RetrogeneDB ID: retro_psin_65

Retrocopy location

• Organism: Chinese softshell turtle (Pelodiscus sinensis)
• Coordinates: JH224635.1:665478..667164(+)
• 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_65
AGAAATGTCAAGCGCAAGTATTTGGACAACTACATCAAATTCGGCCTTACTTGTCAAGAAAAAGAAGGTGTGGATTTGCC
ACAATGTGTTATTTGTTTCAGAGTCTTGGGGAATGACTCAATGAAGCTGGCTAAGCCGAAACTCCATCTCGAAAAGTATC
ACCCCAACTTGTTGCTAAAGGATGAAGATTATTTTGAGCGGCGGTTATCAGGTCTGCAGAACCTCGACTCAATAAGTGCA
TTCTACAATAAGACAAGCAATGCAGTGTGCGCTTCCTACATTGTTGCATACAGACTTGCACAGGCCAAGAAGCCTCATGC
CATCGTACAGCAACTTGTGTTCTCCTGTGCAAAACAGATGATGTGGCTTGTTCTTGGCGAGGAAGCAGCAAGGAAACCGA
ATGATATATCTGTCTTTAACGACACAGCATCGAGACGGATAAATGAGATATCACAGAACATCAATGAACAAGTTGTGGAT
GAAATAAAGAAGTCTCCATTGTTTGCCATACAATTGGATGAACTGACCAATGTCGCATTGTGCTCTCCGCTATTGGTGTT
CGCATGATACGTGGTTGAGGGAGACTTCAGAGATGAGTTTCTTTTTTGTAAGACTCTTGATACCACCAAAAAGGATCAAG
ATGTGATGGAAATTGTTAACAATTTATTTGAAGTACATGGTCTGGCTTGGGTAAATCTTGTGGGTGTCACCACTGATGGT
GCATCTGCCATGCTGGGCTCAAGATCGGGCTTCCAAACACTGGTGAAACAGTGCGCTCCAATGGTAACCGGAGTTCATTG
CTTCATTCATAGGGAAACTTTGGCATCAAAAACATTGCCTGATCAATTGAACATCGTTTTCAAAAGGTTGGTGAAAGTGG
TAAATCACATGAAATCATCGGCTCTGAGCACCAGGCTGTTCAAAAGATTTTGCCTGGACATGGGTTCCGACTTTGATGTG
TTGCTATTCTACACTTCTGTACGGTGGTTGTCAGCAAGGAACGTACTCAATAGACATTTTCAATTGAGAGAGGAGTTGGA
TTTATTTCTCCAGGCTCAAGGAAAAGAGGAATTCCGAAATGTGCTGACACAGTCAAATTTAGAACTTGCGTATCTTGTCA
ATATTTTTGGAATCTTGAACAAACTGAATCTTTAGCTGCAAGGGAAAGGTGCAAATCTGTTCTCTCACCAAAGGATCATC
AAGGCTTTTCTTGAAAAATTGGAACTCTGGATTGTAAGAGTCGAAGGCAATAATTTGGTTCAATTTCCATATGTGGATGC
CATGCTTAGGGAAAAGGAAGCCATTCGGATGCAAATTCTCAATCATTTACGGAAGCTACTAGACAAATTCCAACAATACT
TTCCGGAGGTGGACAGGACAAGGGATGGATTATCTTTCATCAGGAATCCATTTACAACAGATGTTAATAGTGTTCCTGAG
GATCTGCAGGAGGAATTCTTGGATCTGAAAAATGATTTTGCGGCTCAAGTTTGTACCAGAAGTCTACCATAGACAAATTT
TGGTCCAGCATGACCGGGTGTTACCCAAATCTCAGCCCACGCAGTCAGATTTCTTTTGCCATTTGCATCAACTTATATCT
AGTGTGAGACTGGATTTTTGTGTTTGTTGCACGGTAAGTCCAAACAGAGGAATCGGCTTTCAGTGAAAAGCGATATTCGT
TGTGCA

