RetrogeneDB ID: retro_psin_43

Retrocopy location

• Organism: Chinese softshell turtle (Pelodiscus sinensis)
• Coordinates: JH208050.1:67335..69297(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

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

Sequence

>retro_psin_43
TCTGGGCAGATTCGCTACTCGATCCCGGAGGAAACGGAGAGAGGCGTTTTCGTGGGGGACATCGCGCAGGACCTGGGGCT
GGACGCGGAGCAGCTCTCGGAGCGCGGAGTCCGAATCGTTTCCGGAGGTAGGACGCAGTACTTTGCTCTCAATGCGGAGA
GCGGCCATTTGATCACCGCGGAGCGCATAGACAGGGAGCGGATCTGCGGCCGGGCGGGGAAGTGTCTGCTGAGCTGTGAG
CTCATAGTGGAGGATACAATGAAGCTGTACGGAGTGGAAGTGGAAATCACGGACATTAATGACAACGCCCCCAGCTTCCC
GGCGGAAGAAATGGAGTTAAAAGTCAGCGAGACAACGGCGCCGGGATCGCGGTTTTCTTTGAGTGACGCTCAGGACTCCG
ATGTGGGCATTAATTCCCTGCAGAGCTACCAGCTCGGCAGCGACGGGCATTTCTCACTGGATGTTCAGACAGGCCCGGAT
GGCGTGAAACACGCCGACCTGGTGCTGGAAAAGTCCCTGGACCGGGAAGAACAAGCCGTTCACACGCTGATCCTCACGGC
CACTGATGGGGGAGACCCGGTCAGATCCGGCACTGCGCAGATCCGCGTTACTGTCCTCGATGCTAATGACAACGCGCCGG
TTTTCAGTCAGCCTGTCTACACGGTGAGTGTGTGGGAAAATGTGCCGGCAGGGTCCACGGTTCTCACAGTAAAGGCCACC
GACCTGGATGAAGGAGTCAACAAAGAGGTGACCTACTCTTTCCACCAAATCACAGACAAAGCTGCTCAAACATTCCACTT
GGACTCTGAGACGGGGGAAGTGACACTGGTGGGGAACTTGGACTTCGAGGAATCGGCGTTGTATGAAATCGAGGTGAAAG
CGCAAGACGGGGGAGGCCGATACGACAAATCGAGAATTGAAATCATGGTTACCGATGTGAATGACAACGCCCCGGAAATC
GCTGTCAGGTCCCTCGTAAGCGCGATCCCCGAGGACGCTCCCCCCGGGACTGTGGTCGCCCTTCTAAACGTCCAGGATCC
GGATTCGGGGGAGAACGGGGAGGTCACGTGCTCCATACCCAGCAGCCTCCCCTTCCAGCTGAGGCGGTCGCTGGACAAGT
ACTACAGCCTGGTGACCGAGCGAGCCCTGGACAGGGAGCAGGTGGCCGCCTACAACATCACAGTCACCGCCACGGACAGC
GGGACTCCGCCCCTTGCCACCGCCATCACCATCCCGCTCCGGGTCCTGGACACCAACGACAACGCTCCGCTCTTCGGCCA
AGCGTCCTACACCGCCTACGTGCCGGAGAACAACCCCAGCGGGGCCTCCGTGTGCTCCGTGAGGGCCACTGACCGCGACT
GGGGGGAGAACGCCCGAGTGACTTACTCTCTGCTGGAGGGCGAGGGCCGCGAAGCTCCGCTCTCCTCCGCCGTGTCCATT
AACTCGGAGACCGGGGCTGTGTACGCGCTGCGCTCCTTCGACTACGAGCAGCTGCGGGAGCTTCGGTTCCGGGTGCAGGC
TCGGGACGGGGGGTCCCCGCCGCCCCGCCGGCATGTCTCCGTCAGGCTCCTGGTGCTGGACCAGAATGACAACAGCCCGC
ACATCCTGCACCCCGCCTCCCCCAGCGATGGCTCCACGGGAGTGGAGCTGGCCCCTCGCTCCTCCGAGCCGGGCTACCTG
GTCACCAAGGTGGTGGCGGTGGATGCGGACTCCGGGCAGAACGCCTGGCTCTCCTACCAGCTGCTGAAGGCCACGGAGCC
GGGGCTCTTCTCGGTCGGAGTCCACAGCGGCGAGGTGCGGACAGCGCGCTACTTTGTGGACAGGGACGGCCTGAAGCAGA
GCCTGGTGGTGCTGGTGAAGGACAACGGGCAGCCCCCTCTCTCGGCCACCGTCACTGTCACGGTGGCGGTGGCTGACAGC
ATCCCCGAGCTCCTGTCGGACCTGAGCAGCCTCTCGGCTCCC

