RetrogeneDB ID: retro_psin_50

Retrocopy location

• Organism: Chinese softshell turtle (Pelodiscus sinensis)
• Coordinates: JH208874.1:16730..17270(+)
• Located in intron of: ENSPSIG00000009494

Retrocopy information

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

Parental gene information

• Parental gene symbol: C9orf171
• Ensembl ID: ENSPSIG00000006088
• Aliases: None
• Description: chromosome 9 open reading frame 171 [Source:HGNC Symbol;Acc:33776]

Sequence

>retro_psin_50
GCTGAGTTAGGAAAGATTCGCCCCAGATGCACACAGTTGCCTGGATCTGATTTTGTGTATGGACTCACCTATCGTAGAGC
TGATGGGGGAGTTCCTGAAGCCATAGGCCACTGGAACACCATAAAACGCATTATCAAGGCCCCAAAGCATCTGCCGCGTA
ATTTTATTGCCATGAACCGTGGAGCAGTCATAGCTGGTCTTGTCACAGCCAAAGAACACTACCGGTACCGCCAAACCCAC
GACATCCACTGTCCAGAAGATGACGAGCGTCACTTTAAAAGGGACCCACCACGCCTCCCTGATGCCATGAGCTATGGAAT
GCCAGCTCGCCCATCCACCCCTATCAGAGATGTTCTCCAGCACAAATACAAGGATCTTTGGATGGAGGCACAGAGAACAG
CGACTCAGGATCATCATAAGGCAAAACAGAAAATCGTGCAGCCAGGGAAGATATACGAAACACATTCCACTATGCTGAAG
AAATACAAACAGCCTATGAAGCTAGATCCGCTTTGGCATTTGCCCCACTTTGAGAAAGTG

Alignment

ORF - retro_psin_50 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.44 %
• Parental protein coverage: 75. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AELGKPRRSCYTLPGYDFAYGLYLHGDDGGVPEAIGHWHSMKPKPPSPREMQRDYKAMNRGALKAGYVTA
          AELGK.R..C..LPG.DF.YGL.....DGGVPEAIGHW...K.....P....R...AMNRGA..AG.VTA
Retrocopy AELGKIRPRCTQLPGSDFVYGLTYRRADGGVPEAIGHWNTIKRIIKAPKHLPRNFIAMNRGAVIAGLVTA

Parental  REFNLYRQWKDIRCNEDDESRFKRAPPKVPPDMTYGMLARPSTPFFDLLQHRYKEVWMEQQRAIVVAQQV
          .E...YRQ..DI.C.EDDE..FKR.PP..P..M.YGM.ARPSTP..D.LQH.YK..WME.QR........
Retrocopy KEHYRYRQTHDIHCPEDDERHFKRDPPRLPDAMSYGMPARPSTPIRDVLQHKYKDLWMEAQRTATQDHHK

Parental  DKKKVTAKRKVYETRTSLLRKQPPPVKLDSLWHMPHFQKV
          .K.K.....K.YET....L.K...P.KLD.LWH.PHF.KV
Retrocopy AKQKIVQPGKIYETHSTMLKKYKQPMKLDPLWHLPHFEKV

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_50 retrocopy.

TSS

Pelodiscus sinensis was not studied using FANTOM5 data.

Lab

retro_psin_50 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Pelodiscus sinensis	ENSPSIG00000006088	1 retrocopy	retro_psin_50 ,