RetrogeneDB ID:

retro_ptro_265

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:1:219288966..219290420(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:HMGCS1
Ensembl ID:ENSPTRG00000016845
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_ptro_265
TCAAAGTTGGAAAAGTATGTTGATATAGATGCTGGAAAGTATACCATTGGCTTGGGCCAGGCCAAGATGGGCTCCTGCAC
ACATGGAGAAGAGATCAACTCTCTTTGCATGCCTGTGGTTCAGAATCTTATGGAGAGAAAAAATCTTTCCTACGATTGCA
CTGGGCGACTGGAAGTTGGAACAGAGACAATCAAGGACAAATCAAAGTCAGTGAAGACTAATTTGATGCAGCTGTTTGAG
GAGTCTGGGAATATAGATATAGAAGGAACCGACACAACTCATGCATGCTGTGGAGGCCCAGCTGCTGTCTTCAGTGCTGT
TAATTGGATTGAGTCCAGCTCCTGGGATGGACAGTTTGCCCTGGAGCTTGTAGGAGATATTGCTGTATATTCCATAGGAA
AAGTTAGACTGACAGGTGGAGTCGGAGCAGTAGCTCTGCTAATTGAGCCAAATGCAACCTTAATTTTTGAACGAGGGCTT
CGTGGGACACATATGCAACACGCCTATGACTTTTATGAGCCTGATATGCCCTCTGAATGTCCTATAGTAGATGGAAAACC
CTCCACACAGTGCTGCTTCAGTGCATTAGATCACTGCTATTCTGTCGACTGCAAAACGATCCATGCCCAGTGGCAGAAAG
ACGGAAATGATAAAGATTTTACCTTGAATAATTTTGGCTTCTTGATACTTCACTCACCATATTGTAAACTGGTGAGTTTA
TCTCTAGCTCGGATGTTGCGGAATGACTTCCTTAATGATCAGAACAGAGATAAAAATAGTGTTTAGAATGTCCTGGAAGC
CTTTGGGAATGTTAAATTAGAAGACATCTATTTTGATACAGATGTGGAGATGGCATTTATGAAGGATAGTTCCGAACTCT
CCCATCAGAAAACAAAGGCATCTTTGCTGTATCCAGTGAAAATGGAAATACGTACACATCGTCAGTATATGGTTCCCCAC
AACTGTCCCAGCACAGTACTCACCTCAGCAATGATCAGGGAAGAGACTGGAGTGTTCTCATACGGTTCTGGTTCAGCCGG
CACCCTGTACTCTCTTAAAGTTACACAAGATGCCACACCAGGGTCTGCTGTTGATAAAATAACAGCAAGCTATGGGATCT
TAAATCAAAGTGTAGCTCAAGAACTTGTGTGGTACCAGATGTCTTTGTTGAAAACATGAAGCTCAGAGAGGACACCCATC
ACTTGGTCAACTCTGTTCCCCGGGGCCCAAGAGATTCACTCTTTGAAGAAACATGGTACTTAGCTAGGGTGGGTGAAAAG
CACAGAAGTTACACTCCGTGTCCTTCTCCAAATGATGACACTTGGGATGAAGGAGTCAGACTTGTGCATTCAAACACAGT
AACTGATCATATTCCAAGCCCTGCTAAGACAGTGCCAAGACTCCCTGCCACAGCAGCAGAAACGGGAGCAGCTGTCATTA
GTAATGGGGAACAT

