RetrogeneDB ID: retro_ptro_3224

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: X:58452416..58454350(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NLRP2
• Ensembl ID: ENSPTRG00000011480
• Aliases: NLRP2, NALP2
• Description: NLR family, pyrin domain containing 2 [Source:HGNC Symbol;Acc:22948]

Sequence

>retro_ptro_3224
ACCCGCACGGGGCTGTTCCTGCGCTTCCTTTGCGGCCGGTTCCCGCAGGGCGCACAGCTCTGGGGCGTGCTGCGGGCGCT
GAGCCTCCTGGCGGCACAGGGCCTGTGGGCGCAGATGTCAGTGTTCCGTGGAGAGGACTTGGCGAGGCTCGGGGTGCAGG
AGTTCAACATCCGCCCGTCCCTGGACAGAGACATCCTCCGCCAGGACAGAGTCTCTAAAGGCTGCTATTCCTACATCCAC
CTCAGCTTCCAGCAGTTTTTCACTGTGCTGTTCCACGCCCTGGAGGAGGAGGAGGAGGAGGAGGACAAGGACGGCCACGC
CTGGGACAATGGAGACGTGCAGAAGCTGCTTTCTAGAGAAGAAAGACTCAAGAACCCCGACCTGATCCAAGCAAGACACT
TCTTATTCGGCTTCGCCAACGAGAAGAGAGCCAAGGAGTTGGAGACCACTTTGGGCTGCCTGATGTCACTGGAGATCAAA
CAGGAATTACTGTGATGAGAGATAAATTGTGAAAAGGTTGGACACTCAACAATGACGAATCCGAAGGAGCTCTTGTGCTG
TCTGTACGAGTCTCAGGAGGAGGAGCTGGTGAAGGGAGTGACGGCTCCGTTCAAAGAAATATCCCTGCACTTAAATGCAG
TAGACATTATGCTGTTTTCAATCTGCCTCAAGCATTGTCGAAACTTGCAGAAAATGCCACTGCAGGCAGCAAAGGCAAAG
CTCCCGGAGAATGTCACTGTGTCTGAATCAGATGCTGAAGTTGAGAGATCCCGGGATGATCAACACATGCTTCCTTTCTG
GACTGACCTTTGTTCCATATTTGGCTCAAATAAGGATCTGATCATTCTAGAAATCAATAATAGCTTTCTTAGTGCCACAT
TAGTAAGGATCCTGTGTGAACAAATAGCTTCTGACACCTGTCGTCTCCAGAGAGTGATGTTCAAAAACATTTCCCCAGCT
GATGCTTATCGGAACCTCTGCCTAGCTCTTTGAGGTCACAAGACTGTAAGATATCTGACCCTTCAAGGCAATGACCAGAA
TGATATGCTTCCTGCATTGTGTGAGGTCTTGAGACACTCAAAATGTAACCTGCAATATCTCAGGTTGGTGTCTTTTTCCA
CCACCACTTAGCAATGGGCTGATCTCTCCTTGGCCCTTGAAGTCAACCAGTCCCTGACATGTGTAAACCTCTCCCACAAT
GAGCTCTTGGATGAGGGTGCCAAGTTGCTGCACACAACTTTGAGACACCCAAAATGCTTCCTGCCGAGGTTGTTGTTGGA
AAACTGTCACTTTATAGAAGCCAATTGCAAGAACTTTGCTGCTGTTTTGGTTGTCAGCGGGGAGCTGACACACCTGTGCT
TGGCCAAGAACCCCCCCCCCCTCGGGGATACATGGGTGATGTTTCTGTGTAAGGGTTTGAGTTACCCCCATTGTAAACTA
CAGACCCTGGTGCTGTGGGACTGTGACATAACTAGCAATGGCTGCTGTTATCTCGCAGAGCTTCTCCAAGAAAAATCAAG
CCTAATGTGCTTGGATCTGGGACTGAATCACATAGGAGTTACTGGAGTGAAGCTCCTATGTGAGGCTTTGAAGAAACCAC
TGTGTAACTTGAGATGTCTGTGGTTGTGGGGGTGTTCCATCCCTCTGTTCAGTTGTGAGGACCTCTGCTCTGTGCTCAGC
TGCAACCACAGCCTCGTTGCTCTGGACCTGAGCCAGAATCCCTTGGGCTCTAGTCGAGTAAAGATGCTGTTTGAAACCTT
GACACATCCAAATTGCACCCTCCAGACACTCAGGTTGAAAATAGATGACTTTAATGATGAACTCGATAAGCTGCTGGAAG
AAATAGAAGAAAACAACCCACAACTGCCTGTTGATAACTGAGAAACATGATCCCTTGGGGGGGAAAAAGGCTTTCTTCTC
ATTACTTCATTATC

