RetrogeneDB ID: retro_psin_48

Retrocopy location

• Organism: Chinese softshell turtle (Pelodiscus sinensis)
• Coordinates: JH208519.1:447014..450224(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPSIG00000001725
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ATP2B1
• Ensembl ID: ENSPSIG00000005441
• Aliases: None
• Description: ATPase, Ca++ transporting, plasma membrane 1 [Source:HGNC Symbol;Acc:814]

Sequence

>retro_psin_48
GGGATAAGGGGGGACCCATTAGATGTAGCCAGAAGGCAAGAAGTTTTTGGGAAGAATTTTATACCCCCTAAAAAACCTAA
ACCATTCCTTCAGCTGATATGGGAGGCATTACAAGATATAACATTAATTATATTGGAAATTGCAGCCATTGTATCACTAG
GACTTTCTTTTTATAGACCTTCACAAGGACAAAATACAGTGTGTGTAGACAGCCATGCTGCTACTGAAGAGGGTGAAAGT
CAGATGGCTTGGATTGAAGGAACTGCAATTCTTTTCTCAGTAGCTTGTGTAGTATTAGTAACAGCTTTCAATGACTGGAG
TAAGGAGAAACAATTTAGGGGGTTACAGCAACATATTGAAAAAGAACAGAAGTTTGCTGTCATCAGAGATGGTCAAGTCA
TACAGATACCCATTGCTGACATAGTAGTGGGGGATATTGTGTATGTCAAATATGGGGACCTTTTACCAGCTGATGGTGTG
CTTCTCCACGGGAATGACCTCAAAATGGATGAGAGTTCACTCACAGGAGAATCTGATCATGTTAAGAAGACTTTGAGTGG
AGATCCTATACTACTTTCTGGTACTCATGTAATGGAAGGCTCTGGAAGAGTGGTAATTACTGCAGTGGGTATAAACTCAC
AGACAGGAATTATCCTCACTTTACTTGGGGTGGGAGGAGAATTAGAGAAGGAGAATGTGAAAAAGAAAAAGAAAAAACAA
GATGGCACTGTTGAGAACAGCAACAAAGCAAAAGCTCAGGATTATGCAGCCAGAGAAATGCTGTTTGGAACTAGTGAAGA
AAGCACTAATGGAGAAGAGATGGCCAACAGGCAATCACATTTACCAAAAAAAGAAAAATCAGTTCTACAAGGGAAACTTA
CCAGATTAGCAGTTCAGATTGGCAAAGCAGGGTTGGCAATGTCAACAATCACAGTGGTTGTCCTTGTAGTTTATTTTTTA
ATTAAAACATTATTAATTCAGAAGCATACTTGGACTGCTCAGTGTACCCCAATTTATATAAAATATTTTGTGAAGTTCTT
CATTATTGGAGTTACGGTATTGGTGGTGGCCGTGCCAGAGGGTCTCCCACTTGCTGTCACTATCTCACTCGCCTACTCTG
TAAAAGAAATGATGAAAGATAATAACCTAGTACGGCATTTGGATGCTTGTGAAACAATGGGCAATGCAACAACCATTTGC
TCAGATAAAACAGGAACATTAACCATGAACAGAATGACTGTCGTCCAGGCTTTCATCGGAGAAAGGCATCATAAAATTAT
TCCTGCACCTGAATCAATTCCTCAGACTACTCTGAACTATCTTTTAACAGGTATTTCTGTGAATTGTGCGTACACTTCCA
