RetrogeneDB ID: retro_psin_47

Retrocopy location

• Organism: Chinese softshell turtle (Pelodiscus sinensis)
• Coordinates: JH208382.1:141906..143457(-)
• 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_47
TATCTCGAAAAGTGTCACCCCAAATTGTTGCAAAAGGATAAAGATTATTTTGGGCGGTGGTTATCAGGTCTGAAATGGCA
GCGCGTCGACTCAACAAGTGCATTTTACAATAAGACAAGCAATGCAGTGCGCACTTCCTATGTTGTTGCAGACAAAGTTG
CACAGGCCAAGAAGCCTCATACCATTGTAGAGCAACTTGTGCTCTCCTGTGCAAAAGAGATGGTGCGGCTTGTTCTTGGC
GAGGAAGCAGCAAAGAAGCTAAATGATATATCTGTCTCTAACGAAACAGTATCAAGACGGATAAATGAGATATCACAGAA
CATCAGTGAACAAGGTGTAGATGAAATAAAGAAGTCTCCATTGTTTGCCATACAATTGGATGAATCGACCGATGTCGCGT
TGTGCTCTCAGCTATTGGTGTTCACATGATACATGGTTGAGGGAGACTTCAAAGATGAGCTTCTCTTTTGTAAGACTCTT
TATACCACTACAAAGGTTCAGGATGTGATGGAAATTAACAATTTCTTTGAAGTACATGGTCTGGATTGGGTAAATCTTGT
AGGTATCACCAATGATGGTGCACCAGCTATGCTGGGTTCAAGATCGGGCTTCCAAACGCTGGTGAAACAGCGTGCTCCAA
TGGTAACCGGAGTTCATTGCTTCATTCATAGGGAAGCTTTGGCATCAAAAACATTGCCTGATCAACAGAATACCGTTTTC
AAAAGGTTGGTGAAAGTGGTGAATCACATCAAATCATCGGCTCTGAACACCAAGCTGTTCAAAAGATTTTGCCTGGAAAT
GGGTTCTGACTTTGATATGTTCCTGTTCTACACTTCCGTATGGTGGTTGTCAGCAGGGAACGTACTCAACAGAGTTTTTC
AGTTGAGAGAGGAGTTGGATTTATTTCTGCAGGCTCAAGGAAAAGAGGAATTCCGTAATGTGCTGATGCAGTCAAATTTA
GAACTTGGGTATCTTGTCGATATTTTTGGAATCTTGAACAAACTGAATCTTCAGCTGCAAGGGAAAGGTGCAAATTTGTT
CTCTCACCAAAGCATCATCAAGGCTTTTCTTGACAAATTGGAACTCTGGAACATAAGAGTCAAAGGCAGTAATTTGGTTC
AATTTCCATATGTGGATGCCGTGCTCAGGGAAAAGGAAGCCATTCGGACACAAATTCTCGATCATTTACGGAAACTACAA
GATGAATTCCAGTGATACTTTCCAGAGGTGGACAGGACAAGGGATGGATTATCTTTCATCAGGAATCCATTTACAAGAGA
TGTTAATAGTGTTCCAGAGGATCTGCAGGAGGAATTCTTGCATCTGAAAAATCATTTTGTGTCTCAAGACGTGTACCAGC
AGTCTACCATAGAGAAATTTTGGGCCAGCATGACCGGGAGTTACCCAAAGCTGTCAGCACACACAGTCAGATTTCTTTTG
CCATTTGCATCAATTTATATGTGTGAGACTGGATTTTCGTGTTTGTTGCACGTTAAGTCCAAACAGAGGAATCGGCTTGC
AGTGGAAAGCAATATTCATTGTGCATTATCA

