RetrogeneDB ID: retro_psin_39

Retrocopy location

• Organism: Chinese softshell turtle (Pelodiscus sinensis)
• Coordinates: JH207007.1:242389..244087(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

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

Sequence

>retro_psin_39
AGAAATGTCAAGTGCAAGTATTCGGAGGACTACGTCAAATTCGGCTTCACTTGTCAAGAAAAAGAAGGCGTGGATTTGCC
ACAATGTATTGTTTGTTTCAAAGTCTTGGGGAATGACTCAATGAATCTGGCTAAACTGATACTCCATCTCGAAAAGTGTC
ACCCCAACTTGTCACAAAAGGATGAAGATTATTTTGAGCGGCAGTTATCAGGTCTGAAACGGCAGCGCCTCGACTCAACA
AGTGCATTCTACAAGAAGACAAGCAATGCAGTGTGTGCTTCCTACACTGTTGCATACAAAGTTGCACAGGCCAAGAAGCC
TCATACCATTGTAGAGCAACTTGTGCTCCCCTGTGCAAAAGAGATGGTGCGGCTTGTTCTTGGCAAGGAAGCAGCAAGGA
AGCTGAATGATGTATCTGTCTTTAACGACACAGTATCGAGACGGATAAATGAGATATCACAGAACATCAGAGAACAAGTT
GTGGATGAAATAAAGAAGTCTCCGTTGTTTGCCATACAATTGGATGAATTGACCGACATCACATTGTGCTCTAAGCTATT
TGTGTTTGCACAATACATGGTCGAGGCAGACTTCAAAGACGAGTTTCTTTTTTGCAAGACTCTTGATATCACCACAAAGG
CTCAGGATGTGATGGAAATTGTTAACAATTTCTTTGAAGTACATGGTCTGGATTGGGTAAATCTTGTGCGTGTCACCACT
GATGGTGCACCTGCCATGCTGGGCTCAAGATCGGGCTTCTAAATGCTGGTGAAACAGTACGCTCCAATGGTAACCAGAGT
TCATTGCTTCATTCATAGGGAAGCTTTGGCGTCAAAAACATTGCCTGATCAACTGAACGCCATTTTCAAAGGGTTGGTGA
AAGTGGTGAATCACATCAAATCATTGGCTCTGAACACCAGGCTGTTCAAAAGATTTTGCCTGGACATGGGTTCCAACTTT
GATGAGTTACTGTTCTACACTTCTGTACGGTGGTTGTCAGCAGGGAACATACTCAACAGAGTTTTTCAATTGAGAGAGGA
GTTGGATTTATTTCTCCAGGCTCAAGGAAAAGAGGAATTCCGAAATGTGCTGACACAGTCAAATTTAGAACTTGCATACC
TTGTCGATATTTTTGGAATCTTGAACAAACTGAATCTTCAGCTGCAAGGGAAAGGTGCAAATCTGTTCTCTCACCAAAGC
ATCATCAAGGCTTTTCTTGACAAATTGGTACTCTGGATCATAAGAGTCGAAGGCAATAATTTGGTTCAATTTCCATATGT
GGATGCCATGCTCGGGGAAAAGGAAGCCATTCGGATGCAAATTCTCGATCATTTATGGAAGCTATGAGATGAATTCCAAC
GATACTTTCCAGAGATGGAGAGGACAAGGGATGGATTATCTTTCATCAGGAATCCATTTACAACAGATGTTAATAGTGTT
CCAGAGGATCTGCAAGAGGAATTCTTGGATCTGAAAAATGATTTTGAGGCTCAAGGCATGTACCAGCAGTCTACCATAGA
GAAATTTTGGGCCAGTGTGACCGGAAGTTACCCAAATCTGTCAGCACACGCAGTCAGATTTCTTTTGCCATTTGCATCAA
CTTATATGTGTGAGACTGGATTTTCGTGTTTGTTGCATATTAAGTCCAAATAGAGGAATTGGCTTGCAGTGGAAAGCGAT
ATTCATTGTGCATTATCA