AAATATTGGCTCCTGAAAAAGAAAATGGCTTACCACGTCAGGTTGGCAATAAAACTGAATGTGCCTTGCTGGGATTTCTC
CTGAATTTAAAACAGGATTATCAGGCTGTACGAAATCAAATACCAGAAGAAAAGTTGTATAAAGTATATACCTTCAACTC
TGATAGAAAGTCCATGAGTACAGTATTAAAAAAAGTTGATGGTAGTTACCAGATGTTCACCAAGGGTGCTTCTGAGATAG
TGCTTAAAAAATGCAACAAAATCTTGAATGCTGTCGGTGAACCTAAACCATTCAACTCAAAGGACAATACTAATATTTTA
AAAACTGTGGTTGATCCTATGGCTTCTGATGGACTCAGAACCATATGTCTAGCAGTCAAAGATTTCCCAGCTGGGCAGCC
TGAACCAGAATGGGATAATGAAAACAATATTATAATGGAACTCACATGTATTGCAGTTGTTGGCATTGAAGATCCATTGA
GGCCTGAGGTTCCAGATGCAATAACAAAATGCCAGAATGCTGGCATCACAGTGCGTATGGTTACTGGTGACAACATTAAT
ACTGCACGCGCAATTGCTTTGAAATGTGGTATTCTGCATCCTGGGGAGACCTTCCTTTGCTTAGAGGGAAAAGAGTTCAA
CAGACTTATACGTAACGAAAAAGGAGAGATTAAGCAAGAGCTGCTAGACAAGATTTGGCCAAAACTTCGGGTGCTTGCAA
GATCCTCCCCCTCTGATAAACACACATTGGTGAAAGGTATAATTAACAGTACCCTTTCAGAACAGAGACAAGTTGTAGCA
GTAACTGGTGATGGTACTAATGATGCACCAGCATTGAAGGAAGCAGATGTCGGTTTTGCTATGGGCATTGCTGGAACAGA
TGTGGCTAAAGAAGCATCAGATATTATTCTCACAGATGACAACTTCACAAGCACCGTTAAAGCAGTTATGTGGGGCAGAA
ATGTATATGACAGTATCTCCAAATTCCTGCAGTTCCAGCTTACAGTCAATGTAGTAGCAGTAATTGTTGCATTCACAGGA
GCATGTATTACACAAGATTCACCACTAAAAACTGTGCAGATGCTGTGGGTGAATCTCATCATGGACACATTTGCATCTCT
TGCTTTAGCTACAGAAAAACCAACTGAGTCTCTCTTGCTACGGAAGCCTTATGGAAGAAATAAAGCCCTAATCTCCCGCA
CAATGATGAAAAACATTTTAGGTCAGGCATTCTATCAGCTTATAGTCATTTTTACACTTGTTTTTACTGGTGAAAAACTT
TTTGATATTGACAGTGGAAGAAATGCTCCTCTGCATTCCCCTCCCTCCACGCATTACACAATTGTATTCAATAGTTTTGT
GTTAATGCAGATCTGTAATGAAATCAATGCCCGAAAGGTTCATGGTGAAAGGAATGTCTTTGAAGGAATATTCAGTAATA
CAATCTTTTGTGCTATCACTGCTGGTACATTAATTGTACAAATACTTATAGTAGAAGTTGGTGGGAAGCTCTTTAGTTGT
ACTGAGCTTACAGTAGAACAGTGGCTATGGTCACTTTTCCTAGGCATAGGAACGTTGCTGTGGGGACAGCTGATAACAAC
AATTCCAAATAGCTATTTGACGTTCTTGACAGAATTTGGTCATGGACCGCCAAAGGAAGAAATCCTTGAGGAAGAACGAG
CTGAAGATGCAGGAGAGATTGACCATGCTGAAAGAGAATTGCTTCGTGGTCAGATCTTATGGTTTAGGGGAATGTACAGA
ATTCAAGCTCAGAGCCGAGTGGTGAAAGCCTTTCGTACTTCCTTTTACGAAGAGTTAGAAAAACCAGAAACACAAAGCTC
AGTTCGCAGC

