RetrogeneDB ID: retro_psin_14

Retrocopy location

• Organism: Chinese softshell turtle (Pelodiscus sinensis)
• Coordinates: JH208050.1:142628..145469(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPSIG00000000640
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPSIG00000004827
• Aliases: None
• Description: None

Sequence

>retro_psin_14
ATGAAGGAACTGACGCTTACTGACATCTCGGTGTTTCCGACTCGGGATGTGAGTTTCTCGCCTGCAGTTTCCTCCCTGAG
ACTCAGGGTGTCGCTGTTGGCCAACGCCGAGCCAGGGCTGCAGCCGGGAACCGAGCCGAGCCCCTTGCAAAGCTCCGCAC
GGAGCAGATCTCCGGAGAAACGCAGCAGAGAGACAGTGTCGCCGAAACACCAAACCCTCCCTCGGATCGCTGCAATCCGG
CCGGGAAACAGCCGCCATTTCCTCTCACTACGGACCCCGGCACTCCTACAAGCGCAGGGAATTTGGAATGTAGGATCGAT
CACAAGAAAAGCGGCGAGAAAACAGAGACGGGAGATGGAGACCAGGCGCCGGGCGGCCCCACGGCAAGTACTGCTCCTCG
CCTGCTTCTTGCCTTTGTTCTGCCGCGCGGCCCCGGAGCAGACTCGCTACTCGATCCCCGAGGAAATGGCCAAAGGCTCC
CTCGTGGGGAACCTCGCCCAGGATCTGGGGCTGGAGCTGAGGGAGCTGCCGCTGCGGAAGCTCCGTGTCAGTTCGGAACA
GCAGCACTTCAGTGTGAATGGGGAGAACGGGGACTTGTCTGTGAATGGCCGCATAGACCGGGAGGAGATCTGCGGGAAAT
CACCGACTTGTTTCCTAAATGTAGAAGTTGTGGTTGAAAACCCTTTGAACGTTTTCCACCTGAATGTCGCAGTCCAGGAC
ATTAACGATAATGCACCGCGGTTTGTTAAAAATACGGTTGATTTAGAAATTAATGAATTCGCACAGCCTGGTGCGCGATT
TCCTCTAGAACCTGCTCAAGATCCCGATGTTGGAGCTAATTCGCTGCAGAGCTACCAGCTCAGTCCAAATTCATGCTTTA
GCTTGAAATTGAAGGAAAATCCAGCTGGGAAAAAACAAGCAGAATTAGTGTTAGAGAAAGCTTTGGATAGAGAGAAGCAG
AGTTACCATCACTTGGTTCTGAGGGCTGTGGATGGGGGAGATCCCGTCCGCACTGGAACAGTTCAGATTAACATCAGTGT
CACTGACGCTAATGACAATGCCCCCGCCTTCTCCGAAGAGGTCTACAAAGTCAGCCTGAAGGAAAATCTACCGAATGACT
CCTTAGTGCTTCAGGTTAGAGCCACTGATAAAGATGAGGGCACAAATGCGAAAATAGCATATTCTTTCAGCAACATACCG
CAGAGTGCAAGACAGCTCTTCAGCTTAGCTTCCGATGGAACAATCACAACAAAAGGGTCTCTGGATTTTGAAGAGGCACA
TAATTACATCCTGGGTGTAGAAGCCCGGGATGGCGGCGGTCTGACAGGCCACTGCAACGTTCACATAGAACTTCTGGATG
AGAACGACAATAGTCCCGAAGTGACCTTGACATCCCTGTTTAGTCCCATTCCCGAAGACTCGGTGCCCGGGACAGTGATC
GCGCTGATCAAAGCCCGGGACCCAGACGATGGAGGAAATGAAGAAGTCACGTGTCGCATTCAAGATAATCTGCATTTCAA
AATAGTGTCCTCCTCCAGCAGCTACTACAAGCTGGTGACTGACAGCCCCCTGGACAGGGAGCGGGCCCCGGAGTACAACA
TCACAATCACGGCCACAGACAAGGGCTCCCCCCCGCTCTCCACCCAGAAAACCATCCTCTTGCAGATCTCGGATGTCAAT
GACAACGCCCCTGTCTTCGAGAAACCTTCCTACAGCGCCTACGTGCCCGAGAACAACCCCTCGGGGGCCTCCATTTTCAG
TGTCAAAGCCTCAGACCGGGATCTGGACGGCAACGCCCGGGTCACTTACTCCATCCTGCGCAGCAGCATCCAGGAGCTCC
CTGTCTCCTCCTACGTGTCCATCAACTCCCAGACCGGAGCGCTGTACGCGCAGCGCTCCTTCGACTACGAGCAGTTCCGG
GCGTTCGAGCTGCAAGTGAAGGCCCAAGACGGCGGGTCGCCGCCTCTCAGCAGCAACGTCACCGTCAGCGTGTTTATCCT
GGATCGGAACGACAACGCCCCTCGCATCCTGTATCCCTCGCTCGGGCCCGAGGGCTCGGCCGTGTTCGAGATGGTCCCTC
GCTCTGCCGAGGCGGGTTATCTGGTGACGAAGGTGGTGGCGGTGGATGCGGACTCGGGACACAACGCCTGGCTCTCCTAC
CATGTGCTGCAGGCCACGCAGCCGGCGCTCTTCCAGCTGGGGCTGCACAGCGGGGAGATCCGGACCGCGCGCGCCTTTGC
GGACAGAGATGCGGTGAAGCACCGGCTGGTCGCTCTGGTGAAGGACAACGGGCAGCCGCCTCTCTCCGCCACCGTGACTC
TGAGCCTGGTGTTCGCCGAGAACTTCCAAGAGGCTCTTCCGGAAATGAGCGATCGGTCGGCTGACTCGGCGCCACAGTCT
GATTTGCAGTTCTACTTGGTGTTGGCCTTGGCCTTGGTCTCGTTTCTGTTTCTGCTTTCAGTGATAGCGGTGATAGCCAT
AAGAGTTCGAAGTTCAAACAACTCCCCTTTTCTGCAGTATGCCAGGCCGGCTCTGTATTCCAATGATGATCCCAGATTCC
CGCCAGACTTCAAAGAAGGGACCTTGCCCTATTCCTATAACTTGTGCTTGGCTACAGACTGCGGGAAAAATGTATTTAAT
TTGCTCAAAAGTAGTGACCAAAACTTTACAGCTGATGATATCCTGGGGAATGACACCTCTGGGATTTTACTTGTGAATAA
TTCTGGTTCTGAAGGACCCAAATCCGGATCAGAAACTCTTCTTAAGGTGAGATTTTGCAATATCGATTTACGGTGTCTGT
TCTGTGATTCTGAATTAAATTATTCAGGCAATGAAGAATGA

