RetrogeneDB ID:

retro_ptro_584

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:11:1808184..1808975(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:ACTB
Ensembl ID:ENSPTRG00000018890
Aliases:ACTB, beta-actin
Description:Pan troglodytes actin, beta (ACTB), mRNA. [Source:RefSeq mRNA;Acc:NM_001009945]


Retrocopy-Parental alignment summary:






>retro_ptro_584
ATGGATGATAATATCGCCTTGCTTGTCATAGACAACACCTCTGGCATGTGCAAGGCCAGCTTCGCGGACGACGATGCCCC
CTGGGCCGTCTTCCCCTCCATCGTGGGGTGCCCCAGACACCAGGGCATGACGGTGGGCATGGGTCAGAAGGACTCCTATG
TGGGTGGCGAGGCCCAGAGCGACAGAGGCATCCTGACCCTGAAGTACCCCATCGAGCATGGCATCATTGGCAGCTGGGAT
GACAATGGAGAAGATCTGGCACCACACCTTCTACAACGAGCTGCGGGAGCACCCGGTGCTGCTGACCGAGGCCCCCCGAG
CCCCAAAGCCAATAGAAGGAAGATGACCCAGATCACGTTTGAGACCTTCAACACCTCGGCCATGTACGTGGCCATCCAGG
CCGTGCTGTCCAAGTACTCTCCTGGCCATACCACTGGCATCATGATGAACTCCAGCGACAGGGTCACCCGCACAGTGTCC
ATCTATGAGGGCTACAGCCTCCCCCATGCCATCCTGTGTCTGGACCCGGCTGGCCGGGACCAGACTCACTACCTCACAAA
GATCTCACCGAGCGTGGCTACGGCTTCACCACCACGGCCGAGCGGGCGATCACGTGTGACATTAAGGAGAAGCTGTGCTA
TGTTGCCCTGGACTTCAAGCAGGAGGTGGCCACGGCGACCACCAGCTCCTCCCTGGAGAAGAGCTACGAGCTGCCTGACA
GCCAGGTCATCCCCACTGGCAACGAACGGTTCCGCTGCCCCGAGGAGCCCTTCCTGCCTTCCTTCCGGGGT

ORF - retro_ptro_584 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 78.6 %
Parental protein coverage: 71.47 %
Number of stop codons detected: 0
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalMDDDIAALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYP
MDD.IA.LV.DN.SGMCKA.FA.DDAP.AVFPSIVG.PRHQG..VGMGQKDSYVG.EAQS.RGILTLKYP
RetrocopyMDDNIALLVIDNTSGMCKASFADDDAPWAVFPSIVGCPRHQGMTVGMGQKDSYVGGEAQSDRGILTLKYP
ParentalIEHGIVTNWDD-MEKIWHHTFYNELRVAPEEHPVLLTEAPL-NPKANREKMTQIMFETFNTPAMYVAIQA
IEHGI...WDD.MEKIWHHTFYNELR....EHPVLLTEAP...PKANR.KMTQI.FETFNT.AMYVAIQA
RetrocopyIEHGIIGSWDD>MEKIWHHTFYNELR----EHPVLLTEAPR<SPKANRRKMTQITFETFNTSAMYVAIQA
ParentalVLSLYASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDLAGRDLTDYLMKI-LTERGYSFTTTAERE
VLS.Y..G.TTGI.M.S.D.VT.TV.IYEGY.LPHAIL.LD.AGRD.T.YL.KI.LTERGY.FTTTAER.
RetrocopyVLSKYSPGHTTGIMMNSSDRVTRTVSIYEGYSLPHAILCLDPAGRDQTHYLTKI<LTERGYGFTTTAERA
ParentalIVRDIKEKLCYVALDFEQEMATAASSSSLEKSYELPDGQVITIGNERFRCPEALFQPSFLG
I..DIKEKLCYVALDF.QE.ATA..SSSLEKSYELPD.QVI..GNERFRCPE..F.PSF.G
RetrocopyITCDIKEKLCYVALDFKQEVATATTSSSLEKSYELPDSQVIPTGNERFRCPEEPFLPSFRG

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






(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 .02 RPM 1976 .36 RPM
SRP007412_cerebellum 0 .00 RPM 1129 .84 RPM
SRP007412_heart 0 .00 RPM 382 .11 RPM
SRP007412_kidney 0 .03 RPM 1474 .96 RPM
SRP007412_liver 0 .00 RPM 1774 .09 RPM
SRP007412_testis 0 .00 RPM 315 .31 RPM
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_584 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_584 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_584 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 14 parental genes, and 45 retrocopies.

Species Parental gene accession Retrocopies number
Anas platyrhynchos ENSAPLG000000101471 retrocopy
Canis familiaris ENSCAFG000000160203 retrocopies
Callithrix jacchus ENSCJAG000000000082 retrocopies
Dipodomys ordii ENSDORG000000100791 retrocopy
Equus caballus ENSECAG000000159352 retrocopies
Felis catus ENSFCAG000000067881 retrocopy
Loxodonta africana ENSLAFG000000091671 retrocopy
Macaca mulatta ENSMMUG000000111531 retrocopy
Otolemur garnettii ENSOGAG000000083481 retrocopy
Petromyzon marinus ENSPMAG000000041611 retrocopy
Pan troglodytes ENSPTRG000000028941 retrocopy
Pan troglodytes ENSPTRG00000018890 27 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000068682 retrocopies
Xenopus tropicalis ENSXETG000000251161 retrocopy



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