Alignment

ORF - retro_psin_43 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.24 %
• Parental protein coverage: 82.47 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SGQIRYSIPEETERGAFVGDVAKDLGLHAEQPSERGVRIVSGGRTQYFALNAESGHLITAERIDRERICG
          SGQIRYSIPEETERG.FVGD.A.DLGL.AEQ.SERGVRIVSGGRTQYFALNAESGHLITAERIDRERICG
Retrocopy SGQIRYSIPEETERGVFVGDIAQDLGLDAEQLSERGVRIVSGGRTQYFALNAESGHLITAERIDRERICG

Parental  RAGKCLLSCELIVEDTMKLYGVEVEITDINDNAPSFPTEEMELKVSETTAPGSRILLPEAQDSDLGTNSI
          RAGKCLLSCELIVEDTMKLYGVEVEITDINDNAPSFP.EEMELKVSETTAPGSR..L..AQDSD.G.NS.
Retrocopy RAGKCLLSCELIVEDTMKLYGVEVEITDINDNAPSFPAEEMELKVSETTAPGSRFSLSDAQDSDVGINSL

Parental  QSYQLSSDGHFSLDVQTGPDGVKHAELVLEKSLDREEQAVHTLILTATDGGDPVRSGTAQIRVTVLDAND
          QSYQL.SDGHFSLDVQTGPDGVKHA.LVLEKSLDREEQAVHTLILTATDGGDPVRSGTAQIRVTVLDAND
Retrocopy QSYQLGSDGHFSLDVQTGPDGVKHADLVLEKSLDREEQAVHTLILTATDGGDPVRSGTAQIRVTVLDAND

Parental  NAPVFSQPVYTVSVWENVPAGSTILTVKATDLDEGVNKEIKYSFRKITDKASQIFRLDAKTGDITAMGNV
          NAPVFSQPVYTVSVWENVPAGST.LTVKATDLDEGVNKE..YSF..ITDKA.Q.F.LD..TG..T..GN.
Retrocopy NAPVFSQPVYTVSVWENVPAGSTVLTVKATDLDEGVNKEVTYSFHQITDKAAQTFHLDSETGEVTLVGNL

Parental  NFEESALYEIEVQAQDGGGRFDKSKVVIEVSDVNDNAPEIAVRSLFSLVAEDSVPGTVIALIKVRDPDSG
          .FEESALYEIEV.AQDGGGR.DKS...I.V.DVNDNAPEIAVRSL.S...ED..PGTV.AL..V.DPDSG
Retrocopy DFEESALYEIEVKAQDGGGRYDKSRIEIMVTDVNDNAPEIAVRSLVSAIPEDAPPGTVVALLNVQDPDSG

Parental  KNGEVTCHLQHNLPFTIISSSSSYYKLVTDSPLDRERAPEYNITITATDKGSPPLSTQKTILLQISDVND
          .NGEVTC.....LPF....S...YY.LVT...LDRE....YNIT.TATD.G.PPL.T..TI.L...D.ND
Retrocopy ENGEVTCSIPSSLPFQLRRSLDKYYSLVTERALDREQVAAYNITVTATDSGTPPLATAITIPLRVLDTND

Parental  NAPVFEKPSYSAYVPENNPSGASIFSVRATDRDWGENARVTYSLLEGEGREAPLSSAVSINSETGAVYAL
          NAP.F...SY.AYVPENNPSGAS..SVRATDRDWGENARVTYSLLEGEGREAPLSSAVSINSETGAVYAL
Retrocopy NAPLFGQASYTAYVPENNPSGASVCSVRATDRDWGENARVTYSLLEGEGREAPLSSAVSINSETGAVYAL

Parental  RSFDYEQLRELRFRVQARDGGSPPLRSNVSVRLLVLDQNDNSPHILHPASPSDGSTGVELAPRSSEPGYL
          RSFDYEQLRELRFRVQARDGGSPP.R..VSVRLLVLDQNDNSPHILHPASPSDGSTGVELAPRSSEPGYL
Retrocopy RSFDYEQLRELRFRVQARDGGSPPPRRHVSVRLLVLDQNDNSPHILHPASPSDGSTGVELAPRSSEPGYL

Parental  VTKVVAVDADSGQNAWLSYQLLKATEPGLFSVGVHSGEVRTARYFVDRDGLKQSLVVLVKDNGQPPLSAT
          VTKVVAVDADSGQNAWLSYQLLKATEPGLFSVGVHSGEVRTARYFVDRDGLKQSLVVLVKDNGQPPLSAT
Retrocopy VTKVVAVDADSGQNAWLSYQLLKATEPGLFSVGVHSGEVRTARYFVDRDGLKQSLVVLVKDNGQPPLSAT

Parental  VTVTVAVADSIPELLSDLSSLSAP
          VTVTVAVADSIPELLSDLSSLSAP
Retrocopy VTVTVAVADSIPELLSDLSSLSAP

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_43 retrocopy.

TSS

Pelodiscus sinensis was not studied using FANTOM5 data.

Lab

retro_psin_43 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 ,