RetrogeneDB ID: retro_psin_21

Retrocopy location

• Organism: Chinese softshell turtle (Pelodiscus sinensis)
• Coordinates: JH205389.1:125895..127467(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPSIG00000001496
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPSIG00000007114
• Aliases: None
• Description: None

Sequence

>retro_psin_21
ATGGGACGCCAGCAGGAAGGACCAGAGCAAGTGGCTCCACGTGGGATGTTACTGGGAAGATCTGAAGGGCATGTTTCTCA
GAGTCCTGAGCACGGAGAGACCTGGGAGAGTCATAAGCCAGAAAGGGAGCAGAGAAACCATCCAGAGAAGGGACAGGGTA
AATCCAGTCACAGGAGCAGAAGGCTGGAAAGAAACACAGAAACCATTCAACAGAAAATCCCTCATCAACAAGCCCCCTAT
ACTTGCAGTGACTGTGCAACTCTTATTGAGCATCATAGAATCCACAGAGAGAAACCCTTCAACTGCTCTGACTGTGGGAA
AAGGTTCCGGGAGAGGTCGGAACTTGAAAGACACAGCAGAATCCACACACGGGATAAACCTTTTTACTGCTCTGACTGTG
GGAAAAGCTTCAGTTGGAACTCACATCTTTTGAGACATCAAAGAACTCACACATACGATAAACATTTTAACTGCTCTGAC
CTTGGGAAAAGCTTGAGTGACAGTTCAGACCTTGGTACACACAGGGGAATCCAAAGAGGAGTGAAACCCTTCAACTGCTC
CGACTGTGGGAAAAGCTTCAGATGGAACTCACATCTTTACAGACATCAGAGAACTCACACAGATGAGAAACATTTCAGCT
GCTCTGAGTGTGGGAAAAGCTTCAGTCAGCACTCAAATCTCATTAGACATAAGAGAGGCCACACAAGAGAAAAATCTTTC
AATTGCTCTGACTGCAGGAAAAGCTTCAGTGAGCATTCAGAACTTGTTAGACATAGGAGAATCCGCATAGGAGACAAACC
CTTCAGCTGTTCTGATGCTGCAAAATGCTTAGGTCAGAGCTCAGACCTAATTGAACATCATAGAATCCACATAGGAGAGA
AACCCTACAGCTGCTCTGACTGTGGGAAAAGCTTCAGTAAGAGGTCATACCTTGTCTCACACAGGAGAATCCACAGGGGA
GTGAAACCCTTCAGGTGCTCTGACTGTGGGAGAAGCTTCAGTCAGAACTCAACCCTGATTAAACATCAGAGAATTCACAC
TGGAGAGAAGCCTTTCAACTGCTCTCACTGTGGGAAAAGCTTCAATAGCAACGCACATCTTGTTAGGCATCAGAGAATCC
ACACAGGAGAGAAACCCTTCTCCTGCTCAGACTGTGGGAAAAGCTTCAGTCAGAGGTCAGACCTTGTTAGGCATTGGAGA
GTCCAAACCGGGGAGAAATTCTTTAGCTGCTCTGACTGTGGGAAAAGCTTCAGTAGTTCCTCATATCTTATTAAACATAG
AAAAATCCACACAGGAGAGAGACCTTTCAACTGCTCTGACTGTGGGAAAAGCTTCAGTCAGAGGTCAAGCCTTGTTAGGC
ATAGGAGAATCCACACAGGGGAGAAACCCTTCAGCTGTGGTGACTGTGGGAAGAGCTTCAGGGACAAGTCAGACTTGGTT
AAACATAGGAGAATCCACACAGAAAAAAAACCTTTCAGCTGCTCTAACTGTGGGGGAAACTTCAGTAGGCGCTCAAGTTT
TATAAGTCAGGAGAGAAACCAGACTGAGTTGGAAGCCCTTCATCTGCTCTGA