Alignment

ORF - retro_psin_14 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.58 %
• Parental protein coverage: 89.53 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LLCWMLVTFWDAVSGQIRYSIPEETERGAFVGDVAKDLGLHAEQPSERGVRIVSGGRTQYFALNAESGHL
          LL...L..F..A...Q.RYSIPEE...G..VG..A.DLGL.......R..R..S....Q.F..N.E.G.L
Retrocopy LLACFLPLFCRAAPEQTRYSIPEEMAKGSLVGNLAQDLGLELRELPLRKLRVSS--EQQHFSVNGENGDL

Parental  ITAERIDRERICGRAGKCLLSCELIVEDTMKLYGVEVEITDINDNAPSFPTEEMELKVSETTAPGSRILL
          ....RIDRE.ICG....C.L..E..VE.........V...DINDNAP.F......L...E...PG.R..L
Retrocopy SVNGRIDREEICGKSPTCFLNVEVVVENPLNVFHLNVAVQDINDNAPRFVKNTVDLEINEFAQPGARFPL

Parental  PEAQDSDLGTNSIQSYQLSSDGHFSLDVQTGPDGVKHAELVLEKSLDREEQAVHTLILTATDGGDPVRSG
          ..AQD.D.G.NS.QSYQLS....FSL.....P.G.K.AELVLEK.LDRE.Q..H.L.L.A.DGGDPVR.G
Retrocopy EPAQDPDVGANSLQSYQLSPNSCFSLKLKENPAGKKQAELVLEKALDREKQSYHHLVLRAVDGGDPVRTG