Alignment

ORF - retro_psin_48 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.24 %
• Parental protein coverage: 91.7 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GLSGNPADIERREAVFGKNFIPPKKPKTFLQLVWEALQDVTLIILEIAAIVSLGLSFYQPPGGNEALCGA
          G..G.P.D..RR..VFGKNFIPPKKPK.FLQL.WEALQD.TLIILEIAAIVSLGLSFY.P..G....C..
Retrocopy GIRGDPLDVARRQEVFGKNFIPPKKPKPFLQLIWEALQDITLIILEIAAIVSLGLSFYRPSQGQNTVCVD

Parental  VTVGEEEGEGETGWIEGAAILLSVVCVVLVTAFNDWSKEKQFRGLQSRIEQEQKFTVIRGGQVIQIPVAD
          .....EEGE....WIEG.AIL.SV.CVVLVTAFNDWSKEKQFRGLQ..IE.EQKF.VIR.GQVIQIP.AD
Retrocopy SHAATEEGESQMAWIEGTAILFSVACVVLVTAFNDWSKEKQFRGLQQHIEKEQKFAVIRDGQVIQIPIAD

Parental  IIVGDIAQVKYGDLLPADGVLIQGNDLKIDESSLTGESDHVKKTLDKDPMLLSGTHVMEGSGRMVVTAVG
          I.VGDI..VKYGDLLPADGVL..GNDLK.DESSLTGESDHVKKTL..DP.LLSGTHVMEGSGR.V.TAVG
Retrocopy IVVGDIVYVKYGDLLPADGVLLHGNDLKMDESSLTGESDHVKKTLSGDPILLSGTHVMEGSGRVVITAVG

Parental  VNSQTGIIFTLLGAGGDDEEKEKKDKKSKKQDGAVENRNKAKAQDGAAMEMQPLKSEDGGDGDERDKKKA
          .NSQTGII.TLLG.GG...EKE........QDG.VEN.NKAKAQD.AA.EM....SE....G.E......
Retrocopy INSQTGIILTLLGVGGE-LEKENVXXXXXXQDGTVENSNKAKAQDYAAREMLFGTSEESTNGEEMANRQS

Parental  NLPKKEKSVLQGKLTKLAVQIGKAGLLMSAITVIILILYFVIDTFWVQKRPWLAECTPIYIQYFVKFFII
          .L.....SVLQGKLT.LAVQIGKAGL.MS.ITV..L..YF.I.T...QK..W.A.CTPIYI.YFVKFFII
Retrocopy HLXXXXXSVLQGKLTRLAVQIGKAGLAMSTITVVVLVVYFLIKTLLIQKHTWTAQCTPIYIKYFVKFFII

Parental  GVTVLVVAVPEGLPLAVTISLAYSVKKMMKDNNLVRHLDACETMGNATAICSDKTGTLTMNRMTVVQAYI
          GVTVLVVAVPEGLPLAVTISLAYSVK.MMKDNNLVRHLDACETMGNAT.ICSDKTGTLTMNRMTVVQA.I
Retrocopy GVTVLVVAVPEGLPLAVTISLAYSVKEMMKDNNLVRHLDACETMGNATTICSDKTGTLTMNRMTVVQAFI

Parental  SEKHYKKIPEPDAIPEKTLAYLVTGISVNCAYTSKILPPEKEGGLPRHVGNKTECALLGLLLDLKRDYQD
          .E.H.K.IP.P..IP..TL.YL.TGISVNCAYTSKIL.PEKE.GLPR.VGNKTECALLG.LL.LK.DYQ.
Retrocopy GERHHKIIPAPESIPQTTLNYLLTGISVNCAYTSKILAPEKENGLPRQVGNKTECALLGFLLNLKQDYQA

Parental  IRNEIPEEALYKVYTFNSVRKSMSTVLKNSDGSFRVFSKGASEIVLKKCFKILSANGEPKVFRPRDRDDI
          .RN.IPEE.LYKVYTFNS.RKSMSTVLK..DGS...F.KGASEIVLKKC.KIL.A.GEPK.F...D...I
Retrocopy VRNQIPEEKLYKVYTFNSDRKSMSTVLKKVDGSYQMFTKGASEIVLKKCNKILNAVGEPKPFNSKDNTNI

