RetrogeneDB ID: retro_psin_29

Retrocopy location

• Organism: Chinese softshell turtle (Pelodiscus sinensis)
• Coordinates: JH205794.1:370335..371791(-)
• 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_29
TCGACAAGTGCATTCTATAATAAGACAAGCAATGCAGTGCGCGCTTCCTACATTGTTGTATACAAAGTTGCACAGGCCAA
GAAGCCTCATACCACTGTTGAGTAACTTGTGTTCCCCTGTGCAAAAGAGATGGTGTGGTTTGTTCTTGGCGAGGAAGCAG
CAAGGAAGCTAAATGATATCTCTGTCTCTAACGACACAGTATCGAGACGGATAAATGAGATATCACAGAACATCAGTGAA
CAAGTTGTGGATGAAATAAAGTCTTCATTGTTTGCCATACAATTGTATGAATTGACCGACGTCACATTGTGCTCTCAGCT
ATTGGTGTTTGCACGATACATGGTTGAGGGAGGCTTCAAAGATGAGTTTCTTTTTGTAAGACTCTTGATACCACCACAAA
GACTCAGGATGTGATGGAAATTGTTAACAATTTATTTGAAGTACATAGTCTGGATTGGGTAAATCTAGTGGGCGTCACCA
CTGATGGTGCACCAGCCATGCTGGGTTCAAGATTGGGCTTCCAAACGCTGGTGAAACAGCACGCTTCAGTGATAACCGGA
GTTCATTGCTTCATTCATAAGGAAGCTCTGGCATCAAAAACATTGCCTGATCAACTGAATGCCATTTTCAAAGGGTTGGT
GAAAGTGGTGAATAACATCAAATCATCGGCTCTGAACACCAGGCTGTTCAAAAGATTTGGCAGGACATGGGTTCCGACTT
TGATGTGTTGCTGTTCTACACTTCTGTATTGTGGTTGTCAGCAGGGAATGTACTCAGAGTTTTTCAATTGAGAGAGGAGT
TGGATTTATTTCTCCAGGCTCAAAGGAAAGAGGAATTCCGAAATGTGCTGATGCAGTCAAATTTAGAACTTGCGTATCTT
GTCGATATTTTTAGAATCTTGAACAAACTGAATCTTCAGCTGCAAGGGAAAGGTGCAAATCTGTTCTCTAACCAAAGCAT
CATCAAGGCTTTTCTTGACAAATTGGAACTCTGGATCGTAAGAGTAAAAGGCAATAATTTGGTTCCATTTCCATATGTGG
ATGCAATGCTTAGGGAAAAAGAAGCCATTCGGACACAAATTCTCAATCATTTACGGAAGCTACGAGACGAATTCCAACGA
TACTTTCTGGAGGTGGACAGGACAAGGGATGGATTATCTTTCATCAGGAATCCATTTATAACAGATGGTAATAGTGTTCC
AGAGCATCTGCAGGAGGAATTCTTGGATCTGAAAAATGATTTTGCAGCTTAAGACGTGTACCAGCAGTCTACCATAGAGA
AATTTTGGGCCAGCATGACTAGGAGTTACCCAAATCTGCCAGCACATACAGACAGATTTCTTTTGCCATTTGCATCAACT
TATGTGAGAGAGACTGGATTTTCGTGTCTGTTGCACATTAAATCCAAACAGAGGAATCGGCTTGCAGTGGAAAGCGATAT
TCATTGTATAATATCA

Alignment

ORF - retro_psin_29 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.64 %
• Parental protein coverage: 87.14 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  STSAFYNKTSNAVRASYIVAYKVTQAKKPHTIVEQLVLPCAKEMMRLVLGEEAARKLNDISVSNDTLSRR
          STSAFYNKTSNAVRASYIV.YKV.QAKKPHT.VE.LV.PCAKEM...VLGEEAARKLNDISVSNDT.SRR
Retrocopy STSAFYNKTSNAVRASYIVVYKVAQAKKPHTTVE*LVFPCAKEMVWFVLGEEAARKLNDISVSNDTVSRR

Parental  INELSQNISEQVVDEIKTSPLFTIQLDESTDVALCSRLLVFARYITEGDFKDEFLF-CKTLDTTTKAQDM
          INE.SQNISEQVVDEIK.S.LF.IQL.E.TDV.LCS.LLVFARY..EG.FKDEFLF.CKTLDTTTK.QD.
Retrocopy INEISQNISEQVVDEIKSS-LFAIQLYELTDVTLCSQLLVFARYMVEGGFKDEFLF<CKTLDTTTKTQDV

Parental  MEIVNNFFEV----WSGL-GVTTDGAPAMLSSRLGFQMLVKQHAPMVTGVHCFIHREALASKTLPDPLNA
          MEIVNN.FEV....W..L.GVTTDGAPAML.SRLGFQ.LVKQHA...TGVHCFIH.EALASKTLPD.LNA
Retrocopy MEIVNNLFEVHSLDWVNLVGVTTDGAPAMLGSRLGFQTLVKQHASVITGVHCFIHKEALASKTLPDQLNA

Parental  VFKGLVKVMNHIRSLALNTRLFKRF-CLDMGSNFGNILIEREVGFISPGSRNILNRVFQLREKLDLFLQA
          .FKGLVKV.N.I.S.ALNTRLFKRF...DMGS.F...L....V...S.G..N.L.RVFQLRE.LDLFLQA
Retrocopy IFKGLVKVVNNIKSSALNTRLFKRF<WQDMGSDFDVLLFYTSVLWLSAG--NVL-RVFQLREELDLFLQA

Parental  QGKEEFRNVLTQSNLELAYLVDIFRILNKLNLQLQGKGANLFSHQSIVKAFLDKLELWIIRVEGNTLVQF
          Q.KEEFRNVL.QSNLELAYLVDIFRILNKLNLQLQGKGANLFS.QSI.KAFLDKLELWI.RV.GN.LV.F
Retrocopy QRKEEFRNVLMQSNLELAYLVDIFRILNKLNLQLQGKGANLFSNQSIIKAFLDKLELWIVRVKGNNLVPF

Parental  PYVDAMLREKEAIRTQILHHLQKL----QGYFLEVDRTRDGLSFIRNPFTTDVNSVPEDLQEKFLDLKND
          PYVDAMLREKEAIRTQIL.HL.KL....Q.YFLEVDRTRDGLSFIRNPF.TD.NSVPE.LQE.FLDLKND
Retrocopy PYVDAMLREKEAIRTQILNHLRKLRDEFQRYFLEVDRTRDGLSFIRNPFITDGNSVPEHLQEEFLDLKND

Parental  FAAQDMYQQSTIEKFWASVIRSYQNLSAHAVRFLLPFASTYMCEIGISCLLHVTIDERSRPVLLRRLKCS
          FAA.D.YQQSTIEKFWAS..RSY.NL.AH..RFLLPFASTY..E.G.SCLLH.....R.R........C.
Retrocopy FAA*DVYQQSTIEKFWASMTRSYPNLPAHTDRFLLPFASTYVRETGFSCLLHIKSKQRNRLAVESDIHCI

Parental  IA
          I.
Retrocopy IS

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_29 retrocopy.

TSS

Pelodiscus sinensis was not studied using FANTOM5 data.

Lab

retro_psin_29 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.

---

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,