RetrogeneDB ID: retro_psin_58

Retrocopy location

• Organism: Chinese softshell turtle (Pelodiscus sinensis)
• Coordinates: JH210461.1:281032..281737(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPSIG00000011044
• Aliases: None
• Description: None

Sequence

>retro_psin_58
CTTAAATTTGGGTTTACTACAAACAGAAGTGTGCCCCCTTTTCCACTTTGCGTGATTTGCTGTGAGACTTTATCTAACCA
CTATATGAAACCGTCTCTGTTGAAACGACATCTTAATACAAAGTATTCTACAATAAAAGATAAATCAACTGAATGTTTTA
CAAGAAAACGTGAAGGTATCAATAGATCTATTGCTGTTATGAAAGTGTACGCAAAAAGCTCTCAACAAGCTTTACAAGTT
TCTTATGAAATCACACAAATGATAGCAAAAACAAAGAAACCACATACCATTGCTGAAAAGCTTGTTATTCCAGCTTCTAT
CAGAATCGCTGAAATTATGTTAAGTGAAAAAGAAGTCATCAAAATTAAAAATATCCCACATTCGAATGATACAAAAAGAA
GAAGAATTGACATGATGGCAGAAGACATAATAAAACAAATTACTGAAAAAATTATTCAGAAGAAACAGTTCGCTTTACAA
CTTAACAAATCAACAGATACTTCCAATTGCGCGCCATTAATGGTGTTTGTCAGATACATTGATGACGAAGATGAAAAAGG
AATAAGTGAGCAAATATGCTGCTGTAAAGAATTTGACAGTAAAACAACGGGGGAAGACATTTTTAACTTGTTAAATGAAC
AGATTTTGAAACACGGATTATCATGGGAGTGGTGCATATCTGTGTGTACAGACGGAGCAGCAGCA

Alignment

ORF - retro_psin_58 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.17 %
• Parental protein coverage: 53.41 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LKFGFTTNGSIPPLPFRVICCETLSNHCMKPSLLSPCRRTKHPTLKDKSIEYFTRKGEGINISCSAMKVY
          LKFGFTTN.S.PP.P..VICCETLSNH.MKPSLL.....TK..T.KDKS.E.FTRK.EGIN.S...MKVY
Retrocopy LKFGFTTNRSVPPFPLCVICCETLSNHYMKPSLLKRHLNTKYSTIKDKSTECFTRKREGINRSIAVMKVY

Parental  AKSSQQALQTSYEIAQMIAKTKKPHTIAEKLVIPASIRIAVIMFSEKEV-KIKNIAHSNDT-IRRIDEMM
          AKSSQQALQ.SYEI.QMIAKTKKPHTIAEKLVIPASIRIA.IM.SEKEV.KIKNI.HSNDT..RRID.M.
Retrocopy AKSSQQALQVSYEITQMIAKTKKPHTIAEKLVIPASIRIAEIMLSEKEVIKIKNIPHSNDTKRRRIDMMA

Parental  EDIRKQITVKIIQKKQFTLQPNESTDISNCTQLMVFVRYINDEDEK----EFCC-KEVDIKTTGEEIFNL
          EDI.KQIT.KIIQKKQF.LQ.N.STD.SNC..LMVFVRYI.DEDEK......CC.KE.D.KTTGE.IFNL
Retrocopy EDIIKQITEKIIQKKQFALQLNKSTDTSNCAPLMVFVRYIDDEDEKGISEQICCCKEFDSKTTGEDIFNL

Parental  LNEQI-KYRSSWEWCIPVCTDRAAA
          LNEQI.K...SWEWCI.VCTD.AAA
Retrocopy LNEQILKHGLSWEWCISVCTDGAAA

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_58 retrocopy.

TSS

Pelodiscus sinensis was not studied using FANTOM5 data.

Lab

retro_psin_58 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 3 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Gasterosteus aculeatus	ENSGACG00000003664	1 retrocopy	retro_gacu_23,
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 ,