Parental  TAQIRVTVLDANDNAPVFSQPVYTVSVWENVPAGSTILTVKATDLDEGVNKEIKYSFRKITDKASQIFRL
          T.QI...V.DANDNAP.FS..VY.VS..EN.P..S..L.V.ATD.DEG.N..I.YSF..I...A.Q.F.L
Retrocopy TVQINISVTDANDNAPAFSEEVYKVSLKENLPNDSLVLQVRATDKDEGTNAKIAYSFSNIPQSARQLFSL

Parental  DAKTGDITAMGNVNFEESALYEIEVQAQDGGGRFDKSKVVIEVSDVNDNAPEIAVRSLFSLVAEDSVPGT
          .A..G.IT..G...FEE...Y...V.A.DGGG......V.IE..D.NDN.PE....SLFS...EDSVPGT
Retrocopy -ASDGTITTKGSLDFEEAHNYILGVEARDGGGLTGHCNVHIELLDENDNSPEVTLTSLFSPIPEDSVPGT

Parental  VIALIKVRDPDSGKNGEVTCHLQHNLPFTIISSSSSYYKLVTDSPLDRERAPEYNITITATDKGSPPLST
          VIALIK.RDPD.G.N.EVTC..Q.NL.F.I.SSSSSYYKLVTDSPLDRERAPEYNITITATDKGSPPLST
Retrocopy VIALIKARDPDDGGNEEVTCRIQDNLHFKIVSSSSSYYKLVTDSPLDRERAPEYNITITATDKGSPPLST

Parental  QKTILLQISDVNDNAPVFEKPSYSAYVPENNPSGASIFSVRATDRDWGENARVTYSLLEGEGREAPLSSA
          QKTILLQISDVNDNAPVFEKPSYSAYVPENNPSGASIFSV.A.DRD...NARVTYS.L.....E.P.SS.
Retrocopy QKTILLQISDVNDNAPVFEKPSYSAYVPENNPSGASIFSVKASDRDLDGNARVTYSILRSSIQELPVSSY

Parental  VSINSETGAVYALRSFDYEQLRELRFRVQARDGGSPPLRSNVSVRLLVLDQNDNSPHILHPASPSDGSTG
          VSINS.TGA.YA.RSFDYEQ.R.....V.A.DGGSPPL.SNV.V....LD.NDN.P.IL.P.....GS..
Retrocopy VSINSQTGALYAQRSFDYEQFRAFELQVKAQDGGSPPLSSNVTVSVFILDRNDNAPRILYPSLGPEGSAV

Parental  VELAPRSSEPGYLVTKVVAVDADSGQNAWLSYQLLKATEPGLFSVGVHSGEVRTARYFVDRDGLKQSLVV
          .E..PRS.E.GYLVTKVVAVDADSG.NAWLSY..L.AT.P.LF..G.HSGE.RTAR.F.DRD..K..LV.
Retrocopy FEMVPRSAEAGYLVTKVVAVDADSGHNAWLSYHVLQATQPALFQLGLHSGEIRTARAFADRDAVKHRLVA

Parental  LVKDNGQPPLSATVTVTVAVADSIPELLSDLSSLSAPAQPQSGLTLYLVIAVASVSCVFLTFVIALVALR
          LVKDNGQPPLSATVT.....A....E.L...S..SA...PQS.L..YLV.A.A.VS..FL..VIA..A.R
Retrocopy LVKDNGQPPLSATVTLSLVFAENFQEALPEMSDRSADSAPQSDLQFYLVLALALVSFLFLLSVIAVIAIR

Parental  LRRWRESQLL
          .R....S..L
Retrocopy VRSSNNSPFL

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_14 retrocopy.

TSS

Pelodiscus sinensis was not studied using FANTOM5 data.

Lab

retro_psin_14 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.

---

Parental genes homology:

Parental genes homology involve 3 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000002556	6 retrocopies	retro_eeur_140, retro_eeur_291, retro_eeur_527, retro_eeur_630, retro_eeur_631, retro_eeur_637,
Ficedula albicollis	ENSFALG00000008476	1 retrocopy	retro_falb_10,
Pelodiscus sinensis	ENSPSIG00000004827	2 retrocopies	retro_psin_14 , retro_psin_43,