCCAGTTCTTCCTGACATGTG
ACAAGATGGATTGGCTGGACGGCAAGCACGTGGTATTTGGGGAGGTCACGGAATGCCTGCAAGTCTTGTGACCGATTGAC
GCCCAGGCAGCAAGGACGGGAAATCCAAGCAGAAAGTCA

Alignment

ORF - retro_ttru_1314 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.52 %
• Parental protein coverage: 91.35 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL
          GLAEEVDDKVLHAAFIPFGD.TDIQIPLD.ETEKHRGFAFV.FELAEDAAAA.D.MNE.ELF..TIRVNL
Retrocopy GLAEEVDDKVLHAAFIPFGDSTDIQIPLD*ETEKHRGFAFVAFELAEDAAAAVDSMNEPELFIWTIRVNL

Parental  AKPMRIKEGSSRPVWSDDDWLKKFSGKTLEENKEEEGSEPPKVEAQEGEPAVKKARSNPQVYMDIKIGNK
          AKP.RIKEGSSRPVWS.D.WLKKFSGKTLEENK.EEG.EPPKVE.QEGEPAVKKA.SNPQVYMDIK..NK
Retrocopy AKPIRIKEGSSRPVWSEDGWLKKFSGKTLEENK-EEGTEPPKVETQEGEPAVKKAQSNPQVYMDIKTENK

Parental  PAGRIQMLLRSDIVPMTAENFRCLCTHEKGFGFKGSSFHRIIPQFMCQGGDFTNHNGTG-GKSIYGKKFD
          PAG.IQMLL.S..VPMTAENF.C.CTHEKGFGFKGSSFH.IIPQFMCQG.DFTNH.GTG.GKS.YG.KFD
Retrocopy PAG*IQMLLGSGVVPMTAENFHCPCTHEKGFGFKGSSFHHIIPQFMCQGCDFTNHKGTG<GKSTYGRKFD

Parental  DENFILKHTGTGLLSMANSGPNTNGSQFFLTCDKTDWLDGKHVVFGEITEGLDVLRQIEVSPDTGASKAW
          DENFILKHTG.GLLSMANSGPNTNGSQFFLTCDK.DWLDGKHVVFGE.TE.L.VL..I.......A....
Retrocopy DENFILKHTGPGLLSMANSGPNTNGSQFFLTCDKMDWLDGKHVVFGEVTECLQVL*PIDAQ----AARTG

Parental  GPRKKS
          .P..KS
Retrocopy NPSRKS

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_1314 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1314 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 6 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000007365	1 retrocopy	retro_cpor_560,
Myotis lucifugus	ENSMLUG00000016233	1 retrocopy	retro_mluc_339,
Tursiops truncatus	ENSTTRG00000002964	16 retrocopies	retro_ttru_1176, retro_ttru_1177, retro_ttru_1178, retro_ttru_1232, retro_ttru_1294, retro_ttru_1372, retro_ttru_1429, retro_ttru_1571, retro_ttru_222, retro_ttru_287, retro_ttru_298, retro_ttru_503, retro_ttru_623, retro_ttru_68, retro_ttru_763, retro_ttru_906,
Tursiops truncatus	ENSTTRG00000014385	1 retrocopy	retro_ttru_1314 ,
Vicugna pacos	ENSVPAG00000010049	2 retrocopies	retro_vpac_261, retro_vpac_86,
Xenopus tropicalis	ENSXETG00000018981	1 retrocopy	retro_xtro_20,