Alignment

ORF - retro_psin_47 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.15 %
• Parental protein coverage: 91.85 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  HLEKCHPNLLQKDED----YFECLKRQHFDSTSAFYNKTSNAVRASYIVAYKVTQAKKPHTIVEQLVLPC
          .LEKCHP.LLQKD.D........LK.Q..DSTSAFYNKTSNAVR.SY.VA.KV.QAKKPHTIVEQLVL.C
Retrocopy YLEKCHPKLLQKDKDYFGRWLSGLKWQRVDSTSAFYNKTSNAVRTSYVVADKVAQAKKPHTIVEQLVLSC

Parental  AKEMMRLVLGEEAARKLNDISVSNDTLSRRINELSQNISEQVVDEIKTSPLFTIQLDESTDVALCSRLLV
          AKEM.RLVLGEEAA.KLNDISVSN.T.SRRINE.SQNISEQ.VDEIK.SPLF.IQLDESTDVALCS.LLV
Retrocopy AKEMVRLVLGEEAAKKLNDISVSNETVSRRINEISQNISEQGVDEIKKSPLFAIQLDESTDVALCSQLLV

Parental  FARYITEGDFKDEFLFCKTLDTTTKAQDMMEIVNNFFEV----WSGL-GVTTDGAPAMLSSRLGFQMLVK
          F..Y..EGDFKDE.LFCKTL.TTTK.QD.MEI.NNFFEV....W..L.G.T.DGAPAML.SR.GFQ.LVK
Retrocopy FT*YMVEGDFKDELLFCKTLYTTTKVQDVMEI-NNFFEVHGLDWVNLVGITNDGAPAMLGSRSGFQTLVK

Parental  QHAPMVTGVHCFIHREALASKTLPDPLNAVFKGLVKVMNHIRSLALNTRLFKRFCLDMGSNFGNILIERE
          Q.APMVTGVHCFIHREALASKTLPD..N.VFK.LVKV.NHI.S.ALNT.LFKRFCL.MGS.F...L....
Retrocopy QRAPMVTGVHCFIHREALASKTLPDQQNTVFKRLVKVVNHIKSSALNTKLFKRFCLEMGSDFDMFLFYTS

Parental  VGFISPGSRNILNRVFQLREKLDLFLQAQGKEEFRNVLTQSNLELAYLVDIFRILNKLNLQLQGKGANLF
          V...S.G..N.LNRVFQLRE.LDLFLQAQGKEEFRNVL.QSNLEL.YLVDIF.ILNKLNLQLQGKGANLF
Retrocopy VWWLSAG--NVLNRVFQLREELDLFLQAQGKEEFRNVLMQSNLELGYLVDIFGILNKLNLQLQGKGANLF

Parental  SHQSIVKAFLDKLELWIIRVEGNTLVQFPYVDAMLREKEAIRTQILHHLQKLQG----YFLEVDRTRDGL
          SHQSI.KAFLDKLELW.IRV.G..LVQFPYVDA.LREKEAIRTQIL.HL.KLQ.....YF.EVDRTRDGL
Retrocopy SHQSIIKAFLDKLELWNIRVKGSNLVQFPYVDAVLREKEAIRTQILDHLRKLQDEFQ*YFPEVDRTRDGL

Parental  SFIRNPFTTDVNSVPEDLQEKFLDLKNDFAAQDMYQQSTIEKFWASVIRSYQNLSAHAVRFLLPFASTYM
          SFIRNPFT.DVNSVPEDLQE.FL.LKN.F..QD.YQQSTIEKFWAS...SY..LSAH.VRFLLPFAS.YM
Retrocopy SFIRNPFTRDVNSVPEDLQEEFLHLKNHFVSQDVYQQSTIEKFWASMTGSYPKLSAHTVRFLLPFASIYM

Parental  CEIGISCLLHVTIDERSRPVLLRRLKCSIA
          CE.G.SCLLHV....R.R........C...
Retrocopy CETGFSCLLHVKSKQRNRLAVESNIHCALS

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_47 retrocopy.

TSS

Pelodiscus sinensis was not studied using FANTOM5 data.

Lab

retro_psin_47 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,