RetrogeneDB ID:

retro_ptro_2702

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:8:82786764..82787425(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:PSMC2
Ensembl ID:ENSPTRG00000019553
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_ptro_2702
ACAGACATTGAGGCAGGGATGAAATTTGATGTGGAAGAATGTAAGTATTAAATTCATATTCCCATACTTTCTAAGATTGA
TCCAACAATTACCATGATGCCGGTGGAGTAAAAACCTGATGTCATATACAGTGATGTTGTTGGCTGTAGGGAACAGATTG
AGACATTGTAAGCAGTTGAAACCCCACTACTTCATCCAGAGAGATTTGTTAACCTTGGCGTGGAGCCTCCCAAGAGTGTG
CTCTTTGGTCCACTAGGTGCAAGACACTCTGTGCTTAGGTGGTTGCTAAATAGGACTGATGCTTGCTTCATCGAGTTATT
GGATATTAACTTTTACAGAAATATATCTGCAAAGGGGCTGGAATGGTTCATGAGCTCTTCCCAATGGCCAGAACAAGAAA
CGCCTGCCTTATCTTCTTTGATGAAACTGATGCTATTGGAAGAGCTCAGTTTGATGATGGTGCTGGAGGTGACAATGAAG
TACAGAGAAAAATGTGGGAACTAATTCATCAGTTGGATGGCTTTGACCCTCAAGGCAATATTAAGTGCTGATGGCCACTA
ACAGACCTGATACTTTGGATTCAGCACTGATGAAGCCAGGGAAATTGGATAGAAAGATTGAGTTTAGTTTACCTGATCTA
GAGGGTCAGACTCACATCTTT

ORF - retro_ptro_2702 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 73.89 %
Parental protein coverage: 51.73 %
Number of stop codons detected: 4
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalTDIEEGMRVGVDRNKYQIHIPLPPKIDPTVTMMQVEEKPDVTYSDVGGCKEQIEKLREVVETPLLHPERF
TDIE.GM...V...KY.IHIP...KIDPT.TMM.VE.KPDV.YSDV.GC.EQIE.L...VETPLLHPERF
RetrocopyTDIEAGMKFDVEECKY*IHIPILSKIDPTITMMPVE*KPDVIYSDVVGCREQIETL-*AVETPLLHPERF
ParentalVNLGIEPPKGVLLFGPPGTGKTLCARAVANRTDACFI-RVIGSELVQKYVGEGARMVRELFEMARTKKAC
VNLG.EPPK.V.LFGP.G.......R...NRTDACFI.RVIG..L.QKY...GA.MV.ELF.MART..AC
RetrocopyVNLGVEPPKSV-LFGPLGARHSV-LRWLLNRTDACFI<RVIGY*LLQKYICKGAGMVHELFPMARTRNAC
ParentalLIFFDEIDAIGGARFDDGAGGDNEVQRTMLELINQLDGFDPRGNIK-VLMATNRPDTLDPALMRPGRLDR
LIFFDE.DAIG.A.FDDGAGGDNEVQR.M.ELI.QLDGFDP.GNIK.VLMATNRPDTLD.ALM.PG.LDR
RetrocopyLIFFDETDAIGRAQFDDGAGGDNEVQRKMWELIHQLDGFDPQGNIK<VLMATNRPDTLDSALMKPGKLDR
ParentalKIEFSLPDLEGRTHIF
KIEFSLPDLEG.THIF
RetrocopyKIEFSLPDLEGQTHIF

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 .04 RPM 42 .11 RPM
SRP007412_cerebellum 0 .00 RPM 68 .00 RPM
SRP007412_heart 0 .00 RPM 72 .40 RPM
SRP007412_kidney 0 .03 RPM 56 .33 RPM
SRP007412_liver 0 .00 RPM 70 .38 RPM
SRP007412_testis 0 .00 RPM 104 .96 RPM
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_2702 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_2702 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_2702 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_3980
Gorilla gorilla retro_ggor_2672

Parental genes homology:
Parental genes homology involve 13 parental genes, and 26 retrocopies.

Species Parental gene accession Retrocopies number
Echinops telfairi ENSETEG000000057291 retrocopy
Homo sapiens ENSG000001610572 retrocopies
Gorilla gorilla ENSGGOG000000091673 retrocopies
Myotis lucifugus ENSMLUG000000088531 retrocopy
Macaca mulatta ENSMMUG000000034322 retrocopies
Monodelphis domestica ENSMODG000000172381 retrocopy
Mustela putorius furoENSMPUG000000182683 retrocopies
Nomascus leucogenys ENSNLEG000000092742 retrocopies
Otolemur garnettii ENSOGAG000000051642 retrocopies
Pongo abelii ENSPPYG000000178832 retrocopies
Pan troglodytes ENSPTRG00000019553 2 retrocopies
retro_ptro_1826, retro_ptro_2702 ,
Tarsius syrichta ENSTSYG000000006664 retrocopies
Vicugna pacos ENSVPAG000000089211 retrocopy



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