Alignment

ORF - retro_psin_65 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.26 %
• Parental protein coverage: 99.64 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RNVKRKYLEDYIKFSFTCQEK-GMDLPQCVVS--VLGNDSMKPAKLKLHLEKCHPN-LLQKDEDYFECLK
          RNVKRKYL..YIKF..TCQEK.G.DLPQCV....VLGNDSMK.AK.KLHLEK.HPN.LL.........L.
Retrocopy RNVKRKYLDNYIKFGLTCQEKEGVDLPQCVICFRVLGNDSMKLAKPKLHLEKYHPNLLLKDEDYFERRLS

Parental  R-QHFDSTSAFYNKTSNAVRASYIVAYKVTQAKKPHTIVEQLVLPCAKEMMRLVLGEEAARKLNDISVSN
          ..Q..DS.SAFYNKTSNAV.ASYIVAY...QAKKPH.IV.QLV..CAK.MM.LVLGEEAARK.NDISV.N
Retrocopy GLQNLDSISAFYNKTSNAVCASYIVAYRLAQAKKPHAIVQQLVFSCAKQMMWLVLGEEAARKPNDISVFN

Parental  DTLSRRINELSQNISEQVVDEIKTSPLFTIQLDESTDVALCSRLLVFARYITEGDFKDEFLFCKTLDTTT
          DT.SRRINE.SQNI.EQVVDEIK.SPLF.IQLDE.T.VALCS.LLVFA.Y..EGDF.DEFLFCKTLDTT.
Retrocopy DTASRRINEISQNINEQVVDEIKKSPLFAIQLDELTNVALCSPLLVFA*YVVEGDFRDEFLFCKTLDTTK

Parental  KAQDMMEIVNNFFEV----WSGL-GVTTDGAPAMLSSRLGFQMLVKQHAPMVTGVHCFIHREALASKTLP
          K.QD.MEIVNN.FEV....W..L.GVTTDGA.AML.SR.GFQ.LVKQ.APMVTGVHCFIHRE.LASKTLP
Retrocopy KDQDVMEIVNNLFEVHGLAWVNLVGVTTDGASAMLGSRSGFQTLVKQCAPMVTGVHCFIHRETLASKTLP

Parental  DPLNAVFKGLVKVMNHIRSLALNTRLFKRFCLDMGSNFGNILIEREVGFISPGSRNILNRVFQLREKLDL
          D.LN.VFK.LVKV.NH..S.AL.TRLFKRFCLDMGS.F...L....V...S...RN.LNR.FQLRE.LDL
Retrocopy DQLNIVFKRLVKVVNHMKSSALSTRLFKRFCLDMGSDFDVLLFYTSVRWLS--ARNVLNRHFQLREELDL

Parental  FLQAQGKEEFRNVLTQSNLELAYLVDIFRILNKLNLQLQGKGANLFSHQSIVKAFLDKLELWIIRVEGNT
          FLQAQGKEEFRNVLTQSNLELAYLV.IF.ILNKLNL.LQGKGANLFSHQ.I.KAFL.KLELWI.RVEGN.
Retrocopy FLQAQGKEEFRNVLTQSNLELAYLVNIFGILNKLNL*LQGKGANLFSHQRIIKAFLEKLELWIVRVEGNN

Parental  LVQFPYVDAMLREKEAIRTQILHHLQKL----QGYFLEVDRTRDGLSFIRNPFTTDVNSVPEDLQEKFLD
          LVQFPYVDAMLREKEAIR.QIL.HL.KL....Q.YF.EVDRTRDGLSFIRNPFTTDVNSVPEDLQE.FLD
Retrocopy LVQFPYVDAMLREKEAIRMQILNHLRKLLDKFQQYFPEVDRTRDGLSFIRNPFTTDVNSVPEDLQEEFLD

Parental  LKNDFAAQ-DMYQQSTIEKFWASVIRSYQNLSAHAVRFLLPFASTYM-CEIGISCLLHVTIDERSRPVLL
          LKNDFAAQ...YQ.STI.KFW.S....Y.NLS.............Y..CE.G..CLLH.....R.R....
Retrocopy LKNDFAAQ<SLYQKSTIDKFWSSMTGCYPNLSPRSQISFAICINLYL>CETGFLCLLHGKSKQRNRLSVK

Parental  RRLKCS
          ....C.
Retrocopy SDIRCA

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_65 retrocopy.

TSS

Pelodiscus sinensis was not studied using FANTOM5 data.

Lab

retro_psin_65 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,