ORF - retro_ptro_265 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 78.41 %
Parental protein coverage: 93.65 %
Number of stop codons detected: 2
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalAELEKYDGVDAGKYTIGLGQAKMGFCTDREDINSLCMTVVQNLMERNNLSYDCIGRLEVGTETIIDKSKS
..LEKY...DAGKYTIGLGQAKMG.CT..E.INSLCM.VVQNLMER.NLSYDC.GRLEVGTETI.DKSKS
RetrocopySKLEKYVDIDAGKYTIGLGQAKMGSCTHGEEINSLCMPVVQNLMERKNLSYDCTGRLEVGTETIKDKSKS
ParentalVKTNLMQLFEESGNTDIEGIDTTNACYGGTAAVFNAVNWIESSSWDGRYALVVAGDIAVYATGNARPTGG
VKTNLMQLFEESGN.DIEG.DTT.AC.GG.AAVF.AVNWIESSSWDG..AL...GDIAVY..G..R.TGG
RetrocopyVKTNLMQLFEESGNIDIEGTDTTHACCGGPAAVFSAVNWIESSSWDGQFALELVGDIAVYSIGKVRLTGG
ParentalVGAVALLIGPNAPLIFERGLRGTHMQHAYDFYKPDMLSEYPIVDGKLSIQCYLSALDRCYSVYCKKIRAQ
VGAVALLI.PNA.LIFERGLRGTHMQHAYDFY.PDM.SE.PIVDGK.S.QC..SALD.CYSV.CK.I.AQ
RetrocopyVGAVALLIEPNATLIFERGLRGTHMQHAYDFYEPDMPSECPIVDGKPSTQCCFSALDHCYSVDCKTIHAQ
ParentalWQKEGNDKDFTLNDFGFMIFHSPYCKLVQKSLARMLLNDFLNDQNRDKNSIYSGLEAFGDVKLEDTYFDR
WQK.GNDKDFTLN.FGF.I.HSPYCKLV..SLARML.NDFLNDQNRDKNS....LEAFG.VKLED.YFD.
RetrocopyWQKDGNDKDFTLNNFGFLILHSPYCKLVSLSLARMLRNDFLNDQNRDKNSV*NVLEAFGNVKLEDIYFDT
ParentalDVEKAFMKASSELFSQKTKASLL-VSNQNGNMYTSSVYGS-LASVLAQYSPQQLAGKRI-GVFSYGSGLA
DVE.AFMK.SSEL..QKTKASLL.VS..NGN.YTSSVYGS....V.AQYSPQQ..GKR..GVFSYGSG.A
RetrocopyDVEMAFMKDSSELSHQKTKASLL<VSSENGNTYTSSVYGS<PTTVPAQYSPQQ*SGKRL<GVFSYGSGSA
ParentalATLYSLKVTQDATPGSALDKITAS-LCDLKSRLDSRTGVAPDVFAENMKLREDTHHLVNYIPQGSIDSLF
.TLYSLKVTQDATPGSA.DKITAS.L.DLKS...SRT.V.PDVF.ENMKLREDTHHLVN..P.G..DSLF
RetrocopyGTLYSLKVTQDATPGSAVDKITAS<LWDLKSKCSSRTCVVPDVFVENMKLREDTHHLVNSVPRGPRDSLF
ParentalEGTWYLVRVDEKHRRTYARRPTPNDDTLDEGVGLVHSNIATEHIPSPAKKVPRLPATAAEPEAAVISNGE
E.TWYL.RV.EKH.R.Y...P.PNDDT.DEGV.LVHSN..T.HIPSPAK.VPRLPATAAE..AAVISNGE
RetrocopyEETWYLARVGEKH-RSYTPCPSPNDDTWDEGVRLVHSNTVTDHIPSPAKTVPRLPATAAETGAAVISNGE
ParentalH
H
RetrocopyH

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_prefrontal_cortex 0 .00 RPM 92 .16 RPM
SRP007412_cerebellum 0 .00 RPM 53 .24 RPM
SRP007412_heart 0 .00 RPM 23 .00 RPM
SRP007412_kidney 0 .03 RPM 46 .81 RPM
SRP007412_liver 0 .00 RPM 88 .12 RPM
SRP007412_testis 0 .00 RPM 68 .39 RPM

ChIP-Seq - click to see more details

Pan troglodytes was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_ptro_265 retrocopy.

TSS - click to see more details

Pan troglodytes was not studied using FANTOM5 data.

Lab - click to see more details

retro_ptro_265 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_265 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_328
Pongo abelii retro_pabe_361
Parental genes homology:
Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000013031 retrocopy
retro_cjac_1754,
Echinops telfairi ENSETEG000000035831 retrocopy
retro_etel_526,
Homo sapiens ENSG000001129721 retrocopy
retro_hsap_328,
Pongo abelii ENSPPYG000000154391 retrocopy
retro_pabe_361,
Pan troglodytes ENSPTRG00000016845 1 retrocopy
retro_ptro_265 ,


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