RetrogeneDB ID: retro_ttru_540

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_263:133525..134667(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PWP1
• Ensembl ID: ENSTTRG00000011036
• Aliases: None
• Description: PWP1 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:17015]

Sequence

>retro_ttru_540
AATGAAAAAGAAGTGAAACGTCTTATTGCTGAAGCAAAGGAAAAATTACAAGAAAAAGGTGGCAGTGATGAAGAGGAGAC
AGGCGATCCTTCAGAAGATGGCATGCAGCATGTCTGTACCCAGGCCCGACTTCAGGAGCCCCTGGAGGATGGTGACCCAG
AGGATGATGGGACGCTGGATGATGAGCTGGCTGAGTATGACTTAGATAAATATAATGAAGAAGGTGACCCAGATACTGAA
ACTCTTGGTGAATTTCTTTTGGATCTTACAGTCTATGGGAGTAATGATCAAGATCCTTACGTTACTCTGAAAGATATGGA
GCAGTACGAACGTGAAGTTTTCTTGATTAAGCCCAATGACATTCTCATAGTTTGTGGCAGAGCCGAACAGGACCAATGCA
ATTTAGAGGTACATGTTTATAACCAATAAGAAGATTCTTTTTATGTCCACCATGATATCCTGTTGTCTGCATACCCTTTG
AGTGTTGAATGGCTGAATTTTGATCCTAGCCCAGATGATTCAACTGGAAATTACATTGCTGTGGGAAACATGACCCCCGT
CATTGAAGTGTGGGATTTCGATATAGTGGAACTCTTTAGAGCCAGTCTTTACACTTAGAAATAAGCTATCAAAAAAGAAG
AAAAAGAAAGGAAAGATGAATTCCTCAGCAGATGGGCGTACCAATGCTGTCCTTGACCTTTCTTGGAATAAGCTGATCAG
AAATGTGCCGGCCAGTGCATCAGCTAACACTGTTATTCTGTGGGATACGTCCTTGGGGAAACCAGCAGCCAGCCTTGCCA
TACATACAGACAAGATCCAGACTCTCCAGTTTCATCCATTTGAAGCACAGACTCTGATTTCTGGATCATGTGATAAGTCA
GTGGCTTTGTATGACTGCCGAGGTCCAGAGGAAAGCCATCAACTGTGGCGATTCAGTGGGCAGATTGAGAGTGACTTGGA
ATCACTTTTCACCTTGTCATTTTTTGGCCAGTACAAATGATGGTTTTGTATATAATTTGGATGCATGCTCAGATAAGCCA
ATTTTTACACTTAATGCACACAGGGATGAAATTTCTCGTCTTGATCTAAGCAGTCAAATCAAGGACTGTCTTGTGACTGC
ATCAGCAGACAAGTATGTGAAG

Alignment

ORF - retro_ttru_540 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.49 %
• Parental protein coverage: 76.6 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SKEEVKRLIAEAKEKLQEEGGSDEEETGDPSEDGMQSARTQARPQEPLEDGDPEDDRTLDDDELAEYALD
          ...EVKRLIAEAKEKLQE.GGSDEEETGDPSEDGMQ...TQAR.QEPLEDGDPEDD.TLDD.ELAEY.LD
Retrocopy NEKEVKRLIAEAKEKLQEKGGSDEEETGDPSEDGMQHVCTQARLQEPLEDGDPEDDGTLDD-ELAEYDLD

Parental  KYDEEGDPDTETLGESLLGLTVYGSNDQDPYVTLKDTEQYEREDFLIKPNDNLIVCGRAEQDQCNLEVHV
          KY.EEGDPDTETLGE.LL.LTVYGSNDQDPYVTLKD.EQYERE.FLIKPND.LIVCGRAEQDQCNLEVHV
Retrocopy KYNEEGDPDTETLGEFLLDLTVYGSNDQDPYVTLKDMEQYEREVFLIKPNDILIVCGRAEQDQCNLEVHV

Parental  YNQEEDSFYVHHDILLSAYPLSVEWLNFDPSPDDSTGNYIAVGNMTPVIEVWDLDIVD-SLEPVFTLGSK
          YNQ.EDSFYVHHDILLSAYPLSVEWLNFDPSPDDSTGNYIAVGNMTPVIEVWD.DIV..SLEPVFTL..K
Retrocopy YNQ*EDSFYVHHDILLSAYPLSVEWLNFDPSPDDSTGNYIAVGNMTPVIEVWDFDIVE>SLEPVFTLRNK

Parental  LSKKKKKKGKKNSSADGHTDAVLDLSWNKLIRNVLASASADNTVILWDMSLGKPAASLAIHTDKVQTLQF
          L..........NSSADG.T.AVLDLSWNKLIRNV.ASASA.NTVILWD.SLGKPAASLAIHTDK.QTLQF
Retrocopy LXXXXXXXXXXNSSADGRTNAVLDLSWNKLIRNVPASASA-NTVILWDTSLGKPAASLAIHTDKIQTLQF

Parental  HPFEAQTLISGSYDKSVALYDCRSPEESHRMWRFS-GQIERVTWNHFSPCHFLASTDDGFVYNLDARSDK
          HPFEAQTLISGS.DKSVALYDCR.PEESH..WRFS.G...RVTWNHFSPCHFLAST.DGFVYNLDA.SDK
Retrocopy HPFEAQTLISGSCDKSVALYDCRGPEESHQLWRFS>GRL-RVTWNHFSPCHFLASTNDGFVYNLDACSDK

Parental  PIFTLNAHNDEISGLDLSSQIKGCLVTASADKYVK
          PIFTLNAH.DEIS.LDLSSQIK.CLVTASADKYVK
Retrocopy PIFTLNAHRDEISRLDLSSQIKDCLVTASADKYVK

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_540 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_540 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 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Macaca mulatta	ENSMMUG00000015544	1 retrocopy	retro_mmul_688,
Macaca mulatta	ENSMMUG00000031574	1 retrocopy	retro_mmul_687,
Mus musculus	ENSMUSG00000001785	2 retrocopies	retro_mmus_1600, retro_mmus_3074,
Otolemur garnettii	ENSOGAG00000011940	2 retrocopies	retro_ogar_2999, retro_ogar_3444,
Rattus norvegicus	ENSRNOG00000005350	1 retrocopy	retro_rnor_646,
Tursiops truncatus	ENSTTRG00000011036	1 retrocopy	retro_ttru_540 ,