RetrogeneDB ID:

retro_mmul_2279

Retrocopy
location
Organism:Rhesus macaque (Macaca mulatta)
Coordinates:8:6802355..6804104(+)
Located in intron of:ENSMMUG00000018668
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:PTPN4
Ensembl ID:ENSMMUG00000005610
Aliases:None
Description:tyrosine-protein phosphatase non-receptor type 4 [Source:RefSeq peptide;Acc:NP_001253553]


Retrocopy-Parental alignment summary:






>retro_mmul_2279
CGCTACTAGTATTTTTTACAAATTTAACAAGACATTCTTACTGGAAGATTGCCCTGTTCTTACGATACTACTGCCCTTTT
TCCTTTATTTGCTGTTCAGACTAAACTTGGAGACTACAGTCAGTCAGAGAACTTGCTAGGCCACCTCTCAGGTTATTCTT
TCATTCCTGATCATCCTCAAAAATTTGAAAAATAAATTGTAAAAATGACATCAGCAACATATAGGCTTATGTCCTTGAGA
AGCAGAAGTTAATTACCTAAACACAGCAAGTACCTTAGAACTCGGTGGAGTTGAATTCCACTATGCAAGGAATCGAAGTT
ACAATGAAATTATGATTGGAATGACGTCAAGAGAAATTCTGATTTATAAGAGACTACGAATGAGTACCTTTCCGTGGTTG
AAGATTGTAAAAATTTGTTTTAAGTGCAAACAGTTTTTTATTCAGCTTTGAAAATGGCTTGCATAAATCTGGAGAAAGAT
TATCAGGATTTAATATGATAAATTGTGGAGCATGTAAACGTTTGTGGAAAGCAAGTTTAGAACATCACATATTCTTCTGT
TTGGACAGACCACTTCCAACTAGAAATAATTCTTTTGCACATTATTTTACATTAGGTTCAAAATTCCTAATGCACCGTGG
GAGAACTGAAGTTCAGTTAATTCAGTATGGCAAATAAAAGGCAAATAAAGACAATTTGCAGGATCCTCAAGTAAGCCATT
GACGTGGAAATTAATGAATTGGGAAGTAGTAAGCAGGAATTCAATATCTGATGAAAGGATTGGAAACGTAAAGCCTTCCA
TCACAGCTGCCACCTGGAACAGGAATTTCTACTCATCAAAATTTTGCATTCATACAAGAGGGAACCTGATTATGACCGTC
TTCAGTTGGTCATTTGGTAGATTATGTGGTTCACACTTCTTCCAAAGTATTTGCGAATCAGAGATCACCATTATCAGCAC
AAGCTGATAGCATCACTCTGGAATCATCCACCATTACAGGACACCCCTGAGATAGGTAGTCTCCGGCTTTACCACCCAAA
CAATCTAAGAAAAACAGTTGGAACCAAATTCATTATTTACATTTCCAACAAGATCTGGAAGATCATATTAATGAAACATT
GATATTACATCTTCTCTTAAAAAATCTACTCCTAATGGTGGTGTTCTACATGATCATCTTGTTCTAATCAGAGTGAACCT
GATGAAAATGGAAGGTATGGAGTCAATGTAAAGGGGAATATGGTCAGAAGATGTCTGTGATCGTGTCCTGAGAAGCACCA
GGAACACCTTTGAACTCGGTGACCCTCGATTGAAGAGAAGACCTAGTTGTATTGATCAGTGGTTGGGACTTTACAGACTC
ATCCATGATTGGTTTGTCCTGCTTATTAAAGCTAACTGTGAGAGACATTCTGGGGAACTCATGCTTCTAGTTCTACCTGT
GCTGCATATGATGTAGTGGAAGAAGTGCTAGAAAACGGGACAGACTTCCAGTACATTCTGGAGAAAGACCCACTAGATAG
TGTCCACCAGGATGACCGTTTCCTGTGGGAGTCAGTGATCCAGCTAGCCAAGGGCTTACCGCTGGAACATTCTGGACACA
ATTTGATCAGCTTATCAAAAAGAAAACTTGGAATGACAATGTCTGGTGCCAGATTACCTTAGAACCTTTCCAAAAATAGA
TACAGAGATAGTTTGCCTTATGATACTACATGGATTATTTTAAAAGGTAATGAGGACTACATCAGTGCA

ORF - retro_mmul_2279 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 66.39 %
Parental protein coverage: 63.17 %
Number of stop codons detected: 15
Number of frameshifts detected 11


Retrocopy - Parental Gene Alignment:

ParentalRYQYFLQIKQDILTGRLPCPSNTAALLASFAVQSELGDYDQSENLSGYLSDYSFIPNQPQDFEKEIAKL-
RY.YFLQI.QDILTGRLPC...T.AL...FAVQ..LGDY.QSENL.G.LS.YSFIP..PQ.FEK.I.K..
RetrocopyRY*YFLQI*QDILTGRLPCSYDTTALFPLFAVQTKLGDYSQSENLLGHLSGYSFIPDHPQKFEK*IVKM>
ParentalHQQHIGLSPAEAEFNYLNTARTLELYGVEFHYARDQSNNEIMIGVMSGGILIYKNRVRMNTFPWLKIVKI
HQQHIGL.P.EAE.NYLNTA.TLEL.GVEFHYAR..S.NEIMIG..S..ILIYK.R.RM.TFPWLKIVKI
RetrocopyHQQHIGLCP*EAEVNYLNTASTLELGGVEFHYARNRSYNEIMIGMTSREILIYK-RLRMSTFPWLKIVKI
ParentalSFKCKQFFIQLRK-ELHESRETLLGFNMVNYRACKNLWKACVEHHTFFRLDRPLPPQKN-FFAHYFTLGS
.FKCKQFFIQL.K..LH.S.E.L.GFNM.N..ACK.LWKA..EHH.FF.LDRPLP...N.FF...F....
RetrocopyCFKCKQFFIQL*K>GLHKSGERLSGFNMINCGACKRLWKASLEHHIFFCLDRPLPTRNN<FFCTLFYIRF
ParentalKFRYCGRTEVQSVQYGKEKANKDRVFARSPSKPLARKLMDWEVVSRNSISDDR-LETQSLPSRSPPGT--
K..........SV........K.R.FA.S.SKPL..KLM.WEVVSRNSISD.R.LET.SLPS..PPGT..
RetrocopyKIPNAPWEN*SSVNSVWQIKGK*RQFAGSSSKPLTWKLMNWEVVSRNSISDER>LET*SLPSQLPPGTGI
ParentalPNHRNSAFTQEGTRLRPSSVGHLVDHMVHTSPSEVFVNQRSPSSTQANSIVLESSPSQETPGDGKPPALP
..H.N.AF.QEGT.L.PSSVGHLVD..VHTS.S.VF.NQRSP.S.QA.SI.LESS.....P.D...PALP
RetrocopySTHQNFAFIQEGT*L*PSSVGHLVDYVVHTS-SKVFANQRSPLSAQADSITLESSTITGHP*DR*SPALP
ParentalPKQSKKNSWNQIHYSHSQQDLESHINETF-DIPSSPEKPTPNGGIPHDNLVLIRM-KPDENGRFGFNVKG
PKQSKKNSWNQIHY.H.QQDLE.HINET..DI.SS..K.TPNGG..HD.LVLIR...PDENGR.G.NVKG
RetrocopyPKQSKKNSWNQIHYLHFQQDLEDHINETL<DITSSLKKSTPNGGVLHDHLVLIRV<EPDENGRYGVNVKG
ParentalG-YDQKMPVIVSRVAPGTPADLCVPRLNEGDQVVLINGRDIAEHT-HDQVVLFIKASCERHSGELMLLVR
..Y.QKM.VIVS..APGTP.........E.D.VVLI.G.D......HD..VL.IKA.CERHSGELMLLV.
RetrocopyN<YGQKMSVIVS*EAPGTPLNSVTLD*RE-DLVVLISGWDFTDSS<HDWFVLLIKANCERHSGELMLLVL
ParentalPN-AVYDVVEEKLENEPDFQYIPEKASLDSVHQDDHSLRESMIQLA-EGLITGTVLTQFDQLYRKKP-GM
P..A.YDVVEE.LEN..DFQYI.EK..LDSVHQDD..L.ES.IQLA..GL..GT..TQFDQL..KK..GM
RetrocopyPV<AAYDVVEEVLENGTDFQYILEKDPLDSVHQDDRFLWESVIQLA<QGLTAGTFWTQFDQLIKKKT>GM
ParentalTMSCAKLPQNISKNRYRDISPYDATRVILKGNEDYINA
TMS.A.LP.N.SKNRYRD..PYD.T..ILKGNEDYI.A
RetrocopyTMSGARLP*NLSKNRYRDSLPYDTTWIILKGNEDYISA

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






RNA-Seq - click to see more details

(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
SRP007412_brain 0 .78 RPM 32 .16 RPM
SRP007412_brain_prefrontal_cortex 0 .48 RPM 26 .58 RPM
SRP007412_cerebellum 0 .32 RPM 36 .94 RPM
SRP007412_heart 0 .00 RPM 4 .00 RPM
SRP007412_kidney 0 .12 RPM 5 .52 RPM
SRP007412_liver 0 .00 RPM 3 .64 RPM
SRP007412_testis 1 .24 RPM 17 .75 RPM

ChIP-Seq - click to see more details

Macaca mulatta was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_mmul_2279 retrocopy.

TSS - click to see more details

Macaca mulatta was not studied using FANTOM5 data.

Lab - click to see more details

retro_mmul_2279 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmul_2279 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG000000010151 retrocopy
retro_chof_785,
Macaca mulatta ENSMMUG00000005610 1 retrocopy
retro_mmul_2279 ,




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