RetrogeneDB ID: retro_psin_49

Retrocopy location

• Organism: Chinese softshell turtle (Pelodiscus sinensis)
• Coordinates: JH208680.1:10676348..10676786(-)
• Located in intron of: ENSPSIG00000010156

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPSIG00000010727
• Aliases: None
• Description: None

Sequence

>retro_psin_49
TCCCTTCTTCTCTGCACATTGGTGACAGTGGCCTATTTTACCTTTTATTGTGCTGGAAGGCTAAGGCTAGCGAGAATTCA
GATTGAGAGATACCGACAATTAACAGATGTAAAGAAAGCTATTGGTCAACTTGAGCTTCGCATATTAAAAGAGGGTGACA
AGGAAGCTGATACAGATGCAGAGAACTGTGTAGTGTGTCTGGAAGTATACAAGCCCAAAGACGTAGTACGCATTTTAAGA
TGCAGCCATATTTTCCATAGGTTGTGCATTGACCCTTGGCTGCTACAGCACAGAACATGCCCAGTGTGCAAATGTGACCT
TCTCAAACCTAGTGAAGCTGATCTGCCTGTCAGAAATGAAGCAGAATCTTTACAAGCTGTAGTGCCAAATGAAGCTCTTG
ACACCACTTTGCTTAATGAAGAAGATAGTCATAATGAA

Alignment

ORF - retro_psin_49 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.43 %
• Parental protein coverage: 55.02 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SFFIVTAATVGYFIFYSARRLRVARAQNRRERQLKADAKKAIGQLELRTLKQGDKEIGPDGDSCAVCIDI
          S....T..TV.YF.FY.A.RLR.AR.Q..R.RQL..D.KKAIGQLELR.LK.GDKE...D...C.VC...
Retrocopy SLLLCTLVTVAYFTFYCAGRLRLARIQIERYRQL-TDVKKAIGQLELRILKEGDKEADTDAENCVVCLEV

Parental  YKPNDVVRILTCNHLFHKTCIDPWLLEHRTCPMCKLDILKALGIVEVDIEGEPESLQTTVSNEASNRASL
          YKP.DVVRIL.C.H.FH..CIDPWLL.HRTCP.CK.D.LK...........E.ESLQ..V.NEA.....L
Retrocopy YKPKDVVRILRCSHIFHRLCIDPWLLQHRTCPVCKCDLLKP-SEADLPVRNEAESLQAVVPNEALDTTLL

Parental  NEEDNRSE
          NEED...E
Retrocopy NEEDSHNE

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_49 retrocopy.

TSS

Pelodiscus sinensis was not studied using FANTOM5 data.

Lab

retro_psin_49 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryctolagus cuniculus	ENSOCUG00000012328	1 retrocopy	retro_ocun_37,
Pelodiscus sinensis	ENSPSIG00000010727	1 retrocopy	retro_psin_49 ,
Sus scrofa	ENSSSCG00000012551	1 retrocopy	retro_sscr_597,
Tursiops truncatus	ENSTTRG00000007536	1 retrocopy	retro_ttru_6,