RetrogeneDB ID: retro_psin_53

Retrocopy location

• Organism: Chinese softshell turtle (Pelodiscus sinensis)
• Coordinates: JH209699.1:2470523..2471010(+)
• Located in intron of: ENSPSIG00000016663

Retrocopy information

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

Parental gene information

• Parental gene symbol: HTRA2
• Ensembl ID: ENSPSIG00000004826
• Aliases: None
• Description: HtrA serine peptidase 2 [Source:HGNC Symbol;Acc:14348]

Sequence

>retro_psin_53
GAGCACAATCAGACCTATGCTGCTAGGGATTTCAGGAACTCAGGGAGGCCCCTCAGCTATCTGGGTGGTGAGTGACTGGG
GGGAACACAATGAAGGTGATTTCAGGTATCTCCTTCGACATCCCCTTGGACTGGCCATGGAAATTCTCCCCGAAGGGGGA
ACAGCGCAGGAGCTCCTGGTTCGGCAGTACGGAGATGAAGTGCCACTACGTCGGTGTGATGTACTAATACTGACCCCGTG
TCCTGCCTGAACGCAAGCACTGAGACCCCCGCTTCCCTGATGTCTCGAATGGGGTCCTGATCCCCAAGGTGATCGGTGGC
TCCCTGGCCCATTAGGCAGGTTTGAAGGCTGGTGATGTGCAGGAGATTAATGGCAGGCAGCGTGGTGCGTGGAGGACATC
TGTGGGGCTGCATGGACGCAGAGCAGTCTGGCCATGCTGGAGCTGCACGCCCATGACATGACTCTGGTGAACGTCAGCCC
CGAGGTT

Alignment

ORF - retro_psin_53 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.07 %
• Parental protein coverage: 51.24 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EYIQTDAAIDFGNSGGPLVNLDGE-VIGVNTMKVTSGISFAIPSDRLREFLQKGEQRKSSWFGSTEIKRR
          E..QT.AA.DF.NSG.PL..L.GE.V.G.NTMKV.SGISF.IP.D....F..KGEQR.SSWFGSTE.K..
Retrocopy EHNQTYAARDFRNSGRPLSYLGGE<VTGGNTMKVISGISFDIPLDWPWKFSPKGEQRRSSWFGSTEMKCH

Parental  YIGVMMLTLTPSILAELKLRDPSFPDVSYGVLIHKVIIGSPAHQAGLKAGDVVQEING-QAVRRAEDIYE
          Y.GV.M....P..L.E.K..DP.FPDVS.GVLI.KVI.GS.AH.AGLKAGDV.QEING.QA....EDI..
Retrocopy YVGV-MY*Y*PRVLPERKH*DPRFPDVSNGVLIPKVIGGSLAH*AGLKAGDV-QEING<QAAWCVEDICG

Parental  AVRTHSNLAMLVQRSHDMLLVNVSPEV
          A..T.S.LAML....HDM.LVNVSPEV
Retrocopy AAWTQSSLAMLELHAHDMTLVNVSPEV

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_53 retrocopy.

TSS

Pelodiscus sinensis was not studied using FANTOM5 data.

Lab

retro_psin_53 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	ENSPSIG00000004826	1 retrocopy	retro_psin_53 ,