RetrogeneDB ID: retro_psin_59

Retrocopy location

• Organism: Chinese softshell turtle (Pelodiscus sinensis)
• Coordinates: JH210916.1:588486..590138(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPSIG00000013111
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPSIG00000003379
• Aliases: None
• Description: None

Sequence

>retro_psin_59
AGAAATGTCAAGTGCAAGTACTTGGAGGACTACATCAAATTCGACTTCACTTGTCAAGAAAAAGGCGGCACGGATTTGCC
ACAATGTGTTATTTGTTTCAAAGTCTTGGGGAATGACTCAATGAAGCCGGCTAAGCTGAAACTCCATCTCGAAAAGTGTC
ACCCCACCTTGTTGCAAAAGAATGAAGATTATTTTGAGCGGCAGTTATCAGGTCTGAAATGGCAGTGCCTCAGCTCAACA
AGTGCATTCTACAATAAGACAAGCAATGCAGTGCGCGCTTTCTACATTGTTGCATACAAAGTTGCACAGGCCAAGAAGCC
TCATGCCATCGTAGAGCAACTTGTGCTCTCCTGTGCAAAAGAGATGGTGCAGCTTCCCCTTGGTGAGGAAGCAGCAAGGA
AGCTGAATGATATATCTGTCTCTGAGGACACAGTATCGAGATGGATAAATGAGATATCACAGGACATCAGTGAACAAGTT
GTAGATGAAATGAAGCCTCCATTGTTTGCCATACAATTGGATGAATCAACTGATGTCACATTGTGCTCTCAGCTATTGGT
GTTCGCACGATACATGGTTGAGGGAGACTTCAAAGACGAGTTCCTTTTTTGTAAGGCACTTGATACCACCACAAAGGCTC
AGGATGTGATGGAAATTGTTAATAATTTCTTTGAAGTACATAGTCTGGATTGGGTAAATCTTGTGTGTGTCACCACTGAT
GGTGTACCTGCCACGCTAGGCTCAAGATCGGGCTTCCAAATGCTGGTGAAACAGCGTGCTCCAATGGTAACCAGAGTTCA
TTGCTTCATTCATAGGGAAGCTTTGGCATCAAAAACATTGCCTGATAACTGAATGCCATTTTCAAAGGGTTGGTGAAAGT
GGTGAATCACATCAAATCATCGTCTCTGAACACCAGGCTGTTCAAAAGATTTTGCCTGGACACTGGTTCCGACTTTGATG
TGTTGATGCTCTACACTTCTGTACGGTGGTTGTCATCAGGGAACGTACTCAACAGAGTTTTTCAACTGAGAGAGGAGTTG
GATTTATTTCTCCAGGCTCACAGAAAAGAGGAATTCCAAAATGTGCTGATGCAGTCAAATTTAGAACTTGCGTATCTTGT
CGATATTTTTGGAATCTTGAACAAACTGAATCTTCAGCTGCAAGCGAAAGGTGCCGATCTGTTCTCTCACCAAAGCGTCA
TCAAGGCTTTTCTTGACAAATTGGAACTCTGGATCGTAAAAGTGGAAGGCAATAATTTAGTTCAATTTCTATATGTGGAT
GCCATGCTCGGGGAAAAGGAAACCATTCAAACGCAAATTGTCGATCATTTACAGAAGCTACGAGACGAATTCCAATGATA
CTTTCCAGAGGTGGACAGAACAAGGGATGGATTATCTTTCATCAGGAATCCATTTACAACAGATGTTGTTAGTGTTCCAG
AGGATCTACAGGAGGAATTCTTGGATCTGAGAAATGATTTTGCAGCTCAAGACGTGTACCAGCAATCTACCATGGAGAAA
TTTTGGGCCAGCATGTCCAGGAGTTACCCAAATCTGTCAGCACACGCAGTCAGATTTCTTTTGCCATTTGCATCAACTTA
TATGTGTGAGACTGGATTTTTGTCTTTGTTGCACGTTAAGTCCAAACAAAGG

Alignment

ORF - retro_psin_59 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.3 %
• Parental protein coverage: 97.46 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RNVKRKYLEDYIKFSFTCQEKG-MDLPQCVV--SVLGNDSMKPAKLKLHLEKCHPNLLQKD----EDYFE
          RNVK.KYLEDYIKF.FTCQEKG..DLPQCV....VLGNDSMKPAKLKLHLEKCHP.LLQK.....E....
Retrocopy RNVKCKYLEDYIKFDFTCQEKGGTDLPQCVICFKVLGNDSMKPAKLKLHLEKCHPTLLQKNEDYFERQLS