Parental  VKTVIEPMASEGLRTICLAFRDFPAGEPEPEWDNENDIVTGLTCIAVVGIEDPVRPEVPDAIKKCQRAGI
          .KTV..PMAS.GLRTICLA..DFPAG.PEPEWDNEN.I...LTCIAVVGIEDP.RPEVPDAI.KCQ.AGI
Retrocopy LKTVVDPMASDGLRTICLAVKDFPAGQPEPEWDNENNIIMELTCIAVVGIEDPLRPEVPDAITKCQNAGI

Parental  TVRMVTGDNINTARAIASKCGILNPGEDFLCIEGKDFNRRIRNEKGEIEQERIDKIWPKLRVLARSSPTD
          TVRMVTGDNINTARAIA.KCGIL.PGE.FLC.EGK.FNR.IRNEKGEI.QE..DKIWPKLRVLARSSP.D
Retrocopy TVRMVTGDNINTARAIALKCGILHPGETFLCLEGKEFNRLIRNEKGEIKQELLDKIWPKLRVLARSSPSD

Parental  KHTLVKGIIDSTVSEQRQVVAVTGDGTNDGPALKKADVGFAMGIAGTDVAKEASDIILTDDNFTSIVKAV
          KHTLVKGII.ST.SEQRQVVAVTGDGTND.PALK.ADVGFAMGIAGTDVAKEASDIILTDDNFTS.VKAV
Retrocopy KHTLVKGIINSTLSEQRQVVAVTGDGTNDAPALKEADVGFAMGIAGTDVAKEASDIILTDDNFTSTVKAV

Parental  MWGRNVYDSISKFLQFQLTVNVVAVIVAFTGACITQDSPLKAVQMLWVNLIMDTLASLALATEPPTESLL
          MWGRNVYDSISKFLQFQLTVNVVAVIVAFTGACITQDSPLK.VQMLWVNLIMDT.ASLALATE.PTESLL
Retrocopy MWGRNVYDSISKFLQFQLTVNVVAVIVAFTGACITQDSPLKTVQMLWVNLIMDTFASLALATEKPTESLL

Parental  LRKPYGRNKPLISRTMMKNILGHAFYQLVVVFTLLFAGERIFDIDSGRNAPLHAPPSEHYTIVFNTFVMM
          LRKPYGRNK.LISRTMMKNILG.AFYQL.V.FTL.F.GE..FDIDSGRNAPLH.PPS.HYTIVFN.FV.M
Retrocopy LRKPYGRNKALISRTMMKNILGQAFYQLIVIFTLVFTGEKLFDIDSGRNAPLHSPPSTHYTIVFNSFVLM

Parental  QLFNEINARKIHGERNVFEGIFNNVIFCSIVLGTFIVQVIIVQFGGKPFSCSKLTVEQWLWSVFLGMGTL
          Q..NEINARK.HGERNVFEGIF.N.IFC.I..GT.IVQ..IV..GGK.FSC..LTVEQWLWS.FLG.GTL
Retrocopy QICNEINARKVHGERNVFEGIFSNTIFCAITAGTLIVQILIVEVGGKLFSCTELTVEQWLWSLFLGIGTL

Parental  LWGQLISTIPTSRLKFLKEAGHGTQKEEIPEEELAEDVEEIDHAERELRRGQILWFRGLNRIQTQIRVVN
          LWGQLI.TIP.S.L.FL.E.GHG..KEEI.EEE.AED..EIDHAEREL.RGQILWFRG..RIQ.Q.RVV.
Retrocopy LWGQLITTIPNSYLTFLTEFGHGPPKEEILEEERAEDAGEIDHAERELLRGQILWFRGMYRIQAQSRVVK

Parental  AFRSSLYEGLEKPETRSSIHN
          AFR.S.YE.LEKPET.SS...
Retrocopy AFRTSFYEELEKPETQSSVRS

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_48 retrocopy.

TSS

Pelodiscus sinensis was not studied using FANTOM5 data.

Lab

retro_psin_48 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000014296	1 retrocopy	retro_meug_716,
Monodelphis domestica	ENSMODG00000009874	1 retrocopy	retro_mdom_243,
Pelodiscus sinensis	ENSPSIG00000005441	1 retrocopy	retro_psin_48 ,