RetrogeneDB ID:

retro_ptro_1909

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:3:97080242..97080977(-)
Located in intron of:ENSPTRG00000015132
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RBBP7
Ensembl ID:ENSPTRG00000021702
Aliases:None
Description:retinoblastoma binding protein 7 [Source:HGNC Symbol;Acc:9890]


Retrocopy-Parental alignment summary:






>retro_ptro_1909
ACACACACATTGGATGAACAAAAACATCTTGTTATAGCCAGTGTGCAACTCCCTAATGATGATGCTCATTTTGATGCATC
ACACTATGACAGTGAGAAAGGAGAATTTGGAGGTTTTGGTTCAGTTAGTGGAAAAATTGAAATAGAAATCAAGATCAACC
ATGAAGGAGAAGTAAACAGGGCCCGTTATATGCCCCAGAATCCTTGTATTATCACAACAAAGACTCCTTCCAGTGATGTT
CTTGTCTTGGACTATACAAAACATCCTAAACCAGATCTTTCTGGAGACTGCAACTCAGACTTGCGTCTCCATGGACATCA
GAAAAAAGGCTATGGGCTTTCTTGGCCAAATCTCAGTGGGCACTTACTTAGTGCTTCAGATGATCACACCATCTACCTGT
GGGACATCAGTGCTGTTCCAAAGGAGGGAAATGTGGTGGATGCAAAGACCATCTTTACAGGGCATACAGTAGTAGTAGAA
GATGTTTCCTGGCATCTGTTCCATAAGTCTCTGTTTGGGTCAGTTGCTGATCATCAGAAACTTATGATTTGGGATACTTG
TTCAAACAATACTTCCAAACCAAGCCACTCAGTTGACGCTCACACTGCTGAAGTGAACTGCCTCTCTTTCAATCCTTATA
GTGAGTTCATTCTTGCCACAGGATCAGCTGACAAGACTGTTGCCTTGTGGGATCTGAGAAATCTGAAACTTATGTTGCAT
TCCTCTGAGTCACAT

ORF - retro_ptro_1909 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 83.4 %
Parental protein coverage: 58.67 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalTHTSDEQNHLVVARVHIPNDDAQFDASHCDSDKGEFGGFGSVTGKIECEIKINHEGEVNRARYMPQNPHI
THT.DEQ.HLV.A.V..PNDDA.FDASH.DS.KGEFGGFGSV.GKIE.EIKINHEGEVNRARYMPQNP.I
RetrocopyTHTLDEQKHLVIASVQLPNDDAHFDASHYDSEKGEFGGFGSVSGKIEIEIKINHEGEVNRARYMPQNPCI
ParentalIATKTPSSDVLVFDYTKHPAKPDPSGECNPDLRLRGHQKEGYGLSWNSNLSGHLLSASDDHTVCLWDINA
I.TKTPSSDVLV.DYTKHP.KPD.SG.CN.DLRL.GHQK.GYGLSW..NLSGHLLSASDDHT..LWDI.A
RetrocopyITTKTPSSDVLVLDYTKHP-KPDLSGDCNSDLRLHGHQKKGYGLSW-PNLSGHLLSASDDHTIYLWDISA
ParentalGPKEGKIVDAKAIFTGHSAVVEDVAWHLLHESLFGSVADDQKLMIWDTRSNTTSKPSHLVDAHTAEVNCL
.PKEG..VDAK.IFTGH..VVEDV.WHL.H.SLFGSVAD.QKLMIWDT.SN.TSKPSH.VDAHTAEVNCL
RetrocopyVPKEGNVVDAKTIFTGHTVVVEDVSWHLFHKSLFGSVADHQKLMIWDTCSNNTSKPSHSVDAHTAEVNCL
ParentalSFNPYSEFILATGSADKTVALWDLRNLKLKLHTFESH
SFNPYSEFILATGSADKTVALWDLRNLKL.LH..ESH
RetrocopySFNPYSEFILATGSADKTVALWDLRNLKLMLHSSESH

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 .38 RPM 36 .30 RPM
SRP007412_cerebellum 0 .43 RPM 32 .34 RPM
SRP007412_heart 0 .26 RPM 45 .09 RPM
SRP007412_kidney 0 .37 RPM 48 .41 RPM
SRP007412_liver 0 .07 RPM 28 .35 RPM
SRP007412_testis 0 .53 RPM 63 .76 RPM
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_1909 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_1909 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_1909 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_2814

Parental genes homology:
Parental genes homology involve 11 parental genes, and 21 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000028201 retrocopy
Mus musculus ENSMUSG000000313531 retrocopy
Oryctolagus cuniculus ENSOCUG000000006831 retrocopy
Otolemur garnettii ENSOGAG000000149951 retrocopy
Petromyzon marinus ENSPMAG000000071891 retrocopy
Pan troglodytes ENSPTRG000000017111 retrocopy
Pan troglodytes ENSPTRG00000021702 5 retrocopies
Rattus norvegicus ENSRNOG000000051571 retrocopy
Sorex araneus ENSSARG000000080793 retrocopies
Tupaia belangeri ENSTBEG000000101512 retrocopies
Tarsius syrichta ENSTSYG000000023854 retrocopies



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