Alignment

ORF - retro_psin_39 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.17 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RNVKRKYLEDYIKFSFTCQEK-GMDLPQCVV--SVLGNDSMKPAKLKLHLEKCHPNLLQKD----EDYFE
          RNVK.KY.EDY.KF.FTCQEK.G.DLPQC.V...VLGNDSM..AKL.LHLEKCHPNL.QKD....E....
Retrocopy RNVKCKYSEDYVKFGFTCQEKEGVDLPQCIVCFKVLGNDSMNLAKLILHLEKCHPNLSQKDEDYFERQLS

Parental  CLKRQHFDSTSAFYNKTSNAVRASYIVAYKVTQAKKPHTIVEQLVLPCAKEMMRLVLGEEAARKLNDISV
          .LKRQ..DSTSAFY.KTSNAV.ASY.VAYKV.QAKKPHTIVEQLVLPCAKEM.RLVLG.EAARKLND.SV
Retrocopy GLKRQRLDSTSAFYKKTSNAVCASYTVAYKVAQAKKPHTIVEQLVLPCAKEMVRLVLGKEAARKLNDVSV

Parental  SNDTLSRRINELSQNISEQVVDEIKTSPLFTIQLDESTDVALCSRLLVFARYITEGDFKDEFLFCKTLDT
          .NDT.SRRINE.SQNI.EQVVDEIK.SPLF.IQLDE.TD..LCS.L.VFA.Y..E.DFKDEFLFCKTLD.
Retrocopy FNDTVSRRINEISQNIREQVVDEIKKSPLFAIQLDELTDITLCSKLFVFAQYMVEADFKDEFLFCKTLDI

Parental  TTKAQDMMEIVNNFFEV----WSGLGVTT-DGAPAMLSSRLGFQMLVKQHAPMVTGVHCFIHREALASKT
          TTKAQD.MEIVNNFFEV....W..L...T.DGAPAML.SR.GF.MLVKQ.APMVT.VHCFIHREALASKT
Retrocopy TTKAQDVMEIVNNFFEVHGLDWVNLVRVTTDGAPAMLGSRSGF*MLVKQYAPMVTRVHCFIHREALASKT

Parental  LPDPLNAVFKGLVKVMNHIRSLALNTRLFKRFCLDMGSNFGNILIEREVGFISPGSRNILNRVFQLREKL
          LPD.LNA.FKGLVKV.NHI.SLALNTRLFKRFCLDMGSNF...L....V...S.G..NILNRVFQLRE.L
Retrocopy LPDQLNAIFKGLVKVVNHIKSLALNTRLFKRFCLDMGSNFDELLFYTSVRWLSAG--NILNRVFQLREEL

Parental  DLFLQAQGKEEFRNVLTQSNLELAYLVDIFRILNKLNLQLQGKGANLFSHQSIVKAFLDKLELWIIRVEG
          DLFLQAQGKEEFRNVLTQSNLELAYLVDIF.ILNKLNLQLQGKGANLFSHQSI.KAFLDKL.LWIIRVEG
Retrocopy DLFLQAQGKEEFRNVLTQSNLELAYLVDIFGILNKLNLQLQGKGANLFSHQSIIKAFLDKLVLWIIRVEG

Parental  NTLVQFPYVDAMLREKEAIRTQILHHLQKL----QGYFLEVDRTRDGLSFIRNPFTTDVNSVPEDLQEKF
          N.LVQFPYVDAML.EKEAIR.QIL.HL.KL....Q.YF.E..RTRDGLSFIRNPFTTDVNSVPEDLQE.F
Retrocopy NNLVQFPYVDAMLGEKEAIRMQILDHLWKL*DEFQRYFPEMERTRDGLSFIRNPFTTDVNSVPEDLQEEF

Parental  LDLKNDFAAQDMYQQSTIEKFWASVIRSYQNLSAHAVRFLLPFASTYMCEIGISCLLHVTIDERSRPVLL
          LDLKNDF.AQ.MYQQSTIEKFWASV..SY.NLSAHAVRFLLPFASTYMCE.G.SCLLH.....R......
Retrocopy LDLKNDFEAQGMYQQSTIEKFWASVTGSYPNLSAHAVRFLLPFASTYMCETGFSCLLHIKSK*RNWLAVE

Parental  RRLKCSIA
          ....C...
Retrocopy SDIHCALS

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_39 retrocopy.

TSS

Pelodiscus sinensis was not studied using FANTOM5 data.

Lab

retro_psin_39 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,