Parental  CLKRQHFDSTSAFYNKTSNAVRASYIVAYKVTQAKKPHTIVEQLVLPCAKEMMRLVLGEEAARKLNDISV
          .LK.Q...STSAFYNKTSNAVRA.YIVAYKV.QAKKPH.IVEQLVL.CAKEM..L.LGEEAARKLNDISV
Retrocopy GLKWQCLSSTSAFYNKTSNAVRAFYIVAYKVAQAKKPHAIVEQLVLSCAKEMVQLPLGEEAARKLNDISV

Parental  SNDTLSRRINELSQNISEQVVDEIKTSPLFTIQLDESTDVALCSRLLVFARYITEGDFKDEFLFCKTLDT
          S.DT.SR.INE.SQ.ISEQVVDE.K..PLF.IQLDESTDV.LCS.LLVFARY..EGDFKDEFLFCK.LDT
Retrocopy SEDTVSRWINEISQDISEQVVDEMK-PPLFAIQLDESTDVTLCSQLLVFARYMVEGDFKDEFLFCKALDT

Parental  TTKAQDMMEIVNNFFEV----WSGLGVTT-DGAPAMLSSRLGFQMLVKQHAPMVTGVHCFIHREALASKT
          TTKAQD.MEIVNNFFEV....W..L...T.DG.PA.L.SR.GFQMLVKQ.APMVT.VHCFIHREALASKT
Retrocopy TTKAQDVMEIVNNFFEVHSLDWVNLVCVTTDGVPATLGSRSGFQMLVKQRAPMVTRVHCFIHREALASKT

Parental  LPDP-LNAVFKGLVKVMNHIRSLALNTRLFKRFCLDMGSNFGNILIEREVGFISPGSRNILNRVFQLREK
          LPD..LNA.FKGLVKV.NHI.S..LNTRLFKRFCLD.GS.F........V...S.G..N.LNRVFQLRE.
Retrocopy LPDN<LNAIFKGLVKVVNHIKSSSLNTRLFKRFCLDTGSDFDVLMLYTSVRWLSSG--NVLNRVFQLREE

Parental  LDLFLQAQGKEEFRNVLTQSNLELAYLVDIFRILNKLNLQLQGKGANLFSHQSIVKAFLDKLELWIIRVE
          LDLFLQA..KEEF.NVL.QSNLELAYLVDIF.ILNKLNLQLQ.KGA.LFSHQS..KAFLDKLELWI..VE
Retrocopy LDLFLQAHRKEEFQNVLMQSNLELAYLVDIFGILNKLNLQLQAKGADLFSHQSVIKAFLDKLELWIVKVE

Parental  GNTLVQFPYVDAMLREKEAIRTQILHHLQKL----QGYFLEVDRTRDGLSFIRNPFTTDVNSVPEDLQEK
          GN.LVQF.YVDAML.EKE.I.TQI..HLQKL....Q.YF.EVDRTRDGLSFIRNPFTTDV.SVPEDLQE.
Retrocopy GNNLVQFLYVDAMLGEKETIQTQIVDHLQKLRDEFQ*YFPEVDRTRDGLSFIRNPFTTDVVSVPEDLQEE

Parental  FLDLKNDFAAQDMYQQSTIEKFWASVIRSYQNLSAHAVRFLLPFASTYMCEIGISCLLHVTIDER
          FLDL.NDFAAQD.YQQST.EKFWAS..RSY.NLSAHAVRFLLPFASTYMCE.G...LLHV....R
Retrocopy FLDLRNDFAAQDVYQQSTMEKFWASMSRSYPNLSAHAVRFLLPFASTYMCETGFLSLLHVKSKQR

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Pelodiscus sinensis was not studied using RNA-Seq expression data.

ChIP-Seq

Pelodiscus sinensis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_psin_59 retrocopy.

TSS

Pelodiscus sinensis was not studied using FANTOM5 data.

Lab

retro_psin_59 was not experimentally validated.

Homology

Retrocopy orthology:

Pelodiscus sinensis 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 2 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Pelodiscus sinensis	ENSPSIG00000003379	5 retrocopies	retro_psin_29, retro_psin_39, retro_psin_47, retro_psin_59 , retro_psin_65,
Pelodiscus sinensis	ENSPSIG00000011044	1 retrocopy	retro_psin_58,