Alignment

ORF - retro_ptro_3224 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.93 %
• Parental protein coverage: 60.17 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TRTGLFLRFLCSRFPQGAQLRGALRTLSLLAAQGLWAQTSVLHREDLERLGVQESDLRLFLDGDILRQDR
          TRTGLFLRFLC.RFPQGAQL.G.LR.LSLLAAQGLWAQ.SV...EDL.RLGVQE...R..LD.DILRQDR
Retrocopy TRTGLFLRFLCGRFPQGAQLWGVLRALSLLAAQGLWAQMSVFRGEDLARLGVQEFNIRPSLDRDILRQDR

Parental  VSKGCYSFIHLSF-QQFLTALFYALEKEEEEDRDGHTSDIGDVQKLLSGVERLRNPDLIQAGYYYFGLAN
          VSKGCYS.IHLSF.Q.F................DGH..D.GDVQKLLS..ERL.NPDLIQA....FG.AN
Retrocopy VSKGCYSYIHLSFQQFFTVLFHAXXXXXXXXXKDGHAWDNGDVQKLLSREERLKNPDLIQARHFLFGFAN

Parental  EKRAKELEATFGCRMSPDIKQELLRCDISC-KGGHSTVTDLQELLGCLYESQEEELVKEVMAQFKEISLH
          EKRAKELE.T.GC.MS..IKQELL...I.C.K.GHST.T...ELL.CLYESQEEELVK.V.A.FKEISLH
Retrocopy EKRAKELETTLGCLMSLEIKQELL**EINCEKVGHSTMTNPKELLCCLYESQEEELVKGVTAPFKEISLH

Parental  LNAVDVVPSSFCVKHCRNLQKMSLQVIKENLPENVTASESDAEVERSQDDQHMLPFWTDLCSIFGSNKDL
          LNAVD....S.C.KHCRNLQKM.LQ..K..LPENVT.SESDAEVERS.DDQHMLPFWTDLCSIFGSNKDL
Retrocopy LNAVDIMLFSICLKHCRNLQKMPLQAAKAKLPENVTVSESDAEVERSRDDQHMLPFWTDLCSIFGSNKDL

Parental  MGLAINDSFLSASLVRILCEQIASDTCHLQRVVFKNISPADAHRNLCLALRGHKTVTYLTLQGNDQDDMF
          ..L.IN.SFLSA.LVRILCEQIASDTC.LQRV.FKNISPADA.RNLCLAL.GHKTV.YLTLQGNDQ.DM.
Retrocopy IILEINNSFLSATLVRILCEQIASDTCRLQRVMFKNISPADAYRNLCLAL*GHKTVRYLTLQGNDQNDML

Parental  PALCEVLRHPECNLRYLGLVSCSATTQQWADLSLALEVNQSLTCVNLSDNELLDEGAKLLYTTLRHPKCF
          PALCEVLRH..CNL.YL.LVS.S.TT.QWADLSLALEVNQSLTCVNLS.NELLDEGAKLL.TTLRHPKCF
Retrocopy PALCEVLRHSKCNLQYLRLVSFSTTT*QWADLSLALEVNQSLTCVNLSHNELLDEGAKLLHTTLRHPKCF

Parental  LQRLSLENCHLTEANCKDLAAVLVVSRELTHLCLAK--NPIGNTGVKFLCEGLRYPECKLQTLVLWNCDI
          L.RL.LENCH..EANCK..AAVLVVS.ELTHLCLAK.....G.T.V.FLC.GL.YP.CKLQTLVLW.CDI
Retrocopy LPRLLLENCHFIEANCKNFAAVLVVSGELTHLCLAKXXXXXGDTWVMFLCKGLSYPHCKLQTLVLWDCDI

Parental  TSDGCCDLAKLLQEKSSLSCLDLGLNHIGVKGMKFLCEALRKPLCNLRCLWLWGCSIPPFSCEDLCSALS
          TS.GCC.LA.LLQEKSSL.CLDLGLNHIGV.G.K.LCEAL.KPLCNLRCLWLWGCSIP.FSCEDLCS.LS
Retrocopy TSNGCCYLAELLQEKSSLMCLDLGLNHIGVTGVKLLCEALKKPLCNLRCLWLWGCSIPLFSCEDLCSVLS

Parental  CNQSLVTLDLGQNPLGSSGVKMLFETLTCSSGTLRTLRLKIDDFNDELNKLLEEIEEKNPQLIID-TEKH
          CN.SLV.LDL.QNPLGSS.VKMLFETLT....TL.TLRLKIDDFNDEL.KLLEEIEE.NPQL..D.TEKH
Retrocopy CNHSLVALDLSQNPLGSSRVKMLFETLTHPNCTLQTLRLKIDDFNDELDKLLEEIEENNPQLPVD>TEKH

Parental  H-PW-EERPSSHDFMI
          ..PW...R.SSH.F.I
Retrocopy D>PWGGKRLSSHYFII

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	0.09 RPM	0.00 RPM
SRP007412_cerebellum	0.04 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.00 RPM	25.50 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3224 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3224 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3224 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017689	2 retrocopies	retro_cjac_1321, retro_cjac_3184,
Myotis lucifugus	ENSMLUG00000015486	1 retrocopy	retro_mluc_1353,
Pan troglodytes	ENSPTRG00000011480	1 retrocopy	retro_ptro_3224 ,