Alignment

ORF - retro_psin_21 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.33 %
• Parental protein coverage: 75.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GMLSENHEKSLQQEIIEKEGESEWLQSPEQGETCESQCTPQRWQGNYTGEGQGKSSHRSKGVKTNTETVQ
          G...E..E............E....QSPE.GET.ES...P.R.Q.N....GQGKSSHRS.....NTET.Q
Retrocopy GRQQEGPEQVAPRGMLLGRSEGHVSQSPEHGETWESH-KPEREQRNHPEKGQGKSSHRSRRLERNTETIQ

Parental  QKIPHQQSPCTCSDCATLFKHEKEHTGEKPFKCSFCGTSFSESSDLDKHNKSHTGEKPFSCSDCGKSFSH
          QKIPHQQ.P.TCSDCATL..H...H..EKPF.CS.CG..F.E.S.L..H...HT..KPF.CSDCGKSFS.
Retrocopy QKIPHQQAPYTCSDCATLIEHHRIHR-EKPFNCSDCGKRFRERSELERHSRIHTRDKPFYCSDCGKSFSW

Parental  SSNFVAHRRTHTGEKPFSCSDCGKSFSQRSHLLRHRRSHTGEKPFSCSDCRKSFKERSDLVKHERSHTGE
          .S....H.RTHT..K.F.CSD.GKS.S..S.L..HR....G.KPF.CSDC.KSF...S.L..H.R.HT.E
Retrocopy NSHLLRHQRTHTYDKHFNCSDLGKSLSDSSDLGTHRGIQRGVKPFNCSDCGKSFRWNSHLYRHQRTHTDE

Parental  KPFSCSDCGKSFSCSSHRIEHWRSHRGEKPYSCSDCGKSFSLQSNLARHKRIHKGEKPFSCSDCGKSFSC
          K.FSCS.CGKSFS..S..I.H.R.H..EK...CSDC.KSFS..S.L.RH.RI..G.KPFSCSD..K....
Retrocopy KHFSCSECGKSFSQHSNLIRHKRGHTREKSFNCSDCRKSFSEHSELVRHRRIRIGDKPFSCSDAAKCLGQ

Parental  SSHLIIHWRSHKGEKPFTCSDCGKSFSLQSNLTRHKRIHKGEKPFSCSDCGKCFSRRSHLIDHQKAHTGE
          SS.LI.H.R.H.GEKP..CSDCGKSFS..S.L..H.RIH.G.KPF.CSDCG..FS..S.LI.HQ..HTGE
Retrocopy SSDLIEHHRIHIGEKPYSCSDCGKSFSKRSYLVSHRRIHRGVKPFRCSDCGRSFSQNSTLIKHQRIHTGE

Parental  KPFTCSDCGKSFSQRSHLIRHRRTHTGEKPFTCSYCRKSFKERSDLAKHEGIHTREKTFTCSDCGKYFGQ
          KPF.CS.CGKSF....HL.RH.R.HTGEKPF.CS.C.KSF..RSDL..H....T.EK.F.CSDCGK.F..
Retrocopy KPFNCSHCGKSFNSNAHLVRHQRIHTGEKPFSCSDCGKSFSQRSDLVRHWRVQTGEKFFSCSDCGKSFSS

Parental  HSDLIDHQIKHTRETLHNCSDCGKAFKQRSHFIQHKRAHTGEKPFSCSDCRKSFKERSDLVKHERSHTVE
          .S.LI.H...HT.E...NCSDCGK.F.QRS....H.R.HTGEKPFSC.DC.KSF...SDLVKH.R.HT..
Retrocopy SSYLIKHRKIHTGERPFNCSDCGKSFSQRSSLVRHRRIHTGEKPFSCGDCGKSFRDKSDLVKHRRIHTEK

Parental  KPFSCSDCGKSFSQRSHLVRHKRIHT
          KPFSCS.CG..FS.RS......R..T
Retrocopy KPFSCSNCGGNFSRRSSFISQERNQT

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_21 retrocopy.

TSS

Pelodiscus sinensis was not studied using FANTOM5 data.

Lab

retro_psin_21 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	ENSPSIG00000007114	1 retrocopy	retro_psin_21 ,